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VIVO : Enabling National Networking of Scientists ( NIH Grant Proposal )
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Permanent Link: http://ufdc.ufl.edu/UF00094181/00001
 Material Information
Title: VIVO : Enabling National Networking of Scientists ( NIH Grant Proposal )
Physical Description: Book
Language: English
Creator: George A. Smathers Libraries, University of Florida
Publication Date: 2009
Copyright Date: 2009
 Record Information
Source Institution: University of Florida
Holding Location: University of Florida
Rights Management: All rights reserved by the source institution and holding location.
System ID: UF00094181:00001

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UF UNIVERSITY of

UF FLORIDA
The Foundation for The Gator Nation


College of Medicine
Department of Epidemiology and Health Policy Research
Division of Biomedical Informatics


105 NW 16th St
PO Box 14823
Gainesville, FL 32604
352-273-1007
352-273-1469 Fax


Sheryl K. Brining, Ph.D.
Office of Review
National Center for Research Resources
6701 Democracy Boulevard, Room 1072
Bethesda, MD 20817

June 26, 2009

Dear Dr. Brining,

We are pleased to revise and resubmit the enclosed proposal entitled "VIVO: Enabling National
Networking of Scientists" in response to RFA-RR-09-009: Recovery Act 2009 Limited Competition:
Enabling National Networking of Scientists and Resource Discovery (U24). We are responding
under the heading Research Networking.

This multidisciplinary proposal includes faculty from biomedical informatics and library science,
particularly in the areas of institutional adoption of technology, ontology development, community
software development and deployment, semantic web, and social networking.

All consortium agreements, conflict of interest statements and other required forms are included
in this submission.

Best Regards,






Mike Conlon, PhD
Interim Director of Biomedical Informatics










The Foundation for The Gator Nation
An Equal Oporl r itvy nstituti n







Form Approved Through 11/30/2010 OMB No. 0925-0001
LEAVE BLANK-FOR PHS USE ONLY.
Department of Health and Human Services
Public Health Services Type Activity Number
Grant Apn Review Group Formerly
Grant Application
Do not exceed character length restrictions indicated. Council/Board (Month, Year) Date Received
1. TITLE OF PROJECT (Do not exceed 81 characters, including spaces and punctuation.)
VIVO: Enabling National Networking of Scientists
2. RESPONSE TO SPECIFIC REQUEST FOR APPLICATIONS OR PROGRAM ANNOUNCEMENT OR SOLICITATION [ NO YES
(If "Yes," state number and title)
Number: RFA-RR-09-009 Title: Recovery Act 2009 Limited Competition: Enabling National Networking of Scientists

3. PROGRAM DIRECTOR/PRINCIPAL INVESTIGATOR New Investigator [ No Yes
3a. NAME (Last, first, middle) 3b. DEGREE(S) 3h. eRA Commons User Name
Conlon, Michael BA M. Stat PhD MCONLON
3c. POSITION TITLE 3d. MAILING ADDRESS (Street, city, state, zip code)
Interim Director of Biomedical Informatics 105 NW 16 Street, Room 334
3e. DEPARTMENT, SERVICE, LABORATORY, OR EQUIVALENT PO Box 14823
Biomedical Informatics Gainesville, FL 32604
3f. MAJOR SUBDIVISION
College of Medicine
3g. TELEPHONE AND FAX (Area code, number and extension) E-MAIL ADDRESS:
TEL: 352-273-1007 FAX: 352-273-1469 mconlon@ufl.edu
4. HUMAN SUBJECTS RESEARCH 4a. Research Exempt If "Yes," Exemption No.
N No D Yes ] No D Yes
4b. Federal-Wide Assurance No. 4c. Clinical Trial 4d. NIH-defined Phase III Clinical Trial
] No Yes ] No D Yes
5. VERTEBRATE ANIMALS N No D Yes 5a. Animal Welfare Assurance No.
6. DATES OF PROPOSED PERIOD OF 7. COSTS REQUESTED FOR INITIAL 8. COSTS REQUESTED FOR PROPOSED
SUPPORT (month, day, year-MM/DD/YY) BUDGET PERIOD PERIOD OF SUPPORT
From Through 7a. Direct Costs ($) 7b. Total Costs ($) 8a. Direct Costs ($) 8b. Total Costs ($)
9/1/2009 8/31/2011 $4,001,591 $6,071,796 $8,072,119 $12,265,886
9. APPLICANT ORGANIZATION 10. TYPE OF ORGANIZATION
Name University of Florida Public: ] Federal N State O Local
Address University of Florida Board of Trustees Private: -4 Private Nonprofit

Division of Sponsored Research For-profit: D General D Small Business
219 Grinter Hall O Woman-owned O Socially and Economically Disadvantaged
P.O. Box 115500 11. ENTITY IDENTIFICATION NUMBER
Gainesville, Florida 32611-5500 59-6002052
DUNS NO. 969663814 Cong. District FL-006
12. ADMINISTRATIVE OFFICIAL TO BE NOTIFIED IF AWARD IS MADE 13. OFFICIAL SIGNING FOR APPLICANT ORGANIZATION
Name Name Brian Prindle
Title Title Associate Director for Sponsored Research
Address Address P.O. Box 115500

Gainesville, Florida 32611-5500


Tel: FAX: Tel: 352-392-1582 FAX: 352-846-1839
E-Mail: E-Mail: ufproposals@ufl.edu
14. APPLICANT ORGANIZATION CERTIFICATION AND ACCEPTANCE: I certify that SIGNATURE OF OFFICIAL NAMED IN 13. DATE
the statements herein are true, complete and accurate to the best of my knowledge, and (In ink. "Per" signature not acceptable.)
accept the obligation to comply with Public Health Services terms and conditions if a grant
is awarded as a result of this application. I am aware that any false, fictitious, or fraudulent
statements or claims may subject me to criminal, civil, or administrative penalties.


P HS 398 (Rev. 11 /07)


Face Page


Form Page 1







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael
PROJECT SUMMARY (See instructions):
The proposed work will establish national networking of scientists by providing a new software system
(VIVO) and support for scientists using VIVO. Scientists using VIVO will be able to find other scientists and
their work. Conversely, scientists using VIVO will be found by other scientists doing similar or complimentary
work. VIVO leverages work done over the past five years by Cornell University, supporting researchers and
finding of researchers by representing data about them and their activities including publications, awards,
presentations and partners. VIVO is fully extensible and based on Sematic Web concepts insuring sound
data representation, vastly improved search over existing text based methods and integration of data with
other applications. Support for researchers using VIVO will be done by librarians of the research institutions.
Librarians provide an existing and fully integrated resource for enabling researchers and the national
network.

The project will provide six deliverables: 1) A first release of the software to be used at the seven
participating institutions focused on insitutitonal resources. This release will be used to help establish
internal support for the system and build undersatdning of system value; 2) A second release incorporating
all national networking features which will be used by the seven participating institutions to demonstrate the
viability and utility of national deployment; 3) A third release incoporporating features requested by the NIH
and the project's Executive Advisory Board, fully integrated with the corresponding resource discovery
solution, enabling full national networking capability; 4) a community support process to insure
sustainability; 5) a sustainable, open product development process; and 6) a national, on-going governance
process. The national networking of scientists enabled by VIVO will provide a fundamental new capability to
improve biomedical research and human health.


RELEVANCE (See instructions):
Establishing national networking of scientists will significantly improve all of biomedical research in the United
States by providing opportunities across all disciplines to identify existing and on-going work, identify
potential new collaborations and improve and extend existing collaborations. National networking gives
scientists critical new information regarding current scientific activity to improve science, knowledge and
human health.
PROJECT/PERFORMANCE SITE(S) (if additional space is needed, use Project/Performance Site Format Page)
Project/Performance Site Primary Location
Organizational Name: University of Florida
DUNS: 969663814
Street 1: PO Box 115500, 219 Grinter Hall Street 2:
City: Gainesville County: Alachua State: FL
Province: Country: USA Zip/Postal Code: 32611-5500
Project/Performance Site Congressional Districts: Florida 6th Congressional District
Additional Project/Performance Site Location
Organizational Name: Cornell University
DUNS: 872612445
Street 1: 201 Olin Library Street 2:
City: Ithaca County: Tompkins State: NY
Province: Country: USA Zip/Postal Code: 14853-5301
Project/Performance Site Congressional Districts: 22nd District NY


P HS 398 (Rev. 11 /07)


Page 2


Form Page 2








Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

SENIOR/KEY PERSONNEL. See instructions. Use continuation pages as needed to provide the required information in the format shown below.
Start with Program Director(s)/Principal Investigator(s). List all other senior/key personnel in alphabetical order, last name first.
Name eRA Commons User Name Organization Role on Project
Conlon, Michael MCONLON UF PI
Barnes, Christopher UF Dev Lead
Borner, Katy KBORNER IU Site Lead
Cole, Curtis L. CLCOLE WCMC Site Lead
Corson-Rikert, Jonathan W. Cornell Ithaca Dev Lead
Davis, Valrie I. UF Site Team Lead
Devare, Medha Cornell Ithaca Project Lead
Ding, Ying DINGYING IU Ontology
Hack, George O. UF Ed Tech Team Lead
Holmes, Kristi L. WUSTL Outreach Lead
Joyce, Gerald F. GJOYCE Scripps Site Lead


OTHER SIGNIFICANT CONTRIBUTORS
Name


Organization


Role on Project


Human Embryonic Stem Cells E No [ Yes
If the proposed project involves human embryonic stem cells, list below the registration number of the specific cell lines) from the following list:
http://stemcells.nih.gov/research/registry/. Use continuation pages as needed.
If a specific line cannot be referenced at this time, include a statement that one from the Registry will be used.
Cell Line


PHS 398 (Rev. 11/07)


Page 3


Form Page 2-continued
Number the following pages consecutively throughout
the application. Do not use suffixes such as 4a, 4b.







Program Director/Principal Investigator (Last, First, Middle):


SENIOR/KEY PERSONNEL CONTINUED


eRA Commons Username


Organization


Role on Project


King, Paula
Krafft, Dean B.
McDonald, Robert H.
Mclntosh, Leslie D.
Nagarajan, Rakesh
Noel Jr., Richard J.
Russell Gonzalez, Sara A.
Tennant, Michele R.


RAKESH
RJNOELJR

TENNANTM


Scripps
Cornell Ithaca
IU
WUSTL
WUSTL
Ponce
UF
UF


Dir. Library
Site Lead
IMP Lead
IMP Lead
Site Lead
Site Lead
UF Team Lead
UF Team HSC Lead


PHS 398 (Rev. 11/07) Page 4 Form Page 2 continued


Name


Conlon, Michael


Page 4


P HS 398 (Rev. 11 /07)


Form Page 2 continued







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

Use only if additional space is needed to list additional project/performance sites.

Additional Project/Performance Site Location
Organizational Name: The Trustees of Indiana University
DUNS: 60-300-7902
street 1: IU Digital Library Program Street 2: Wells Library, 1320 E. Tenth Street
City: Bloomington County: Monroe State: IN
Province: [Country: USA Zip/Postal Code: 47405
Project/Performance Site Congressional Districts: IN 009

Additional Project/Performance Site Location
Organizational Name: Ponce School of Medicine
DUNS: 105742043
Street 1: 395 Industrial Reparada, Zona 2 Street 2:
City: Ponce County: Ponce State: PR
Province: Country: USA Zip/Postal Code: 00716-2347
Project/Performance Site Congressional Districts: 0-0000

Additional Project/Performance Site Location
Organizational Name: The Scripps Research Institute
DUNS: 7816134920000
Street 1: 10550 North Torrey Pines Road Street 2:
City: LaJolla County: LaJolla State: CA
Province: Country: USA Zip/Postal Code: 92037
Project/Performance Site Congressional Districts: CA 053

Additional Project/Performance Site Location
Organizational Name: Washington University
DUNS: 06-855-2207
Street 1: 660 South Euclid Avenue Street 2:
City: St. Louis County: St. Louis State: MO
Province: Country: USA Zip/Postal Code: 63110
Project/Performance Site Congressional Districts: 01

Additional Project/Performance Site Location
Organizational Name: Joan & Sanford I. Weill Medical College of Cornell University
DUNS: 060217502
Street 1: 1300 York Avenue Street 2:
City: New York County: New York State: NY
Province: Country: USA Zip/Postal Code: 10065
Project/Performance Site Congressional Districts: 14


PHS 398/2590 (Rev. 11/07)


Page 5


Project/Performance Site Format Page







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael
The name of the program director/principal investigator must be provided at the top of each printed page and each continuation page.
RESEARCH GRANT

TABLE OF CONTENTS


F
Face Page.............................................................................................................................................
Description, Project/Performance Sites, Senior/Key Personnel, Other Significant Contributors,
and Human Em bryonic Stem Cells....................................................................................................
Table of Contents ................................................................................................................................
Detailed Budget for Initial Budget Period .........................................................................................
Budget for Entire Proposed Period of Support.......................................................................................
Budgets Pertaining to Consortium/Contractual Arrangements ..................................... .............
Biographical Sketch Program Director/Principal Investigator (Not to exceed four pages each).........
Other Biographical Sketches (Not to exceed four pages each See instructions)............................
Resources ............................................................................................................................................
Checklist....................................................................................................................................................

Research Plan......................................................................................................................................

1. Introduction to Resubmission Application, if applicable (Not to exceed three pages.), or Introduction to
Revision Application, if applicable (Not to exceed one page.) ................................................................. ...........................
2. Specific Aims ..... ..................................
3 B a ckg ro u nd a nd S ig n ifica nce .. .... ............ ...................... ................... .................................................. ....
4. Preliminary Studies/Progress Report (Items 2-5: not to exceed 25 pages)..........................
5 R research D esig n and M ethods ................................................ I ... ........................................................................................ ,l ,.
5. Research Design and Methods..
6. Inclusion Enrollment Report (Renewal or Revision applications only)................................... ...............................................
7. Bibliography and References Cited/Progress Report Publication List..............................................................................
8 P ro te ctio n o f H u m a n S u bje c ts ....................................................................................................................................................
9. Inclusion of Women and Minorities ..............................
10 T a rgete d/P la nne d E n ro llm e nt T a b le .............. .......................................................... ..........................................................
1 1 In c lu s io n o f C h ild re n ...................................................................................................................................................................
12 V e rte brate A nim als ...................... ..... .... ...................................................
1 3 S e le c t A g e n t R e s e a rc h ...............................................................................................................................................................
14. Multiple PD/PI Leadership Plan.................... .................................. ............. ...............................
15. C consortium /C contractual A rrangem ents ....................................................................... .... .................................................
16 Lette rs o f S u p p o rt (e .g ., C o n su lta nts) .................................................................................................... .... .........................
17. Resource Sharing Plan (s) .......................................

Appendix (Five identical CDs.) F


PHS 398 (Rev. 11/07)


'age Numbers
1

2
6
7
11
15
43
NA
89
97

98


NA


NA
138
NA
NA
NA
NA
NA
NA
NA
142
148
159

Check if
Appendix is
Included


Page 6


Form Page 3







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 9/1/2009 8/31/2010
PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

Conlon, Michael PD/PI 6 170,394 85,197 19,719 104,916

Barnes, Christopher Dev Lead 6 109,269 54,634 15,830 70,464

Botero, Cecilia MeSH Expert 3 69,543 17,386 5,008 22,394

Buhler, Amy ite Support 2 49,980 8,330 3,459 11,789
Librarian
UF Team
Bushousen, Ellie HCTm 1.2 44,447 4,445 1,362 5,807
HSC
Site Team
Davis, Valrie Tead 9.6 51,903 41,522 17,119 58,641
Lead
UF Team
Ferree, Nita HCTm 1.2 49,849 4,985 1,516 6,501
HSC

SUBTOTALS 983,126 330,268 1,313,394
CONSULTANT COSTS

EQUIPMENT (Itemize)
8 servers @ 6,200/each=49,600; 10 workstations @2,000/each=20,000;
6 storage @ 3,000/each=18,000
87,600
SUPPLIES (Itemize by category)
Small items



6,000
TRAVEL
Pl=4,800; Governance=19,200; Support=36,000; Developer=4,800 64,800
PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)

OTHER EXPENSES (Itemize by category)






CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS 2,529,798

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 4,001,591

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 1,356,805

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 5,358,396
PHS 38 (Re. 1107) Pge5,Formage6


P HS 398 (Rev. 11 /07)


Page 7


Form Page 4







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 09/1/2009 08/31/2010
PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

Ed Tech
Hack, George Team Lead 2.4 70,110 14,022 4,862 18,884

UF Team
Jesano, Rae HCTm 1.2 49,721 4,972 1,483 6,455
HSC
UF Team
Johnson, Margeaux Librari 1.2 43,860 4,386 1,368 5,754

UF Team
Russell, Sara G. Leam 6 52,294 26,147 8,203 34,350
Lead
UF Team
Schaefer, Nancy FHSC 1.2 56,375 5,638 1,617 7,255

UF Team
Tennant, Michele HS Lea 3 80,070 20,018 5,508 25,526
HSC Lead

SUBTOTALS 983,126 330,268 1,313,394
CONSULTANT COSTS

EQUIPMENT (Itemize)



SUPPLIES (Itemize by category)





TRAVEL

PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)


OTHER EXPENSES (Itemize by category)






CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS 2,529,798

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 4,001,591

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 1,356,805

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 5,358,396
PHS 38 (Re. 1107) Pge5,Formage6


PHS 398 (Rev. 11/07)


Page 8


Form Page 4







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 09/1/2009 08/31/2010
PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

Research
Turner, Alicia eseh 6 41,838 20,919 7,358 28,277
Asst
Site Support
Williams, Stephen V. e S t 12 54,361 54,361 17,105 71,465
~~~TBEA ~Team Lead 6 90,000 45,000 14,187 59,187

TBA Team Lead 6 90,000 45,000 14,187 59,187


TBA Developer 12 85,000 85,000 27,430 112,430


TBA Developer 12 85,000 85,000 27,430 112,430
TBA Developer 12 85,000 85,000 27,430 112,430

SUBTOTALS 983,126 330,268 1,313,394
CONSULTANT COSTS

EQUIPMENT (Itemize)



SUPPLIES (Itemize by category)





TRAVEL

PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)


OTHER EXPENSES (Itemize by category)






CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS 2,529,798

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 4,001,591

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 1,356,805

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 5,358,396
PHS 38 (Re. 1107) Pge5,Formage6


PHS 398 (Rev. 11/07)


Page 9


Form Page 4







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 09/1/2009 08/31/2010
PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

TBA Developer 12 85,000 85,000 27,430 112,430


TBA Developer 12 85,000 85,000 27,430 112,430


TBA Site Support 12 36,000 36,000 18,173 54,173
PA

TBA Inst Designer 12 53,295 53,295 21,440 74,735

Marketing
TEA Marketing 12 43,575 43,575 19,604 63,179
BA Comm Coord

Metadata
TBA Metata 12 53,295 53,295 21,440 74,735
Expert

SUBTOTALS 983,126 330,268 1,313,394
CONSULTANT COSTS

EQUIPMENT (Itemize)



SUPPLIES (Itemize by category)





TRAVEL

PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)


OTHER EXPENSES (Itemize by category)






CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS 2,529,798

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 4,001,591

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 1,356,805

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 5,358,396
PHS 38 (Re. 11/7) Pge 10Formage6


PHS 398 (Rev. 11/07)


Page 10


Form Page 4







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BUDGET FOR ENTIRE PROPOSED PROJECT PERIOD
DIRECT COSTS ONLY
INITIAL BUDGET ADDITIONAL YEARS OF SUPPORT REQUESTED
BUDGET CATEGORY PERIOD
TOTALS (from Form Page 4) 2nd 3rd 4th 5th
PERSONNEL: Salary and fringe
benefits. Applicant organization
only. 1,313,394 1,352,796

CONSULTANT COSTS

EQUIPMENT 87,600

SUPPLIES 6,000 6,000

TRAVEL 64,800 64,800

PATIENT INPATIENT
CARE
COSTS OUTPATIENT

ALTERATIONS AND
RENOVATIONS

OTHER EXPENSES
CONSORTIUM/
CONTRACTUAL DIRECT 2,646,932
COSTS 2,529,798 2,646,932
SUBTOTAL DIRECT COSTS
(Sum = Item 8a, Face Page) 4,001,591 4,070,528
CONSORTIUM/
CONTRACTUAL F&A
CORACTUAL F&A1,356,805 1,461,590
COSTS
TOTAL DIRECT COSTS 5,358,396 5,532,118

TOTAL DIRECT COSTS FOR ENTIRE PROPOSED PROJECT PERIOD$ 10

JUSTIFICATION. Follow the budget justification instructions exactly. Use continuation pages as needed.
Budget Justification Year 1


Personnel


Michael Conlon, PhD (6 calendar months) Dr. Conlon is Director of Biomedical Informatics and will serve
as the Principal Investigator for this project. He will coordinate all project related activities. Dr. Conlon is
also Associate Director of the Clinical and Translational Sciences Institute. He has extensive experience
with university investigators, research processes and the development of large scale software. Dr. Conlon
led the team that developed the INVEST Clinical Trial electronic data capture software used at over 860 sites
and 14 countries.


Alicia Turner (6 calendar months) Research Assistant to Dr. Conlon. Ms. Turner has extensive experience
in project management, change management, research administration and organizational development. She
will coordinate personnel and budget efforts related to the proposal.


PHS 398 (Rev. 11/07)


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Form Page 5







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Christopher Barnes (6 calendar months) Leads the software engineering teams at Clinical and Translational
Informatics Program (CTRIP). He will lead two teams of developers in the implementation of interfaces for
VIVO and packaging of the VIVO software for distribution to the participating institutions. Mr. Barnes has
extensive informatics experience in both academic and corporate environments. He has developed dozens of
research applications at UF and has presented his findings at the American Medical Informatics Association.

TBA (6 calendar months) A development team lead is needed to manage a "packaging" team which will
provide ready to install versions of VIVO to participating institutions. The packaging team will work closely
with developers at Cornell and Indiana to insure that all VIVO software works smoothly. The packaging team
also coordinates the versions of Apache and MySQL software used in VIVO, writes installations scripts and
installation guides. The packaging team insures that VIVO works smoothly with various versions of the
various operating systems that participating institutions will use to host VIVO. The development team lead
will report to Mr. Barnes.

TBA (12 calendar months) Software developer is needed to participate in the development of VIVO
packaging activities described above.

TBA (12 calendar months) A second software developer is needed to ensure VIVO packaging as described
above.

TBA (6 calendar months) Development team lead is needed to manage an interface team developing the
interfaces of VIVO to specific software products including Drupal, Sakai, PeopleSoft and Shibboleth. The
team lead reports to Mr. Barnes. The team lead will insure that all appropriate software development
practices are followed and that the software produced addresses the use cases and functionality required.

TBA (12 calendar months) A software developer is needed to serve on the interface team.

TBA (12 calendar months) A second developer is needed to work on the interface team to provide the
appropriate level of manpower needed to generate the interfaces described in the proposal.

Valrie Davis (9.6 calendar months) -- Ms. Davis will serve as site liaison, coordinating implementation of VIVO
at participating schools, including all "help desk" type activities. She will guide schools in their implementation
and use of VIVO and, with Mr Williams, will travel as required to any site requesting implementation
assistance. She will also coordinate the development of a community of implementation support network,
ensuring that all types of implementation support needs are met with implementation and use processes. She
will also provide appropriate feedback to Dr. Conlon, to the Cornell and UF development teams, and to the
Washington University evaluation team regarding the implementation of all VIVO releases at partner sites.
She will also manage the local UF Libraries project budget. She will meet regularly with the UF
Implementation (Dr. Gonzalez) and Outreach (Dr. Tennant) Leads to review progress and discuss changes in
the local UF implementation plan.

Sara Russell Gonzalez (6 calendar months) -- Dr. Gonzalez will lead the Implementation team at UF to
implement the existing VIVO database at UF in the first year and the VIVOweb in the second year. She will
coordinate the ingest and harvesting of participant data into the VIVO database, in consultation with the
Outreach Lead (Dr. Tennant). She will work closely with Dr. Ying Ding (Indiana University), the UF
Metadata/Ontologist Expert, and Ms. Cecilia Botero (UF MeSH authority) to develop a robust ontological
structure for use both in the UF VIVO and for adoption at implementation sites. Dr. Gonzalez will also work
closely with Dr. Tennant and UF outreach librarians to develop a marketing strategy to optimize adoption by
the UF research community. She will work with Dr. Leslie Mclntosh (WU) to coordinate project evaluation.

TBA (12 calendar months) -- Metadata Expert/Ontologist. This individual will work under the direction of Dr.
Gonzalez to develop (in collaboration with Cornell) and maintain a commonly agreed upon metadata


PH S 398 (Rev. 11 /07)


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


vocabulary that reflects the needs of our local ontology users but is also interoperable and geographically,
administratively, and functionally scalable with the national interface. S/he will evaluate local usability of
metadata and refine the metadata in a manner that facilitates access.

Michele R. Tennant (3 calendar months) -- Dr. Tennant will lead the researcher support and outreach efforts
at the UF. As research support, Dr. Tennant will provide onsite and email assistance in the use of VIVOweb
to UF biomedical researchers. As Outreach Lead, Dr. Tennant will coordinate the work of the UF Libraries'
liaisons (see section on Outreach Team below). Dr. Tennant will also perform these activities for genetic-,
molecular-, and bioinformatics-related researchers at the UF Health Science Center. Dr. Tennant will work
closely with team leader Dr. Medha Devare, and will present and exhibit at some of the conferences listed in
section C4.b, assist in recruiting new schools, help create a national online presence, and be the primary
contact for library associations that are medical in nature. Finally, in support of the ontology team, she will
provide feedback from researchers to the Implementation Team led by Dr. Sara Russell Gonzalez.

Outreach Team: These UF Libraries Liaisons will comprise the Outreach Team led by Dr. Tennant, and will
work closely with their respective researchers in a variety of ways. They will be responsible for marketing
VIVO and getting buy-in from UF researchers to use the resource; they will present at departmental meetings,
teach how to use the resource one-on-one, and make use of the marketing and instructional tools created by
the Instructional Designer and Marketing/Communications Coordinator. They will work closely with
researchers to determine and then communicate to the technical team researchers' opinions of VIVOweb -
what works, what doesn't, and what is missing or unnecessary. They will also work with clients to perform
data evaluation. All liaisons have forged strong relationships with their research clients.

Ellie Bushhousen (1.2 calendar months) -- Outreach clientele: College of Dentistry, College of Veterinary
Medicine.

Nita Ferree (1.2 calendar months) -- Outreach clientele: College of Medicine.

Rae Jesano (1.2 calendar months) -- Outreach clientele: College of Pharmacy.

Nancy Schaefer (1.2 calendar months) -- Outreach clientele: College of Public Health and Health Professions.

Amy Buhler (2 calendar months) -- Outreach clientele: College of Engineering (Biomedical Engineering,
Agricultural & Biological Engineering, and Nuclear & Radiological Engineering, Nanotechnology).

Margeaux Johnson (1.2 calendar months) -- Outreach clientele: College of Engineering (Distance Educ. Sites)

George Hack, PhD (2.4 calendar months) -- As National Educational Technology Team Leader, Dr. Hack will
coordinate all national instructional designer and marketing/communication activities. This includes the
development of a comprehensive suite of educational materials for both VIVO users and implementation and
support teams. These materials will include both text-based and video tutorials which range in complexity
from basic needs to more complicated or innovative use of the application.

TBA (12 calendar months) An instructional designer is needed to work with Dr. George Hack to create the
comprehensive suite of instructional materials to be used on a national basis. The position will design and
develop instructional material for VIVOweb utilizing effective needs analysis, project management, course
development, and evaluation skills, and will collaboratively develop entry and advanced level courses for both
internal and external audiences. This position will serve as liaison between Research & Development and
Instructional Design in determining needs of the instruction and appropriate method of delivery, providing
instructional and program design expertise for the development, and support of online courses and
specialized educational delivery modes.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


TBA (12 calendar months) A Marketing/Communications Coordinator is needed to work with Dr. George
Hack to create the comprehensive suite of marketing materials to be used on a national basis. This position
will be responsible for managing marketing and communications processes, and the design and production of
resources in a variety of formats including web, print, graphics, audio, video, and animation technologies to
support curriculum offerings and promote VIVO. The position will work closely with liaisons in the adoption
strategies, use of best practices to identify change agents, promotion and marketing of the characteristics of
VIVO as a new innovation, and to establish the key elements of a change process that will facilitate adoption.

Stephen Williams (12 calendar months) -- Mr. Williams, Technology/Systems Site Support, will work with the
Site Lead (Ms. Davis) to meet the technical needs of all implementation sites. Mr. Williams was the technical
lead for the UF VIVO implementation and has experience with MySQL, Java, Perl, C#, and .Net with both UF
Libraries.

TBA (12 calendar months) A Program Assistant will be supervised by Ms. Davis and will provide assistance
to Ms. Davis, Dr. Gonzalez and Dr. Tennant with communication and planning. S/he will also be responsible
for compiling and maintaining project documentation and reports.

Cecilia Botero (3 calendar months) -- Ms. Botero, a MeSH expert, will work closely with Dr. Ying Ding
(Indiana University), the UF Metadata/Ontologist Expert, and Dr. Gonzalez (UF Implementation Lead) to
develop a robust ontological structure, ensure that MeSH terms will be integrated properly into the standard
ontology and that the proper mapping occurs.

Equipment
Eight servers are needed to provide fall tolerant development test and production environments for the
integrated work to be done with VIVO by the development teams at UF. These will be Dell R710 or similar.
Servers will be housed in the existing library information technology services area. Servers will be supported
by existing staff of Library Information Services.

Ten workstations are requested for new employees assigned 100% to the VIVO project.

Seven raw Terabytes of storage are requested to support the development work of the project and to house
the indices used by the national VIVO web. This will be a Dell Equiologic PS6000 or similar with mixed drives
for performance and storage. Storage will be backed up using an existing Quantum Tape Library. Storage
and backup will be operated by existing staff of Library information services.

Supplies
Small items, books, removable media, miscellaneous software and office supplies are needed to support the
staff being hired under this proposal.

Travel
Four trips are requested for the Principal Investigator to attend governance process meetings of the project.
Sixteen trips are requested to support the executive advisory board meetings. Travel would be provided for
the executive advisory board members. Thirty trips are requested for support activities related to the
implementation of VIVO at the participating institutions. Four trips are requested for the developers to attend
training and participate in outreach activities.

Budget Justification Year 2
Salaries
All salaries are increased by 3%.

Travel
All travel continues at the same levels as in Year 1.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 9/1/2009 8/31/2010
PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

Krafft, Dean Site Lead 1.2 153,768 15,377 5,228 20,605


Caruso, Brian Team Lead 6 60,300 30,150 13,598 43,748


Corson-Rikert, Jon Dev Lead 3 96,432 24,107 10,872 34,979


Devare, Medha Project Lead 6 54,036 27,019 12,186 39,205


Lowe, Brian Team Lead 7.2 60,300 36,180 16,317 52,497


Mistlebauer, Holly Project Mgr 3 88,692 22,174 10,000 32,174

SUBTOTALS 767,607 344,483 1,112,090
CONSULTANT COSTS

EQUIPMENT (Itemize)
3 Servers @ 15,000/each=45,000; 1 PolyComm @ 20,000=20,000

65,000
SUPPLIES (Itemize by category)
Small items, 9 staff computers @ 2,500 = 22,500



27,499
TRAVEL
5 trips for 6 travelers @ 1,600/each=48,000; Conference = 5,000 53,000
PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)


OTHER EXPENSES (Itemize by category)






CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 1,257,589

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 680,128

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 1937,717
PHS 38 (Re. 11/7) Pge 15Formage7


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Form Page 4







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 9/1/2009 8/31/2010
PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

Worthington, Miles Team Lead 12 49,776 49,776 22,448 72,224


TBAProject 12 50,256 50,256 22,665 72,921
Coordinator

TBA Metadata 12 55,272 55,272 24,928 80,200
TA Librarian

TBA Developer 12 65,328 65,328 29,463 94,791


TBA Developer 12 65,328 65,328 29,463 94,791


TBA Developer 12 65,328 65,328 29,463 94,791

SUBTOTALS 767,607 344,483 1,112,090
CONSULTANT COSTS

EQUIPMENT (Itemize)



SUPPLIES (Itemize by category)





TRAVEL

PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)


OTHER EXPENSES (Itemize by category)






CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 1,257,589

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 680,128

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 1,937717
PHS 38 (Re. 11/7) Pge 16Formage7


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Form Page 4







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 9/1/2009 8/31/2010

PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

TBA Developer 12 65,328 65,328 29,463 94,791


TBA Developer 12 65,328 65,328 29,463 94,791


TBA Developer 12 65,328 65,328 29,463 94,791

Technical
TBA ProManager 12 65,328 65,328 29,463 94,791
Proj Manager






SUBTOTALS 767,607 344,483 1,112,090
CONSULTANT COSTS

EQUIPMENT (Itemize)



SUPPLIES (Itemize by category)





TRAVEL

PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)


OTHER EXPENSES (Itemize by category)






CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 1,257,589

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 680,128

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 1,937717
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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BUDGET FOR ENTIRE PROPOSED PROJECT PERIOD
DIRECT COSTS ONLY
INITIAL BUDGET ADDITIONAL YEARS OF SUPPORT REQUESTED
BUDGET CATEGORY PERIOD
TOTALS (from Form Page 4) 2nd 3rd 4th 5th
PERSONNEL: Salary and fringe
benefits. Applicant organization
only. 1,112,090 1,197,964

CONSULTANT COSTS

EQUIPMENT 65,000 15,000

SUPPLIES 27,499 20,008

TRAVEL 53,000 79,900

PATIENT INPATIENT
CARE
COSTS OUTPATIENT

ALTERATIONS AND
RENOVATIONS

OTHER EXPENSES
CONSORTIUM/
CONTRACTUAL DIRECT
COSTS
SUBTOTAL DIRECT COSTS
(Sum = Item 8a, Face Page) 1,257,589 1,312,872
CONSORTIUM/
CONTRACTUAL F&A680,128 710,011
COSTS 680,128 710,011
TOTAL DIRECT COSTS 1,937,717 2,022,883

TOTAL DIRECT COSTS FOR ENTIRE PROPOSED PROJECT PERIOD $ 39,600
|$ 3,960,600
JUSTIFICATION. Follow the budget justification instructions exactly. Use continuation pages as needed.
Key Personnel:


Dean Krafft, PhD, Cornell Principal Investigator, (Effort: 1.2 person months/yr) is the Chief Technology
Strategist at the Cornell University Library. Dr. Krafft will oversee the Cornell effort, working with other
members of the team and our partners on planning, management, and reporting. He will also coordinate and
chair the Technical Advisory Board and oversee technical development at Cornell. As the former Director of
IT for Computing and Information Science at Cornell and the former Principal Investigator on the National
Science Digital Library project, he has extensive experience in managing large software development
projects, in IT support and production, and in working in large, complex virtual organizations.


Medha Devare, PhD, National project coordinator, (Effort: 6 person months/yr) is the Bioinformatics and Life
Sciences Librarian at Cornell's Mann Library. Medha coordinates the VIVO project at Cornell, and will
employ her skills and outreach experience to ensure adoption, usage, and maintenance of VIVOweb across
institutions.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Holly Mistlebauer, MLS, Cornell site project manager, (Effort: 3 person months/yr) is the Head of Operations
for Information Technology Services at Cornell's Mann Library and brings extensive project
management skills to the team. Holly has also managed the acquisition and de-duplication of publication
citations for The Essential Electronic Agriculture Library (TEEAL) project1 since its inception in 1999.

Jonathan Corson-Rikert, BA, Development coordinator, (Effort: 3 person months/yr) is Head of Information
Technology Services at Cornell's Mann Library and the originator and technical lead for the VIVO
project. He has worked since 2002 on developing and enhancing VIVO, supervising a team of
programmers and designers to do so. Jon will continue to supervise the development team at Cornell
and serve as the principal coordinator of the four development teams on the project.

Brian Caruso, BS, VIVO system architect, (Effort: 6 person months in year 1, 7.8 person months in year 2)has
worked on the VIVO project since December, 2004 as the core system designer responsible for broad
areas of development including search, data ingest, interactive editing, web services, access controls,
performance optimization, reliability, and integration with Fedora. As lead for an architecture and
systems sub-group at Cornell, Brian will coordinate VIVO system documentation, installation packaging,
and data ingest efforts with UF and lead implementation of VIVOweb features supporting distributed
indexing, query, and analysis in close coordination with Dr. Borner's analysis and visualization group.

Brian Lowe, BA, Semantic Web programmer, (Effort: 7.2 person months in year 1, 12 person months in year
2) joined the VIVO team in 2005 and was instrumental in rewriting VIVO to align with Semantic Web
standards, integrating the Pellet reasoning engine, and developing formalized bi-directional interchange
between VIVO's internal RDF format and external XML schemas. As lead of a Semantic Web sub-group
at Cornell, Brian will coordinate semantic interoperability across VIVOweb installations and with the
Linked Open Data cloud, extend VIVO's reasoning capabilities and SPARQL query support, address
scalability, and coordinate closely with Dr. Ying Ding's team at Indiana to implement ontology extensions
as necessary at the local and national level.

Miles Worthington, BA, Interface designer, (Effort: 12 person months/yr) joined the VIVO team in early 2008
and has designed two websites at Cornell re-purposing VIVO data for media communications and
graduate student recruitment, most recently using the Drupal2 open source content management
system. Miles will plan and conduct user testing, work closely with the support, implementation, and
evaluation teams to define requirements; design and implement interface enhancements to VIVO, and
develop tools to support using VIVO data in course management systems, collaboration tools, and
general-purpose content management systems. He will also work closely with Dr. Borner and Dr. Ding at
Indiana to address usability in the context of ontology, analysis, and visualization.

Additional programmers will be hired (Effort: 6 at 12 person-months/yr) to work under the immediate direction
of the lead programmers at Cornell, addressing the following areas and additional priorities based on
feedback from implementation teams:
Design, deployment, testing and documentation of VIVO installation packages, in collaboration with
the UF development team
Modifications and extensions to VIVO core code to support and streamline automated data ingest and
associated workflow tools, in collaboration with UF.
Extensions to VIVO core infrastructure to fully support Linked Open Data standards and seamless
cross-site references and navigation
Implementation and testing of Hadoop3 computing cluster to support distributed indexing, network data
analysis, and visualization


Continuation Format Page


1 http://www.teeal.org
2 http://drupal.org
3 http://hadoop.apache.org
PHS 398 (Rev. 11/07)


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Implementation of distributed query capability across one or more SPARQL endpoints; evaluation of
commercial and open-source technologies to support scalability across a distributed network
Integration of data analysis and visualization tools developed by the Indiana University team into core
VIVO
Support for data export as schema-compliant XML and implementation of additional web services
optimized to support data sharing and integration into other institutional applications at distributed
sites

Rapidly scaling up any development group presents challenges that must be carefully addressed in project
planning. We propose to hire the services of an experienced technical project manager (Effort: 12 person-
months/yr) with agile development training to support requirements analysis, define and schedule
programming tasks, coordinate small-team work assignments and progress assessments, and facilitate
communication with development and implementation teams at other institutions through issue tracking
systems, team wiki spaces, and other collaboration tools as they prove useful.

A metadata librarian will be hired to work on ontology issues that arise as institutions install VIVO and modify
the core ontology for local accuracy. This person will collaborate with the ontology team at Indiana University
and the MeSH expert at the University of Florida, and communicate needs and feedback to the development
team.

A project coordinator will be hired to support all Cornell personnel involved in the project by facilitating
communication and collaboration, scheduling, outreach, and other logistic needs.

The equipment budget includes 3 Linux servers to be acquired in year 1 and 1 Linux server to be acquired in
year 2 at Cornell to provide redundant test and development servers and to experiment with virtual server
configuration as part of a distributed computing cluster. We have also included funds to purchase a
PolyComm Internet-based, multi-point videoconferencing system to allow open videoconferencing links
between Cornell, Florida, and Indiana development teams and to provide optimal technical support for
implementation teams at other sites.

The budget includes funds for travel to VIVOweb implementer sites, and other project-related meetings as
well as for presentation at conferences.

The budget includes funds for miscellaneous project specific supplies such as computers for programmers
and project staff, and supplies for data backup.


Continuation Format Page


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 9/1/2009 8/31/2010
PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

Borner, Katy Site Lead 1 88,878 8,888 2,092 10,980

Ding, Ying Ontology 1 75,750 7,875 1,854 9,729

Dunn, Jon Project 0.35 86,762 2,534 880 3,414
Oversight

McDonald, Robert H. IMP 0.1 90,000 750 260 1,010

Walsh, Alan Identity Mgt 1.2 76,800 7,680 2,666 10,346

Sr.
TBA D er 12 70,000 70,000 24,304 94,304
Developer

SUBTOTALS 436,192 135,067 571,259
CONSULTANT COSTS

EQUIPMENT (Itemize)
5 workstations @ $3,000/each = $15,000

15,000
SUPPLIES (Itemize by category)
Small items



4,000
TRAVEL
Borner, 4@1,000/ea=4,000; Ding, 4@1,000/ea=4,000; Implementation, 2@1,000/ea=2,000 10,000
PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)

OTHER EXPENSES (Itemize by category)
1 tuition waiver @ $21,625/each = $21,625



21,625
CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 621,884

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 324,140

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 946,024
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Form Page 4







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 9/1/2009 8/31/2010
PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

TBA Developer 12 65,000 65,000 22,568 87,568


TBA Developer 12 65,000 65,000 22,568 87,568

Database
TBA Datase 12 65,000 65,000 22,568 87,568
Expert

TBA intent Dev 12 55,000 55,000 19,096 74,096
& Assess
Interface
TBA Interface 0.5 47,163 1,965 682 2,647
Developer

TBA PhD Student 12 18,000 18,000 2,162 20,162

SUBTOTALS 436,192 135,067 571,529
CONSULTANT COSTS

EQUIPMENT (Itemize)



SUPPLIES (Itemize by category)





TRAVEL

PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)


OTHER EXPENSES (Itemize by category)






CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 621,884

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 324,140

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 946,024
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Form Page 4







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 9/1/2009 8/31/2010

PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

TBA Student Asst 12 30,000 30,000 30,000

Project
TBA _Maneent 266,000 11,000 3,819 14,819
Management

TBAProgrammer, 6 55,000 27,500 9,548 37,048
Connectivity









SUBTOTALS 436,192 135,067 571,259
CONSULTANT COSTS

EQUIPMENT (Itemize)



SUPPLIES (Itemize by category)





TRAVEL

PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)


OTHER EXPENSES (Itemize by category)






CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 621,884

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 324,140

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 946,024
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Form Page 4







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BUDGET FOR ENTIRE PROPOSED PROJECT PERIOD
DIRECT COSTS ONLY
INITIAL BUDGET ADDITIONAL YEARS OF SUPPORT REQUESTED
BUDGET CATEGORY PERIOD
TOTALS (from Form Page 4) 2nd 3rd 4th 5th
PERSONNEL: Salary and fringe
benefits. Applicant organization
only. 571,259 585,146
CONSULTANT COSTS

EQUIPMENT 15,000

SUPPLIES 4,000 4,000

TRAVEL 10,000 10,000

PATIENT INPATIENT
CARE
COSTS OUTPATIENT

ALTERATIONS AND
RENOVATIONS

OTHER EXPENSES 21,625 25,299
CONSORTIUM/
CONTRACTUAL DIRECT
COSTS
SUBTOTAL DIRECT COSTS
(Sum = Item 8a, Face Page) 621,884 624,445
CONSORTIUM/
CONTRACTUAL F&A324,140 324,823
COSTS 324,140 324,823
TOTAL DIRECT COSTS 946,024 949,268

TOTAL DIRECT COSTS FOR ENTIRE PROPOSED PROJECT PERIOD $ 18,292
$ 1,895,292
JUSTIFICATION. Follow the budget justification instructions exactly. Use continuation pages as needed.
Three teams from Indiana University will participate. Their separate budget justifications are given below.


TEAM1: Social Networking, Lead by Borner, SLIS, Indiana University
Personnel
Katy Borner will hire and supervise the work, conduct the proposed research on data analysis and
visualization, disseminate the project results. The listed summer salary corresponds to 4 weeks or 10% of
her annual base salary.


Other Personnel
A senior programmer, a programmer, and a database expert will be employed to perform the proposed work.
One hourly graduate student will be hired. This student will work approximately 20 hours per week for 30
weeks during the Fall and Spring, and 40 hours per week for 10 weeks during the Summer (10 weeks), at an
hourly rate of $15/h (in total, $15,000).


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Fringe Benefits
The current summer salary fringe benefit rate for Borner is 23.54%, for programmers is 34.72% as
established by the University.

Travel
Project results will be presented to NSF and at international conferences, workshops or related events.

Supplies
Materials and supplies comprise printing, duplication, postage at $2000 each year. Three computers will be
purchased one for each full time programmer. This work cannot be done without a computer.

Indirect Costs
The federally negotiated indirect cost rate for on-campus research is 54%.

TEAM2: Ontology Development, Lead by Ding, SLIS, Indiana University
Dr. Ding will be scientifically in charge of ontology development. She will hire and supervise programmers and
graduate students, report the project to NIH, disseminate the project results and validate the proposed work.
The listed summer salary corresponds to her 4 weeks or 10% of her annual base salary.

Other Personnel
One skilled programmer will be hired to clean data, process data, convert data into semantic formats and
provide integrated functions to other VIVOwebs. The salary for skilled programmer will be around $65K per
year.

One PhD student will be supported and focused on theoretical efficiency about ontology management. The
cost includes the stipend, 24 credit hours out of state tuition fee and health insurance.

One hourly graduate student will be needed to support the work of PhD student and skilled programmer. This
student will work approximately 20 hours per week for 30 weeks during the Fall and Spring, and 40 hours per
week for 10 weeks during the Summer (10 weeks), at an hourly rate of $15/h (in total, $15,000).

Fringe Benefits
The current summer salary fringe benefit rate for Borner, Ding and Barnett is 22.89% which is established by
the University. Hourly graduate students are subjected to FICA/non-enrollment withholding at 7.06%.

Fee Remission
SAA fee remission is based on current rate for 24 credit hours at out of state rate, with a 6% increase each in
years 1 and 2.

Travel
We need to present the project results at international conferences, workshops or related events. A total travel
budget of $8000 is requested for the two year project period, with $4000 in year 1 and $4000 in year 2.

Supplies
We claimed $2000 per year as the cost for the publications, documentation and distributions of the project
results.

Two computers will be acquired at total of $6000 (at $3K each) in year 1 to allow the hired programmer and
PhD student to work. These computers should have high memory space and disk space in order to handle
large scale data computing. They will be used to store, process, analyze data and other daily reporting and
documenting usage.


Continuation Format Page


PH S 398 (Rev. 11 /07)


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Indirect Costs
The federally negotiated indirect cost rate for on-campus research is 54%.

TEAM: The VIVO@IUB Team
Robert McDonald, Project Oversight for the implementation of VIVO at the Indiana University Bloomington
Campus, will be responsible for coordinating all aspects of the implementation of the Cornell VIVO at the IUB
campus within the IU Digital Library Program infrastructure, including oversight of all grant personnel,
coordination with the IUB Dean of Faculties, the IUB Libraries, IU School of Library and Information Science
and institutions, and coordination with technical implementation. (0.10 Calendar months)

Jon Dunn, Project Oversight, will be responsible for project oversight of this project within the IU Digital
Library Program for technical coordination among the IU Digital Library Program technical personnel and will
assist Mr. McDonald in overall management of the project. (0.35 Calendar months)

TBN, Project and Technical Management, this position will be responsible for technical coordination among
Cornell technical staff installing VIVO, the Indiana University Digital Library Program technical staff and
project management coordination, and the IU SLIS and other institutional technical implementation. (2.0
Calendar months)

Alan Walsh, Senior Investigator, is the Manager of Identity Management for Indiana University. He will
provide technical consultation and support for the implementation of Federated Identities for the consortium
institutions. He will continue his efforts to assist other consortium members to establish their own federated
identity systems so authentication can be shared and so that users can be more easily disambiguated for
networking and assessment purposes.

TBN, User Interface Specialist, this position will be responsible for enabling the multiple user interfaces to the
VIVO implementation for the IUB campus. Other work will be done in integrating the various interfaces within
the IU campus portal OneStart.

The Content Developer and Assessment professional, TBN, will be responsible for internal promotion of the
VIVO implementation across the Indiana University Bloomington campus, for organizational coordination and
advocacy for VIVO implementation, and for evaluation and assessment. These latter activities include
identifying use cases for Indiana, fleshing them out, and coordinating with leads at other federated
institutions. (12 Calendar months per year)

The Programmer, TBN, will be responsible for customization of the VIVO software so it functions efficiently in
the context of the Indiana University Bloomington data environment (including federated identity support,
ontology support for content, and integration with IUB data sources). These features are well beyond the
extension of VIVO undertaken by Cornell, but will provide features important for uptake at the IUB campus.
This person will also provide technology integration for other Indiana expertise databases, notably the Indiana
Database of University Research Expertise (INDURE), used by Purdue and Notre Dame Universities and will
work on integration for such bibliographic tools as the Journal Citation Reports API. (6.0 Calendar months per
year)

Indiana University fringe benefit rates for faculty and professional staff are currently 34.72%.

Salary and related fringe benefits were inflated by 3% for year 2.

Travel funds are requested for two persons to attend consortium coordinating meetings each year. ($2000 in
year 1, $2000 in year 2)


Continuation Format Page


PH S 398 (Rev. 11 /07)


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 9/1/2009 8/31/2010
PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

Noel, Richard J. Site Lead .5 146,000 6,083 1,095 7,178


Espada, Ricardo Developer 6 30,000 15,000 2,700 17,700
Assistant

Torres, Damaris IMP Lead 2 55,000 9,167 1,650 10,817










SUBTOTALS 30,250 5,445 35,695
CONSULTANT COSTS

EQUIPMENT (Itemize)
Data server $8000; Web server $7000

15,000
SUPPLIES (Itemize by category)





TRAVEL
Two trips from Puerto Rico to US for training/tech on VIVO and for consortium administration 4,000
PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)


OTHER EXPENSES (Itemize by category)
Additional hardware



2,000
CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 56,695

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 28,199

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 84,894
PHS398(Re. 1/07 Pae 2 Fom Pge4,9


P HS 398 (Rev. 11 /07)


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Form Page 4







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BUDGET FOR ENTIRE PROPOSED PROJECT PERIOD
DIRECT COSTS ONLY
INITIAL BUDGET ADDITIONAL YEARS OF SUPPORT REQUESTED
BUDGET CATEGORY PERIOD
TOTALS (from Form Page 4) 2nd 3rd 4th 5th
PERSONNEL: Salary and fringe
benefits. Applicant organization
only. 35,695 36,766

CONSULTANT COSTS

EQUIPMENT 15,000

SUPPLIES

TRAVEL 4,000 4,000

PATIENT INPATIENT
CARE
COSTS OUTPATIENT

ALTERATIONS AND
RENOVATIONS

OTHER EXPENSES 2,000 2,000
CONSORTIUM/
CONTRACTUAL DIRECT
COSTS
SUBTOTAL DIRECT COSTS
(Sum = Item 8a, Face Page) 56,695 42,766
CONSORTIUM/
CONTRACTUAL F&A28,199 29,045
COSTS 28,199 29,045
TOTAL DIRECT COSTS 84,894 71,811

TOTAL DIRECT COSTS FOR ENTIRE PROPOSED PROJECT PERIOD$ 5
$ 156,705
JUSTIFICATION. Follow the budget justification instructions exactly. Use continuation pages as needed.
Personnel:
Richard J. Noel Jr., PhD, Project Director/Ponce Leader will devote 0.5 calendar months. He is an Associate
Professor of Biochemistry and has been on the PSM faculty for nearly 10 years. In addition he serves as the
Molecular Biology Core Laboratory Director and has developed an excellent network of contacts within the
research community Ponce School of Medicine. He will primarily be responsible for overall administration of
the subcontract at the Ponce School of Medicine. This will include supervision of all personnel related to the
project as well as reporting progress back to the principal investigator (Dr. Conlon). He also serve as a
liaison for communication between Ponce and all other members of the consortium, particularly with respect
to the community and participation aspects.


Damaris Torres, BSIS Implementation Coordinator, will devote two calendar months for the early adoption
of VIVO at the Ponce School of Medicine. Ms. Torres currently serves as the Director of the Management of
Information Systems for the institution and is a key position to support a smooth implementation of this
national network at PSM. She will coordinate all tasks related to the technical part of the implementation
including configuring network and security access to the system. She will be primarily responsible for


PHS 398 (Rev. 11/07)


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Form Page 5






Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Budget Justification continued


implementing any needed changes to existing systems configuration to provide access to VIVO. She will
oversee the security of the systems and access by users and will directly supervise the work of the
implementation developer. She will maintain a secondary role in providing assistance and training to users. Ms.
Torres will also serve as the technical liaison between PSM and the consortium.
Ricardo Espada, BS- Implementation Developer, will devote 6 calendar months to the early adoption of VIVO
at PSM. Mr. Espada is a network specialist at the Ponce school of medicine and will be in charge of the
installation, configuration and maintenance of the VIVO servers. His tasks will include: installation and
configuration of the operating system, and the VIVO software of the Database and the web server. Configure
and administration of the backup/restore software. Server Maintenance, install updates and upgrades to the
server. Monitor traffic to VIVO. Provide training to users.
*Personnel budget is increased by 3% cost of living for year two.
Equipment:
$15,000 requested. Implementation of VIVO at the Ponce School of Medicine will require the support through
additional hardware of a server to hold data and in independent server to surf the web access. A suitable Web
server with the proper technical specifications (such as the IBM system X. 3550 M2 7946 MC1) was recently
quoted for $7000. An appropriate database server (such as the IBM system X. 3650 M2 7947 MC1) was
recently quoted for $8000.
Travel:
$4000 requested. Half of these funds will support travel for Dr. Noel to meet with the PI (Dr. Conlon) in order to
facilitate proper coordination and administration of the early adoption of VIVO at the Ponce School of Medicine.
A second trip for Ms. Torres to interact in person with members of the technical implementation of this
consortium is budgeted to facilitate a fluid adoption of this technology. These trips are intended to assist with
both the community adoption and technical implementation of this national network.
Other expenses:
$2000 requested. Additional hardware such as cables, small media storage/sharing, and a laptop to assist in
the training of network members is requested. These materials will be particularly relevant in facilitating the
addition of off-site faculty, such as clinicians, who do participate in research but do not have regular access to
the physical PSM campus to facilitate interactions with the scientific community.


Continuation Format Page


P HS 398 (Rev. 11 /07)


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 09/01/2009 08/31/2010

PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

Joyce, Gerald Site Lead 0.24 196,700 3,934 984 4,918


King, Paula Dir. Library 1.80 128,357 19,254 4,814 24,068


TBN Programmer 3.0 70,000 17,500 4,375 21,875


TBN Programmer 3.0 70,000 17,500 4,375 21,875







SUBTOTALS 58,188 14,548 72,736
CONSULTANT COSTS

EQUIPMENT (Itemize)



SUPPLIES (Itemize by category)





TRAVEL

PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)


OTHER EXPENSES (Itemize by category)






CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 72,736

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 65,390

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 138,126
PHS 38 (Re. 11/7) Pge 30Formage6


PHS 398 (Rev. 11/07)


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Form Page 4








Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BUDGET FOR ENTIRE PROPOSED PROJECT PERIOD
DIRECT COSTS ONLY

INITIAL BUDGET ADDITIONAL YEARS OF SUPPORT REQUESTED
BUDGET CATEGORY PERIOD
TOTALS (from Form Page 4) 2nd 3rd 4th 5th
PERSONNEL: Salary and fringe
benefits. Applicant organization
only. 72,736 74,917

CONSULTANT COSTS

EQUIPMENT

SUPPLIES

TRAVEL


PATIENT INPATIENT
CARE
COSTS OUTPATIENT

ALTERATIONS AND
RENOVATIONS

OTHER EXPENSES

CONSORTIUM/
CONTRACTUAL DIRECT
COSTS
SUBTOTAL DIRECT COSTS
(Sum = Item 8a, Face Page) 72,736 74,917
CONSORTIUM/
CONTRACTUAL F&A65,390 67,350
COSTS 65,390 67,350
TOTAL DIRECT COSTS 138,126 142,267


TOTAL DIRECT COSTS FOR ENTIRE PROPOSED PROJECT PERIOD$ 280,

JUSTIFICATION. Follow the budget justification instructions exactly. Use continuation pages as needed.


See next page.


PHS 398 (Rev. 11/07)


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Form Page 5







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Budget Justification


Personnel

Gerald Joyce, Principal Investigator (effort = 0.24 calendar months) will provide overall direction for the TSRI
effort on both campuses (Florida and California) as complemented in his role as Dean of the Faculty to assure
a robust implementation, assure the quality and integrity of faculty data collection, and provide valuable
critique of the value and impact of the VIVO system to promote robust research collaborations.


Paula King, Director of Libraries (effort = 1.80 calendar months) will provide day-to-day leadership and
monitoring of the "early implementor" effort while working closely with the working groups from all the
participating institutions. Her participation will be essential to evaluate the interchange of institutional data
with the shared data resources, as well as provide a critique of the utility and robustness of the system for a
research-intensive institute. Paula will also serve as the primary interface for the "community and
sustainability" aspects of the TSRI implementation.


TBN, Programmer (effort = 3.0 calendar months) will act as the primary technical resource for TSRI working
with the collaboration partners to install, implement, configure and secure the system.


TBN, Programmer (effort = 3.0 calendar months) will provide the database and data interchange expertise
necessary to integrate and leverage faculty information from the local campus systems to the VIVO system as
appropriate and will additionally support the primary technical resource (above).


Continuation Format Page


P HS 398 (Rev. 11 /07)


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 9/1/2009 8/31/2010
PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

Nagarajan, Rakesh Site Lead 0.6 0 0 0

Outreach
Holmes, Kristi ueah 6 28,490 5,637 34,127
Lead

Houchins, Caerie Systems 2.4 13,826 2,441 16,267
Admin

Joseph, George DBA 2.4 13,731 3,394 17,125

Mclntosh, Leslie IMP Lead 6 38,819 6,427 45,246

Meyer, Rekha Support 1.2 4,894 1,629 6,523
Specialist

SUBTOTALS 141,124 28,432 169,556
CONSULTANT COSTS

EQUIPMENT (Itemize)



SUPPLIES (Itemize by category)
Computer servers, 3 x $4,000=$12,000; Computer storage, $3,000;
Five workstations/laptops, 5 x $1,100=$5,500; Posters, educational materials, $3,000

23,500
TRAVEL
Lead Travel, $2,400; Outreach Travel, $3,600; Implementation Travel, $3,600 9,600
PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)

OTHER EXPENSES (Itemize by category)
Data entry service to back load faculty profiles @ $10/hour, $62,400



62,400
CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 265,056

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 92,770

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 357,826
PHS 38 (Re. 11/7) Pge 33Formage6


P HS 398 (Rev. 11 /07)


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Form Page 4







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 9/1/2009 8/31/2010

PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

Software
Narkar, Sujay So3.96 21,557 3,931 25,488
Engineer
Jr Biomed
TBN JrBio ed 6 19,807 4,973 24,780
Info Speclist.


+ + 4 i 4 i


SUBTOTALS I 141,1241 28,432 169,556
CONSULTANT COSTS

EQUIPMENT (Itemize)



SUPPLIES (Itemize by category)





TRAVEL

PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)


OTHER EXPENSES (Itemize by category)






CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 265,056

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 92,770

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 357,826
PHS 38 (Re. 11/7) Pge 34Formage6


P HS 398 (Rev. 11 /07)


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Form Page 4







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BUDGET FOR ENTIRE PROPOSED PROJECT PERIOD
DIRECT COSTS ONLY
INITIAL BUDGET ADDITIONAL YEARS OF SUPPORT REQUESTED
BUDGET CATEGORY PERIOD
TOTALS (from Form Page 4) 2nd 3rd 4th 5th
PERSONNEL: Salary and fringe
benefits. Applicant organization
only. 169,556 200,383

CONSULTANT COSTS

EQUIPMENT

SUPPLIES 23,500 3,000

TRAVEL 9,600 9,600

PATIENT INPATIENT
CARE
COSTS OUTPATIENT

ALTERATIONS AND
RENOVATIONS

OTHER EXPENSES 62,400 16,640
CONSORTIUM/
CONTRACTUAL DIRECT
COSTS
SUBTOTAL DIRECT COSTS
(Sum = Item 8a, Face Page) 265,056 229,623
CONSORTIUM/
CONTRACTUAL F&A92,770 80,368
COSTS 92,770 80,368
TOTAL DIRECT COSTS 357,826 309,991

TOTAL DIRECT COSTS FOR ENTIRE PROPOSED PROJECT PERIOD$ 667,

JUSTIFICATION. Follow the budget justification instructions exactly. Use continuation pages as needed.
Rakesh Nagarajan, Principal Investigator (0.6 calendar months, Years 1-2, No salary requested)
Dr. Nagarajan's oversight in this project will be supported under the existing CTSA award, and thus no
additional salary support is requested for Dr. Nagarajan. He is the Biomedical Informatics Program director
of the Washington University's (WU) CTSA, termed the Institute of Clinical and Translational Sciences
(ICTS), which has one of its subaims to implement research networking solutions. In this project, Dr.
Nagarajan will oversee the activities of the WU VIVO Adoption Team. He will meet with the Outreach (Dr.
Holmes) and Implementation (Dr. McIntosh) Leads to review progress, address changes in the
implementation plan, and finalize the ontological framework at WU. Dr. Rakesh Nagarajan is trained as a
physician-scientist and conducted his doctoral research in molecular neuroscience and oncology and has
signficiant experience developing and applying biomedical informatics tools to facilitate clinical and
translational research. In addition to his role in the WU CTSA, he is leading the biomedical informatics
infrastructure development effort at Washington University as co-director of the Alvin J. Siteman Cancer
Center (SCC) Bioinformatics Core, Neuroscience Blueprint Biomedical Informatics Core, and co-director of
the Center for Kidney Disease Research (CKDR) Translational Research Core. Under the direction of Dr.
Nagarajan, these separate informatics groups as well as others have been brought together through the


P HS 398 (Rev. 11 /07)


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Form Page 5






Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


establishment of the WU Center for Biomedical Informatics (CBMI). Dr. Nagarajan and his group are
implementing a common informatics infrastructure to support the diverse needs of physician-
scientists and bench researchers.

Kristi Holmes, Outreach Lead, (6 calendar months, Years 1-2)
Dr. Holmes will lead the outreach efforts at WU. It is expected that she will support the release of the
VIVO application at WU, oversee data entry personnel who will bulk load faculty profiles using
existing resources (e.g. administrative systems, departmental faculty profiles, graduate training
program-based profiles, etc.), coordinate and deliver training sessions to academic departments and
divisions, maintain oversight of project assessment and evaluation efforts at WU, customize training
materials for WU, liaise with other institutions participating in the project, and development of the
ontological framework on a local level at.WU. It is expected that Dr. Holmes will participate in weekly
conference calls with other Outreach Leads and will provide comments to the project coordinators on
project assessment and evaluation as well as feedback on training materials. Dr. Holmes will work
closely with the WU Implementation Lead, Dr. Mclntosh, to coordinate implementation of VIVO at
WU. Dr. Holmes received her PhD in Biochemistry and joined the Washington University's Becker
Medical Library, where she is involved in the development and implementation of the Library's
Bioinformatics@Becker program. This program includes the development and presentation of
bioinformatics resource workshops for the university community, integration of molecular biology
information resources into medical school and graduate-level curricula, and application of
bioinformatics resources to research problems through individualized consultations and collaborative
relationships. She has also served as a course developer and instructor for the NCBI Advanced
Workshop for Bioinformatics Information Specialists offered by the National Center for Biotechnology
Information. Dr. Holmes works in close partnership with the ICTS to develop and support cross-
disciplinary initiatives which aim to facilitate campus-wide educational and professional
development goals. Dr. Holmes's professional interests center upon promotion and support of
collaborative tools and initiatives at the institutional level and beyond. Toward this end she
successfully managed the implementation and assessment of a pilot faculty profiling application at
WU and actively seeks innovative approaches to promote collaboration in the translational research
setting.

Leslie Mclntosh, Implementation and Evaluation Lead, (6 calendar months, Years 1-2)
Dr. Mclntosh will serve as the project implementation and evaluation lead. She will participate in
weekly conference calls with other Implementation Leads and will provide feedback to the project
coordinators on the implementation process at WU. She will also coordinate the deployment and roll
out of VIVO at WU. This will include working closely with Dr. Holmes to plan training sessions,
working with technical personnel (Mr. Houchins, Mr. Joseph, and Mr. Narkar) to deploy VIVO in test
and production environments, and supporting the oversight of data entry personnel who will back load
faculty profile information. Dr. Mclntosh will also serve as the evaluation lead and will work closely
with the TBD Junior Biomedical Informatics Specialist to answer questions such as: 1) How effective
VIVO is in identifying potential collaborators; 3) how useful investigators find VIVO; and 3) How
much personnel, resource, and financial support is required to operate and maintain VIVO. Dr.
Mclntosh obtained her Master's in Public Health and PhD in Epidemiology from Saint Louis University
conducting her dissertation work on the psychometrics of quality of life survey instruments. Dr.
Mclntosh's research interests include using technology to translate and disseminate health data; for
example, developing on-line and computer aided surveys in order to reduce input errors, decreasing
the time to collect survey data, and increasing user accessibility of the survey. She has been a co-
investigator on a grant that used text analysis to evaluate the global youth online discussion forums


Continuation Format Page


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


and consulted with the FBI in methods in social network data collection. She has three years
experience developing and assessing measurement instruments using structural equation modeling
and hierarchical cluster analysis in assessing the psychometric properties of the Medicare Short Form
(SF-36) and the National Eye Institute Visual Functioning Questionnaire (NEI-VFQ) in persons with
and without disabilities. For two years she coordinated, attended, and evaluated state, national, and
international Evidence-Based Public Health (EBPH) training sponsored by state and local health
agencies, the CDC, and Countrywide Initiative Non-communicable Disease Initiative (CINDI) program
within the WHO. Dr. Mclntosh also developed databases, websites, and on-line surveys for both
educational and private institutions.

Caerie Houchins, Systems Administrator (2.4 calendar months, Years 1-2)
Mr. Houchins is responsible for design, deployment, and maintenance of servers and associated
hardware (e.g. RAID arrays and backup tape libraries) in the CBMI. He will be responsible for
creating and managing the hardware infrastructure required to house VIVO on test and production
environments. He has over ten years experience as a software engineer as well as systems
engineering experience. He has worked for several Fortune 500 companies administrating hundreds
of servers of various types and operating systems. Prior to joining CBMI Mr. Houchins was the
Global Team Lead for IT at a medical software company where he specialized in web based
applications hosted on Unix and Linux servers utilizing Java, PHP, Perl, Apache, JBoss, and Tomcat.
He has experience in large scale IT security utilizing IDS systems, various firewalls, log scraping
utilities, packet level inspection techniques. Mr. Houchins has training with both HIPAA regulations
and Sarbanes-Oxley.

George Joseph, Database Administrator (2.4 calendar months, Years 1-2)
Mr. Joseph is responsible for design, deployment, and maintenance of databases in the CBMI. Thus,
he will serve as the database administrator for the project where he will deploy, manage, and secure
the MySQL databases required for the VIVO application in test and production environments. Mr.
Joseph has experience with MySQL and Oracle database management and administration as well as
a strong software engineering background. He has a strong conceptual background of databases,
data warehouse systems, and extract-transform-load tools.

Suiay Narkar, Software Engineer (3.96 calendar months, Years 1-2)
Mr. Narkar will serve as the software engineer for the project. This includes integration of the VIVO
application with local systems at WU including HR databases and integrating the application with a
single institutional sign-on, WUSTL KEY. Mr. Narkar has over four years experience developing
Java, J2EE, web-based applications, including biomedical informatics systems such as the clinical
studies data management system being utilized within the ICTS.

Rekha Meyer, Support Specialist (1.2 calendar months, Years 1-2)
Rekha Meyer will provide technical and end user support for the VIVO application. She will be
responsible for both email-based and telephone consultations and will work closely with other
technical personnel to answer any questions that may be raised by faculty and personnel who will test
and utilize the VIVO application at WU. Dr. Meyer has a PhD degree in Biochemistry from the
University of Tennessee and joined the CBMI in January 2006. Dr. Meyer has an extensive research
background in genomics and molecular biology. Aside from domain expertise, she has software
engineering experience while at the Washington University Genome Sequencing Center. Dr Meyer is
primarily responsible for all technical support issues for applications developed or supported by the
CBMI including all requests to the help desk at help(abmi.wustl.edu. Specific support issues involve


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


responding to desktop support calls, data loading, data submissions to public repositories, database
querying, and application installation and testing. In addition to end user support, she also provides
application level support for tools such as caArray (microarray data management system) and
caTissue (biospecimen informatics system)

TBD, Junior Biomedical Informatics Specialist, (6 calendar months in Year 1 and 12 calendar months
in Year 2)
This individual will work under the direction of Dr. Mclntosh to execute the evaluation plan of the
VIVO consortium. S/he will conduct interviews with scientists and the WU VIVO Adoption Team at
our site in collaboration with Dr. Holmes and will acquire interview data (from local scientists and the
site-specific adoption team) from other sites through the Outreach Lead. S/he will then analyze these
data sets in collaboration with Dr. Mclntosh and prepare quarterly reports. These reports will be
made available to the Executive Advisory Board.

Supplies ($23,500 in Year 1, $3,000 in Year 2)
Funds ($15,000) are requested for servers ($12,000) and storage ($3,000) on RAID arrays. We
expect to have a production environment with an Apache web server, two application servers hosting
Tomcat which will provide failover capability, and a MySQL database server. In addition, the test
environment will include an Apache web server, a single Tomcat server, and a MySQL database
server. These seven servers will be constructed within our virtual machine environment, and thus
$12,000 is requested for this infrastructure. Storage to persist faculty profiles and other required
information in VIVO will be provided by RAID array slices, and thus $3,000 is requested for these
resources.

Supplies ($3,000) for posters that will be presented at VIVO full group meetings and
evaluation/assessment and educational materials are requested in Years 1 and 2. In addition, five
laptops ($1,100/laptop = $5,500) are required for the Outreach Lead and four data entry personnel to
review/edit training materials, to review/edit ontologies, and to execute the overall project (Outreach
Lead) as well as to back load faculty profiles (data entry personnel).

Travel ($9,600 in Years 1 and 2)
Funds ($7,200 in Years 1 and 2) are requested for two trips each year for the PI, Outreach Lead, and
Implementation Lead to the University of Florida where the entire VIVO team will meet to review
progress, evaluate new features in VIVO, and present end user feedback. In addition, funds ($2,400)
are requested for travel to two conferences where the Outreach Lead or the Implementation Lead will
present the WU adoption of VIVO.

Other expenses ($62,400 in Year 1 and $16,640 in Year 2)
Four data entry personnel will work to back load faculty profiles from existing sources such as
center/departmental/school profile pages or paper content. It is anticipated that these members will
work 30 hours/week (4 personnel $10/hour 30 hours/week 52 weeks/year = $62,400) in Year 1
and 8 hours/week (4 personnel $10/hour 8 hours/week 52 weeks/year = $16,640) in Year 2.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 9/1/2009 8/31/2010
PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

Cole, Curtis L. Site Lead 0.30 196,700 4,918 1,377 6,295


Alpert, Paul Info Arch 2.4 63,402 12,680 3,551 16,231


Dickinson, Dan Dev Mgr 1.2 91,800 9,180 2,570 11,750


Michelini, Peter Project Mgr 1.2 119,600 11,960 3,349 15,309

Site
Ruffing, John Interat 1.2 116,282 11,628 3,256 14,884
Integration

Turner, Jessie DBA 0.60 103,032 5,152 1,442 6,594

SUBTOTALS 1 178,389 49,949 228,338
CONSULTANT COSTS

EQUIPMENT (Itemize)
Test Server=7,500; PCs/Printers=3,500; Development Server=7,500

18,500
SUPPLIES (Itemize by category)
Miscellaneous=1,000
Programmer Productivity Software=500


1,500
TRAVEL
Round trip travel to Ithaca and National Meetings/ Conferences 7,500
PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)


OTHER EXPENSES (Itemize by category)






CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 255,838

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 166,178

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 422,016
PHS 38 (Re. 11/7) Pge 39Formage6


P HS 398 (Rev. 11 /07)


Page 39


Form Page 4







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

DETAILED BUDGET FOR INITIAL BUDGET PERIOD FROM THROUGH
DIRECT COSTS ONLY 9/1/2009 8/31/2010
PERSONNEL (Applicant organization only) Months Devoted to Project DOLLAR AMOUNT REQUESTED (omit cents)
ROLE ON Cal. Acad. Summer INST.BASE SALARY FRINGE
NAME PROJECT Mnths Mnths Mnths SALARY REQUESTED BENEFITS TOTAL

PD/PI

TBN Unix Sys 1.2 95,000 9,500 2,660 12,160
Admin
BizTalk
TBN Programmer 0.24 101,065 2,021 566 2,587
Programmer
SAP Proc
TBN SAP Proc 0.24 92,500 1,850 518 2,368
Programmer

TBH Programmer 12 90,000 90,000 25,200 115,200

User Support
TBH Access 3.60 65,000 19,500 5,460 24,960
Access




SUBTOTALS 122,871 34,404 152,275
CONSULTANT COSTS

EQUIPMENT (Itemize)



SUPPLIES (Itemize by category)





TRAVEL

PATIENT CARE COSTS INPATIENT
OUTPATIENT
ALTERATIONS AND RENOVATIONS (Itemize by category)


OTHER EXPENSES (Itemize by category)






CONSORTIUM/CONTRACTUAL COSTS DIRECT COSTS

SUBTOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD (Item 7a, Face Page) $ 255,838

CONSORTIUM/CONTRACTUAL COSTS FACILITIES AND ADMINISTRATIVE COSTS 166,178

TOTAL DIRECT COSTS FOR INITIAL BUDGET PERIOD $ 422,016
PHS 38 (Re. 11/7) Pge 40Formage6


PHS 398 (Rev. 11/07)


Page 40


Form Page 4







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BUDGET FOR ENTIRE PROPOSED PROJECT PERIOD
DIRECT COSTS ONLY
INITIAL BUDGET ADDITIONAL YEARS OF SUPPORT REQUESTED
BUDGET CATEGORY PERIOD
TOTALS (from Form Page 4) 2nd 3rd 4th 5th
PERSONNEL: Salary and fringe
benefits. Applicant organization
only. 228,338 351,309

CONSULTANT COSTS

EQUIPMENT 18,500 2,000

SUPPLIES 1,500 1,500

TRAVEL 7,500 7,500

PATIENT INPATIENT
CARE
COSTS OUTPATIENT

ALTERATIONS AND
RENOVATIONS

OTHER EXPENSES
CONSORTIUM/
CONTRACTUAL DIRECT
COSTS
SUBTOTAL DIRECT COSTS
(Sum = Item 8a, Face Page) 255,838 362,309
CONSORTIUM/
CONTRACTUAL F&A166,178 249,993
COSTS 166,178 249,993
TOTAL DIRECT COSTS 422,016 612,302

TOTAL DIRECT COSTS FOR ENTIRE PROPOSED PROJECT PERIOD $ 1 ,318
$~ 1,034,318
JUSTIFICATION. Follow the budget justification instructions exactly. Use continuation pages as needed.
PERSONNEL. Funds are requested for the following existing staff:
Curtis Cole, WCMC PI/ PD (0.025 FTE). Dr. Cole is the Chief Information Officer at WCMC and Core
Director of the CTSC Biomedical Informatics Key Function. As the PI/PD for this site, Dr. Cole will provide
overall direction and management of the project and personnel.


John Ruffing, Site Integration Manager (0.10 FTE). Mr. Ruffin is the Operations Manager for WCMC and
currently coordinates WCMC's participation in the Ithaca VIVO installation. He will continue in that now
expanded role as we share new semantic concepts to the VIVO collaboration.


Peter Michelini, Project Manager (0.10 FTE). Mr. Michelini is a certified project manager who has managed
several research oriented information technology projects at WCMC including the Research Profile System
(RPS) and implementation of the clinical trial management system. He will coordinate all project activities,
equipment, schedules, and staff.


PHS 398 (Rev. 11/07)


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Form Page 5






Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BUDGET JUSTIFICATION CONTINUED

Dan Dickinson, Development Manager (0.10 FTE). Mr. Dickinson leads the central WCMC development group
which includes the Content Management System (CMS) and RPS. He will manage the technical resources and
approach to the VIVOweb implementation.

Paul Alpert, Digital Service Librarian (0.20 FTE). Mr. Alpert is a Librarian in the Samuel J. Wood Library and
will serve as the central content expert managing and mapping the VIVO taxonomy to internal systems.

Jessie Turner, Senior Database Administrator (0.05 FTE). Ms. Turner currently manages WCMC's core
Oracle infrastructure and will manage the database portion of the VIVO implementation.

The following resources will be utilized as needed from pools of existing central information technology staff:
- Unix System Administrator (0.10 FTE)
- BizTalk programmer (0.02 FTE)
- SAP Process Integration Engineer (0.02 FTE)
- Partner Site Integrator (1.00 FTE). In the second year after the core infrastructure is established, the
integrator will work with CTSC partner institutions and non-WCMC investigators on implementaiton and use of
VIVOweb through the CTSC Portal.

The following staff will be recruited to for the project:
Programmer (1.00 FTE) for implementation of the VIVO system and integration into Cerebro and RPS.
Senior User Support Technician (0.30 FTE) will develop documentation for the implementation, help the test
users, and manage local access control.

NON PERSONNEL
WCMC intends to continue using the Cornell Ithaca production instance of VIVOweb until federation services
are developed that make this less desirable. However, to assist in the creation of such services and to align
our internal system semantics with VIVOweb we will implement test and development instances of VIVOweb
locally. Two servers (or virtual machines) will be needed for this. New TBN staff will need PCs and developers
with need software tools for their work. Travel for several of the technical staff and leadership between NY and
Ithaca several times a year is anticipated as well as travel for national meetings of the VIVOweb development
consortium members.


PHS 398 (Rev. 11/07) Page 42 Continuation Format Page


Page 42


P HS 398 (Rev. 11 /07)


Continuation Format Page







Principal Investigator/Program Director (Last, First, Middle): Conlon, Michael


BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
Conlon, Michael Director of Biomedical Informatics, University of
eRA COMMONS USER NAME Florida

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION (if a ) YEAR(s) FIELD OF STUDY
Bucknell University, Lewisburg, PA B.A. 1975 Mathematics
Bucknell University, Lewisburg, PA B.A. 1975 Economics
University of Florida, Gainesville, FL M.Stat 1979 Statistics
University of Florida, Gainesville, FL Ph.D. 1982 Statistics
A. Positions and Honors
Positions and Employment
1980-83 Director, Statistical Consulting Center, Center for Instructional and Research Computing Activities
1982-83 Asst. Dir. of Acad. Computing, Ctr for Instr. and Research Computing Activities, Univ. of Florida
1992-08 Research Associate Professor, Department of Statistics, University of Florida
1993-07 Director, Information Resources and Technology Prog, Liberal Arts and Sciences, Univ. of Florida
1997-02 Assistant Vice President for Health Affairs, Academic Information Systems and Support and Chief
Information Officer, University of Florida Health Science Center
2002- Director of Data Infrastructure, University of Florida
2002-03 Co-founder and Chief Technology Officer, MarCon Global Data Solutions, Incorporated
2005-09 PeopleSoft Implementation Officer, University of Florida
2008- Director, Biomedical Informatics, University of Florida
2008- Associate Director, Clinical and Translational Science Institute, University of Florida
2008- Director, Clinical and Translational Informatics Program, University of Florida
2008- Research Associate Professor, Epidemiology and Health Policy Research, University of Florida
2009- Associate CIO IT Architecture, University of Florida
Other Experience
1985 Member, MedComp Southeast
1986-90 Reviewer, Technometrics.
1987-88 Member, General Clinical Research Center Advisory Board
1989-92 Member, University of Florida Institutional Review Board
1990-92 Vice Chairman, University of Florida Institutional Review Board
1991 Secretary/Treasurer, Statistical Computing and Graphics Section, American Statistical Association
1991-02 Member, Health Science Center Instructional Support Committee
1992-95 Scientific Reviewer, NIH National Heart, Lung and Blood Institute
1993 Reviewer, American Statistician.
1993-96 Chair, University Academic Computing Committee
1994-96 Scientific Reviewer, NIH National Cancer Institute
1994-02 Member, University Distance Learning Council
1995-96 Founding Editor, AmStat OnLine. American Statistical Association.
1996-00 Member, Electronic Learning Forum
1997 Associate Editor, Journal of Quality Technology
1997-02 Member, Shands Hospital Clinical Computing Committee
1997-02 Member, Campus Network Advisory Committee
1997-02 Member, University Video Advisory Council
1998-02 Member, Faculty Advisory Committee, University of Florida Brain Institute
PHS 398 (Rev. 11/07) Page 43 Biographical Sketch Format Page






Principal Investigator/Program Director (Last, First, Middle): Conlon, Michael
1998-02 Chair, Health Science Center Network Advisory Group
1999-02 Project Director, UF IAIMS
1999-03 Member, American Statistical Association Electronic Publications Committee
1999-03 Associate Editor, AmStat OnLine, American Statistical Association
1999-03 Member, American Statistical Association Publications Committee
2000-01 Member, University Information Technology Review Task Force
2000-02 Board of Directors, National Institute of Statistical Sciences.
2001-02 Member, University Telehealth Advisory Board
2001-02 Member, University High Performance Computing Committee
2001-02 Member, University Distance Education Advisory Committee
2001-02 Member, University Information Technology and Advisory Council
2001-03 Member, Microsoft National Higher Education Advisory Group
2002- Member, Information Technology Advisory Committee, Data Infrastructure and Administrative
Computing
2002-03 Chair, University Directory Services Committee
2003- Chair, Information Technology Advisory Committee on UF Active Directory
2003-05 Editor, AmStat OnLine, American Statistical Association
2004- Member, Educause Working Group on Identity Management
2006- Member, Educause Identity Management Steering Committee
2007-08 Member, Health Science Center Information Architecture Committee
2008- Chair, University Planning Group on Computational Biology
2008- Chair, Health Science Center Information Architecture Committee
2008- Member, Health Science Center Information System Advisory Council
2008- Member, InCommon Workgroup, Research Administration
Honors
1975 Phi Beta Kappa
1975 Pi Mu Epsilon
1975 Graduate Council Fellow, University of Florida
1982 Departmental honors, qualifying exam, University of Florida

B. Selected Peer-Reviewed Publications (in chronologic order)
1. Khuri, A. I. and Conlon, M. "Simultaneous Optimization of Multiple Responses Represented by Polynomial
Regression Functions," Technometrics, 23, 1981, pp 363-376.
2. Conlon, M. "Incorporating Statistical Relationships in Data Management," Proceedings of the Statistical
Computing Section of the American Statistical Association, 1984, pp 76-79.
3. Conlon, M. "Implementing IMSL Routines as SAS Functions," Proceedings of the 1985 SUGI Conference,
1985, pp 163-164.
4. Conlon, M. "The Design and Implementation of a Software Library for Statistical Research and Practice,"
Proceedings of the Statistical Computing Section of the American Statistical Association, 1986, pp 212-
217.
5. Conlon, M. "MLIB: A Statistical Computing Library for the IBM/PC," American Statistician, 41, 1987, pp
329.
6. Conlon, M. "Software Tools for Implementing Network Algorithms," Proceedings of the Statistical
Computing Section of the American Statistical Association, 1987, pp 374-378.
7. Conlon, M. "Calling Sequences for Statistical Computing," Computer Science and Statistics: Proceedings
of the 19th Symposium on the Interface, 1987, pp 353-356.
8. Conlon, M. "Review of STAT, a program by Gary Perlman," The American Statistician, 43, 1989, pp 171-
174.
9. Conlon, M. and Thomas, R. G. "A New Confidence Interval for the Difference of Two Binomial
Proportions," Computational Statistics and Data Analysis 9, 1990, pp 237-241.
10. Conlon, M. and Anderson, G. C. "Three Methods of Random Assignment: Comparison of Balance
Achieved on Potentially Confounding Variables," Nursing Research, 39, 1990, pp 376-379.


Biographical Sketch Format Page


PH S 398 (Rev. 11 /07)


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Principal Investigator/Program Director (Last, First, Middle): Conlon, Michael
11. Stewart, R. B., Conlon, M., Hale, W. E., Marks, R. G., Moore, M. T., and May, F. E. "Factors Predicting
One Year Mortality Among an Ambulatory Elderly Population," Journal of Pharmacoepidemiology, 1, 1990,
pp 3-19.
12. Conlon, M. "Evaluating Functions over Lattices," In Page, C. and LePage, R. (Eds.) Computer Science
and Statistics, Proceedings of the 22nd Symposium on the Interface, New York: Springer-Verlag, 1990, pp
315-317.
13. Conlon, M. and Chang, M. N. "An Algorithm for the Exact Distribution of the Kaplan-Meier Estimator Under
the Proportional Hazards Model," American Statistical Association, Anaheim, 1990.
14. Mladinich, C. R. J., Buergelt, C. D., and Conlon, M. "Evaluation and Comparison of Automated and
Manual Biopsy Devices," American Association for Laboratory Animal Science Bulletin, 30, 1991, pp 9-11.
15. Conlon, M. and Sincich, T. L. DellenStat: Statistical Software to Accompany Statistics by Example, 4th
edition, Dellen Publishing Co., San Francisco, CA, 1991, 266 pages.
16. Conlon, M. "A Network Algorithm for Exact and Approximate Computation of Coefficients of Product
Polynomials," Proceedings of the Statistical Computing Section of the American Statistical Association,
1992, pp 156-159.
17. Thomas, R. G. and Conlon, M. "Sample Size Determination Based on Fisher's Exact Test for Use in
Comparative Trials with Small Events Rates," Controlled Clinical Trials. 13, 1992, pp 134-147.
18. Conlon, M. "The Controlled Random Search Procedure for Function Optimization," Communications in
Statistics -Simulation and Computation. 21(3), 1992, pp 919-923.
19. Thomas, R. G. and Conlon, M. "An Algorithm for the Rapid Evaluation of the Power Function for Fisher's
Exact Test," Journal of Statistical Computation and Simulation. 44, 1992, pp 63-73.
20. Conlon, M. and Thomas, R. G. "Algorithm AS 280: The Power Function for Fisher's Exact Test," Applied
Statistics. 42(1), 1993, pp 258-260.
21. Eyler, F. D., Behnke, M., Conlon, M., Woods, N. S., and Frentzen, B. "Consequences of Prenatal Cocaine
Use in a Rural Setting: A Comparison of Neonates matched on Maternal Risk Factors," Neurotoxicology
and Teratology, 16, 1994, pp 81-87.
22. Behnke, M., Eyler, F. D., Conlon, M., Woods, N. S., and Casanova, O. Q. "Multiple Risk Factors Do Not
Identify Cocaine Use in Rural Obstetrical Patients," Neurotoxicology and Teratology, 16, 1994, pp 479-484.
23. Conlon, M. "Statistical and Methodological Issues in the Longitudinal Study of Maternal Substance Abuse
and Perinatal/Developmental Outcomes," Epidemiology and Public Health Research in Florida, Gainesville,
FL, 1995.
24. Conlon, M. "Planning for Data Management," American Statistical Association, Chicago, IL, 1996.
25. Behnke, M. Eyler, F. D., Conlon, M., Casanova, O. Q., and Woods, N. S. "How Fetal Cocaine Exposure
Increases Neonatal Hospital Costs," Pediatrics, 99(2), 1997, 204-208.
26. Eyler, F. D., Behnke, M., Conlon, M., Woods, N. S., and Wobie, K. "Birth Outcome From a Prospective,
Matched Study of Prenatal Crack/Cocaine Use I: Interactive and Dose Effects on Health and Growth,"
Pediatrics, 101(2), 1998, pp 229-237.
27. Pepine, C., Handberg-Thurmond, E., Marks, R., Conlon, M., Cooper-Dehoff, R., Volker, P, and Ziller, P.
"Rationale and Design of the International Verapamil SR/Trandolapril Study (INVEST): An Internet-Based
Randomized Trial in Coronary Artery Disease Patients with Hypertension," J. American College of
Cardiology, 32(5), 1998, pp 1228-1237.
28. Behnke, M., Eyler, F. D., Conlon, M., Wobie, K., Woods, N. S., and Cumming, W. "Incidence and
Description of Structural Brain Abnormalities in Newborns Exposed to Cocaine," Journal of Pediatrics,
132(2), 1998, pp 291-4.
29. Marks, R. and Conlon, M. "INVEST A Web Based Clinical Trial," Florida Chapter Meeting of American
Statistical Association's meeting, Orlando, FL, February 6, 1998.
30. Conlon, M. "Web-Based Clinical Trials," invited presentation at Informatics and Clinical Research, Quebec,
Canada, October 16, 1998.
31. Conlon, M. "INVEST Study Role of the Internet System," invited presentation on the INVEST Clinical
Trial System, Rome, Italy, October 22, 1998.
32. Conlon, M. "Paradigm Shifts in Internet Clinical Trials," invited presentation at the 23rd Annual Meeting of
the Association for Clinical Research Professionals, Washington, DC, May 26, 1999.
33. Conlon, M. "E-Commerce for the Management of Clinical Trials," invited presentation at Basic E-
Commerce Strategy for the Pharmaceutical Industry, London, England, March 17, 2000.
PHS 398 (Rev. 11/07) Page 45 Biographical Sketch Format Page






Principal Investigator/Program Director (Last, First, Middle): Conlon, Michael
34. Marks, R., Conlon, M., and Moyer, E. "Clinical Trials Using Internet Technology," invited presentation at
the 3rd Annual Meeting of BioFlorida, Tampa, FL October 16, 2000.
35. Conlon, M. "Experience with a Large Web-Based International Clinical Trial," keynote presentation, Clinical
Trials: The Next Phase!, presented by Access Conferences, London, England, December 14, 2000.
36. Davis-Eyler, F., Behnke, M., Garvan, C., Stewart-Woods, N., Wobie, K., and Conlon, M., "Newborn
Evaluations of Toxicity and Withdrawal Related to Prenatal Cocaine Exposure," Neurotoxicology and
Teratology, 23, 2001, pp 399-411.
37. Conlon, M. and Marks, R. G. "A Vision for Web-based Clinical Trials," in Mitchard, Mervyn (ed) Topics in
Clinical Research, 2001.
38. Marks, R., Bristol, H., Conlon, M., and Pepine, C. J. "Enhancing Clinical Trials on the Internet: Lessons
Learned from INVEST," Clinical Cardiology, 24(V), 2001, V17-V23.
39. Marks, R. G., Conlon, M, and Ruberg, S. J. "Paradigm Shifts in Clinical Trials Enabled by Information
Technology," Statistics in Medicine 20, 2001, pp 2683-2696.
40. Conlon, M. "Web-based Clinical Trials," in Cooper, Elizabeth (ed) Business Briefing: PharmaTech 2001,
World Markets Research Centre, Ltd., London, 2001, pp 77-81.
41. Conlon, M. "Using the Web for Data Collection in Clinical Trials," invited workshop presentation at the
annual meeting of the Society for Clinical Trials, Denver, CO, May 20, 2001.
42. Conlon, M. "The INVEST Web-Based Clinical Trial," invited keynote presentation, International Society for
Clinical Trials, Sydney, Australia, October 22, 2002.
43. Anderson, G. C., Radjenovic, D., Chiu, S.-H., Conlon, M., and Lane A. E. "Development of an
Observational Instrument to Measure Mother-Infant Separation Post Birth," Journal of Nursing
Measurement, 12(3), 2004, pp 215-234.
44. Conlon, M. "GatorAid: Identity Management at the University of Florida," invited presentation at CUMREC
2005, Keystone, CO, May 17, 2005.
45. Conlon, M. "Identity Management at UF," invited presentation at Educause Conference, Orlando, FL,
October 19, 2005.
46. Conlon, M. "Credentialing, Levels of Assurance and Risk: What's Good Enough," invited presentation at
Educause Campus Architectural Middleware Planning (CAMP), Tempe, AZ, February 8, 2006.
47. Conlon, M. "Enterprise Integration at UF," invited presentation at Microsoft Higher Education Executive
Forum, Tampa, FL, June 22, 2006.
48. Conlon, M. "Creating Identity Management Services at the University of Florida," invited presentation at
Third Annual Cal State University Symposium on Identity Management, Los Angeles, CA, July 19, 2006.
49. Conlon, M. "Reality and Response: The Higher-Education Customer Perspective," invited presentation at
MGX2006, Orlando, FL, July 21, 2006.
50. Conlon, M. "Science, Statistics and the Relevance of Colleges and Universities," keynote presentation at
Consortium of College and University Media Centers, Gainesville, FL, October 19, 2007.
51. Barton, T.J., Berman, M., Conlon, M., Haeusser, J. "Minimize Exposure: Correlating Identities Across the
Enterprise," invited panel at Educause and Internet2 Campus Architecture and Middleware Planning:
Bridging Security and Identity Management, Tempe, AZ, February 13, 2008.
52. Conlon, M. "Organizing a Campus Change: Planning for Identity and Access Management Improvements
at UF," invited presentation at Educause Southeast Regional Conference 2008, Jacksonville, FL, June 3,
2008.

C. Research Support
None


Biographical Sketch Format Page


PH S 398 (Rev. 11 /07)


Page 46







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.


EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DE EYEAR(s) FIELD OF STUDY
(if applicable)
Rensselaer Polytechnic Institute, Troy, New York 1992-1993 Electrical Engineering
Santa Fe Community College, Gainesville, 1994-1998 Electrical Engineering
Florida




Please refer to the application instructions in order to complete sections A, B, and C of the Biographical
Sketch.

A. Positions and Honors

Positions and Employment
1999- 2000 Data Analyst, Soldout.com, Darien, Connecticut
2000 2000 Senior Data Analyst, Soldout.com, Darien, Connecticut
2000 2001 Senior Data Analyst, Media Space Solutions, Norwalk, Connecticut
2001 2002 Senior Software Consultant, Geode Software, New Britain, Connecticut
2002 2003 Senior Software Consultant, bFinity Inc., High Springs, Florida
2003 IT Senior (Informatics Manager), College of Medicine, University of Florida,
Gainesville, Florida

Other Experience and Professional Memberships
2001 Microsoft Certified Professional
2001 Microsoft Certified Professional, Microsoft SQL Server Database Implementation and
Design
2003 2004 Member, Technical Security sub-Committee, Security Program for the Information and
Computing Environment
2004 Unit Information Security Manager, Dept. Epidemiology and Health Policy Research,
Research Data Coordinating Center
2006 Guest Lecturer ("How to approach Research Data Management"), Introduction to
Clinical/Translational Research, GMS 6181, General Clinical Research Center, University of Florida
2007 Guest Lecturer ("How to approach Research Data Management"), Introduction to
Clinical/Translational Research, GMS 6181, General Clinical Research Center, University of Florida
2008 Guest Lecturer ("How to approach Research Data Management"), Introduction to
Clinical/Translational Research, GMS 6181, General Clinical Research Center, University of Florida
2008 Florida Center for Aids Research, Executive Committee Member
2008 American Medical Informatics Association

B. Publications
Development of a Tumor Registry Informatics System, for the Florida Center for Brain Tumor
Research (Poster), National Library of Medicine, Integrated Advanced Information Management
Systems (IAIMS) Consortium 2007 Annual Meeting, Chicago Illinois
PHS 398 (Rev. 11/07) Page 47 Biographical Sketch Format Page






Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


C. Research Support
Ongoing Research Support
529-07-0093-00001 (PI: EA Shenkman) 12/13/2007-08/31/2010
State of Texas/Texas Health & Human Services Commission
Evaluating Health Care in Texas Medicaid and Children's Health Insurance Program
The goal of this project is to provide the Texas Health and Human Services Commission with the data and
information they need to fulfill their mission of continuously improving the quality of care provided to Medicaid
and Children's Health Insurance Program recipients in the State of Texas.
Role: Database IT Manager

COQNC (PIs: SK Aydede & EA Shenkman) 02/01/2007-06/30/2008
Florida Department of Health, Children's Medical Services
Care Coordination, Disease Management Guideline and Web-Based Module Development
The goal of this project is the development of organizational tools and techniques that would support and
improve the family-centered, comprehensive and coordinated managed system of care for children with special
health care needs in Florida.
Role: Database IT Manager

P30 AG028740.02 (PI: M Pahor) 04/01/2007-03/31/2012
NIH
Claude D Pepper Older American Independence Center
The goal of this project is to assess the risk factors and better understand the biological reasons for physical
disability in older adults; to develop and test effective prevention and rehabilitation therapies; and to educate
and train new investigators in research on aging and disability, while developing their leadership qualities and
roles.
Role: Database IT Manager

051779 (PI: AC Wagenaar) 10/01/2004-06/30/2008
Robert Wood Johnson Foundation
Reducing Underage Drinking Through Coalitions Evaluation
This goal of this project is to evaluate the Underage Drinking through Coalitions program in 10 states, using a
time-series quasi-experimental design.
Role: Database IT Manager


Completed Research Support
529-03-0012-00001 (PI: EA Shenkman) 08/01/2002-02/29/2008
State of Texas/Texas Health & Human Services Commission
Evaluating Health Care in Texas Medicaid and Children's Health Insurance Program
The goal of this project is to provide the Texas Health and Human Services Commission with the data and
information they need to fulfill their mission of continuously improving the quality of care provided to Medicaid
and Children's Health Insurance Program recipients in the State of Texas.
Role: Database IT Manager

H93 MC00073 (PI: LM Youngbalde) 07/01/2002-06/30/2007
HRSA, Maternal & Child Health Bureau
Outreach to Uninsured Children with Special Health Care Needs (CSHCN): Telemedicine Links Between Title
V and Community Health Centers
The purpose of this project is to reach uninsured CSHCN in Florida and enroll them in insurance, particularly
those in underserved communities that traditionally have faced numerous barriers to care: the black and
Hispanic communities, and children living in rural areas.
Role: Database IT Manager


PH S 398 (Rev. 11 /07)


Page 48


Biographical Sketch Format Page







Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME Victor H. Yngve Associate Professor, School of
Borner, Katy Library and Information Science, Indiana University,
eRA COMMONS USER NAME (credential, e.g., agency login) Bloomington
kborner
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DE EYEAR(s) FIELD OF STUDY
(if applicable)
University of Kaiserslautern Ph.D. 1997 Computer Science
University of Technology, Leipzig MA 1991 Engineering/Electronics


Section A: Positions and Honors:

Skilled Worker, RFT Fernmeldewerk Leipzig, Development Department, Aug. / Sept. 1987
Assistant Worker, University of Technology Leipzig, Department of Electronics, 1988 199.
Practical Course, Westinghouse Controlmatic GmbH, Frankfurt a. M., Oct. Dec. 1990
Research Assistant in BMBF funded projects GOSLER and FABEL, University of Technology Leipzig,
Department of Mathematics and Computer Science, 1991- 1994.
Professional Services (Technical Development), Nov. 1992 June 1998.
Development Engineer, Horiba LTD, Automotive Instruments Development Department, Kyoto, Japan, July /
Aug. 1993
Ph.D. Studies, Boston University, Department of Computer Science, USA, Aug. / Sept. 1994
Research Assistant in the BMBF funded project FABEL, University of Freiburg, Center for Cognitive Science,
1994- 1996
Research Associate and Instructor, University of Bielefeld, Faculty of Technology, 1996 1998
Visiting Assistant Professor, Computer Science Department, Indiana University, Bloomington, Aug. 1998 July
1999
Visiting Assistant Professor, School of Library and Information Science, Indiana University, Bloomington, Aug. -
Dec 1999
Assistant Professor School of Library and Information Science, Indiana University, Jan. 2000 March 2005
Core Cognitive Science Faculty, Indiana University, Bloomington, Jan. 2000 present
Adjunct Associate Professor School of Informatics, Indiana University, Aug. 2001 present
Associate Professor School of Library and Information Science, Indiana University, June 2005 present
Victor H. Yngve Associate Professor School of Library and Information Science, Aug. 2007 present

Member, National Science Foundation, Alan T. Waterman Award Committee (through 5/31/2009)
Guest Editor, Informetrics Special Issue on the Science of Science, Elsevier 3(3), 2009.
Chair, Visualization and Data Analysis Conference, SPIE, San Jose California, January 20-23, 2009
Outstanding Junior Faculty Award, Indiana University, Bloomington, Nov. 2003.
Pervasive Technology Laboratories Fellowship, Indiana University, Sept. 2003 Aug. 2004.
SBC Fellow (formerly Ameritech Fellow), Round 4, 2003/2004.
Trustees Teaching Award for the School of Library and Information Science, Indiana University, 2003.
Ph.D. Fellowship Studienstiftung des Deutschen Volkes e.V., Germany, 1992 1995.
Altstipendiat Konrad Adenauer Stiftung e.V., Germany.


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Section B: Applicable Publications

Journal Articles: Peer-Reviewed

Borner, Katy. (2001). Efficient case-based structure generation for design support. Artificial Intelligence
Review, Kluwer Academic Publishers, 16(2):87-118.
Boyack, Kevin W. and Borner, Katy. (2003). Indicator-Assisted Evaluation and Funding of Research:
Visualizing the Influence of Grants on the Number and Citation Counts of Research Papers, Journal of the
American Society of Information Science and Technology, Special Topic Issue on Visualizing Scientific
Paradigms, 54(5):447-461.
Borner, Katy, Maru, Jeegar and Goldstone, Robert. (2004). The Simultaneous Evolution of Author and Paper
Networks. Proceedings of the National Academy of Sciences of the United States of America,
101(Suppl_1):5266-5273. Also available as cond-mat/0311459
Mane, Ketan K. and Borner, Katy. (2004). Mapping Topics and Topic Bursts in PNAS. Proceedings of the
National Academy of Sciences of the United States of America, 101 (Suppl. 1):5287-5290. Also available as
cs.IR/0402029.
Shiffrin, Richard M. and Borner, Katy. (2004). Introduction: Mapping Knowledge Domains. Proceedings of the
National Academy of Sciences of the United States of America, 101 (Suppl_1):5183-5185
Chen, Chaomei and Borner, Katy. (Feb. 2005). The Spatial-Semantic Impact of a Collaborative Information
Virtual Environment on Group Dynamics. PRESENCE: Teleoperators and Virtual Environments. Special
Issue on Collaborative Information Visualization Environments, 14(1): pp. 81-103. Supplementary Material.
Borner, Katy, Dall'Asta, Luca, Ke, Weimao and Vespignani, Alessandro. (April 2005) Studying the Emerging
Global Brain: Analyzing and Visualizing the Impact of Co-Authorship Teams. Complexity, special issue on
Understanding Complex Systems, 10(4): pp. 58-67. Also available as cond-mat/0502147.
Boyack, Kevin W., Klavans, Richard and Borner, Katy. (2005). Mapping the Backbone of Science.
Scientometrics. 64(3), 351-374.
Holloway, Todd, Bozicevic, Miran and Borner, Katy. (2007) Analyzing and Visualizing the Semantic Coverage
of Wikipedia and Its Authors. Complexity, Special issue on Understanding Complex Systems. 12(3), pp.
30-40. Also available as cs.IR/0512085.
Borner, Katy, Penumarthy, Shashikant, Meiss, Mark and Ke, Weimao. (2006) Mapping the Diffusion of
Scholarly Knowledge Among Major U.S. Research Institutions. Scientometrics. 68(3), pp. 415-426.
Borner, Katy, Hardy, Elisha, Herr, Bruce W., Holloway, Todd and Paley, W. Bradford (July 2007) Taxonomy
Visualization in Support of the Semi-Automatic Validation and Optimization of Organizational Schemas.
Informetrics. 1(3), pp. 214-225.
Borner, Katy (2007). Making Sense of Mankind's Scholarly Knowledge and Expertise: Collecting, Interlinking,
and Organizing What We Know and Different Approaches to Mapping (Network) Science. Environment and
Planning B: Planning and Design. Vol. 34 (5), 808-825, Pion.
Boyack, Kevin W., Borner, Katy and Klavans, Richard. (2009) Mapping the Structure and Evolution of
Chemistry Research. In Scientometrics. 79(1), pp. 45-60.

Books/Book Chapters, Peer-Reviewed

Borner, Katy. (1994). Structural similarity as guidance in case-based design. In Topics in Case-Based
Reasoning Selected Papers from the First European Workshop on Case-Based Reasoning (EWCBR-93).
Wess, S., Althoff, K. D. and Richter, M. M. (Eds.), Lecture Notes in Artificial Intelligence, volume 837,
Springer Verlag, pp. 197-208.
Borner, Katy, Fehr, Rainer, and Wachsmuth, Ipke. (1998). AkuVis: Interactive visualization of acoustic data.
Computer Science for Environmental Protection'98: Networked Structures in Information Technology, the
Environment and Business, Haasis, H. D. and Ranze, K. C. (Eds.), Metropolis Verlag, Volume 1, pp. 722-
728.


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Borner, Katy (2001). Adaptation and Evaluation of 3-Dimensional Collaborative Information Visualizations .
8th International Conference on User Modeling, Bavaria, Germany. July 13-17, pp. 33-40.
Borner, Katy. (2002). Visual Interfaces for Semantic Information Retrieval and Browsing. In Groimenko,
Vladimir and Chen, Chaomei (Eds.), Visualizing the Semantic Web: XML-based Internet and Information
Visualization, Springer Verlag, Chapter 7, pp. 99-115.
Borner, Katy, Chen, Chaomei, and Boyack, Kevin. (2003). Visualizing Knowledge Domains. In Blaise Cronin
(Ed.), Annual Review of Information Science & Technology, Volume 37, Medford, NJ: Information Today,
Inc./American Society for Information Science and Technology, chapter 5, pp. 179-255
Borner, Katy and Penumarthy, Shashikant. (2003). Maps of Virtual Worlds. In Information Desiqn Source Book.
IIDj Institute for Information Design Japan (Ed.), Graphic-Sha, Japan
Borner, Katy, Penumarthy, Shashikant, DeVarco, Bonnie Jean, and Kerney, Carol. (2005). Visualizing Social
Patterns in Virtual Environments on a Local and Global Scale. In Peter van den Besselaar & Satoshi
Koizumi (eds), Digital Cities III. Information Technologies for Social Capital: Cross-cultural Perspectives,
Lecture Notes in Computer Science, Vol. 3081. Springer Verlag, pp. 325-340.
Katy Borner. (2006) Semantic Association Networks: Using Semantic Web Technology to Improve Scholarly
Knowledge and Expertise Management. In Vladimir Geroimenko & Chaomei Chen (eds.) Visualizing the
Semantic Web, Springer Verlag, 2nd Edition, chapter 11, pp. 183-198.
Hook, Peter A. and Borner, Katy. (2005) Educational Knowledge Domain Visualizations: Tools to Navigate,
Understand, and Internalize the Structure of Scholarly Knowledge and Expertise. In Amanda Spink and
Charles Cole (eds.) New Directions in Cognitive Information Retrieval. Springer-Verlag, Netherlands,
chapter 5, pp. 187-208.
Fletcher, George Sheth, Hardik and Borner, Katy. (2005). Unstructured Peer-to-Peer Networks: Topological
Properties and Search Performance. In Gianluca Moro, Sonia Bergamaschi, Karl Aberer (eds.) Agents and
Peer-to-Peer Computing: Third International Workshop, AP2PC 2004, New York, NY, USA, July 19, 2004.
Springer Verlag, pp 14-27
Borner, Katy, Sanyal, Soma and Vespignani, Alessandro. (2007) Network Science. In Blaise Cronin (Ed.),
Annual Review of Information Science & Technoloqy, Volume 41, Medford, NJ: Information Today,
Inc./American Society for Information Science and Technology, chapter 12, pp. 537-607.
Herr, Bruce W., Huang, Weixia, Penumarthy, Shashikant, Borner, Katy. (2007) Designing Highly Flexible and
Usable Cyberinfrastructures for Convergence. In William S. Bainbridge and Mihail C. Roco (Eds.) Progress
in Convergence Technologies for Human Wellbeing. Annals of the New York Academy of Sciences,
Boston, MA, volume 1093, pp. 161-179.

Conference and Workshop Publications Peer-Reviewed

Borner, Katy. (2000). Visible Threads: A smart VR interface to digital libraries. In Robert F. Erbacher, Philip C.
Chen, Jonathan C. Roberts & Craig M. Wittenbrink (eds.) Visual Data Exploration and Analysis VII,
Proceedings of SPIE, San Jose, CA, 23-28 January, Volume 3960, pp. 228-237.
Borner, Katy. (2000). Extracting and visualizing semantic structures in retrieval results for browsing. ACM
Digital Library Conference, San Antonio, Texas, June 2-7, pp. 234-235.
Borner, Katy. (2000). Searching for the perfect match: A comparison of free sorting results for images by
human subjects and by Latent Semantic Analysis, Information Visualisation 2000, Symposium on Digital
Libraries, London, England, 19-21July, pp. 192-197.
Borner, Katy, Dillon, Andrew and Dolinsky, Margaret. (2000). LVis Digital Library Visualizer. Information
Visualisation 2000, Symposium on Digital Libraries, London, England, 19 -21 July, pp. 77-81.
Borner, Katy and Chen, Chaomei. (2001). JCDL Workshop: Visual Interfaces to Digital Libraries Its Past,
Present, and Future. Proceedings of the First ACM+IEEE Joint Conference on Digital Libraries, Roanoke,
VA, USA, p. 482.
Borner, Katy and Zhou, Yuezheng. (2001) A Software Repository for Education and Research in Information
Visualization. Information Visualisation Conference, London, England, July 25-27, pp. 257-262.
Feng, Ying and Borner, Katy. (2002). Using Semantic Treemaps to Categorize and Visualize Bookmark Files.
In Visualization and Data Analysis. Robert F. Erbacher, Philip C. Chen, Matti Grohn, Jonathan C. Roberts,


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Craig M. Wittenbrink (eds), Visual Data Exploration and Analysis VlIII, January 20-25, 2002, San Jose, CA,
Proceedings of SPIE, Volume 4665, pp. 218-227.
Rasmussen E., Atkins H. B., Borner K., McCain K. W. (2002). Visualizing knowledge domains. ASIST 2002:
Proceedings of the ASIST Annual Meeting 39: 476-477, Information Today Inc., Medford.
Mostafa, Javed and Borner, Katy. (2003). International workshop on information visualization interfaces for
retrieval and analysis (IVIRA 2003). Marshall, Chatherine C., Henry, Geneva, Delcambre, Lois (Eds.), Third
ACM+IEEE Joint Conference on Digital Libraries, May 27-31, 2003, Houston, Texas, USA, ACM Press, p.
416.
Borner, Katy & Penumarthy, Shashikant. (2005). Spatio-Temporal Information Production and Consumption
of Major U.S. Research Institutions. In: P. Ingwersen & B. Larsen (Eds.), Proceedings of ISSI 2005.
Stockholm: Karolinska University Press. Vol. 1, pp. 635-641.
La Rowe, Gavin, Ambre, Sumeet, Burgoon, John, Ke, Weimao and Borner, Katy. (2007) The Scholarly
Database and Its Utility for Scientometrics Research. In Proceedings of the 11th International Conference
on Scientometrics and Informetrics, Madrid, Spain, June 25-27, 2007, pp. 457-462.
Mane, Ketan K. and Borner, Katy. (2007) Computational Diagnostics: A Novel Approach to Viewing Medical
Data. Proceedings of the Fifth International Conference on Coordinated and Multiple Views in Exploratory
Visualization (CMV 2007), July 2, IEEE Computer Society Conference Publishing Services, pp. 27-34.
Neirynck, Thomas and Borner, Katy. (2007) Representing, Analyzing, and Visualizing Scholarly Data in
Support of Research Management. In Proceedings of the 11th Information Visualisation Conference, ETH
Zurich, Switzerland, IEEE Computer Society Conference Publishing Services, pp. 124-129.
Boyack, Kevin W. Klavans, Richard, Paley, W. Bradford & Borner, Katy. (2007). Mapping, Illuminating, and
Interacting with Science. In ACM Siggraph 2007 Sketches, ACM.

C. Research Support

James S. McDonnell Foundation, 21st Century Science Special Initiative: Studying Complex Systems
Identification, mapping and visualization of emergent scientific endeavors, fields, and the inter-relationships
of science specialties and sub-specialties
NSF SBE 0738111 TLS: Towards a Macroscope for Science Policy Decision Making
The development of large-scale visualization techniques based upon real-time data on scientific fields; the
promotion and development of a scholarly "marketplace" for wide dissemination of current research and
trends.
NIH RM-07-004 EpiC: A Cyberinfrastructure that Supports the Plug-and-Play of Datasets and Algorithms
Needed for the Study and Analysis of Epidemic Processes.
The creation of a repository and marketplace for epidemiologists and associated researchers to share real-
time data, to harness data streams on epidemic reporting, to house algorithms and datasets to share
across projects and to explore data mining techniques to better enable forecasting
NSF IIS-0715303 Creative Metaphors to Stimulate New Approaches to Visualizing, Understanding and
Rethinking Large Repositories of Scholarly Data.
Investigation into the intersection of humanities and science, the application of artistic techniques to
understanding scientific data streams and storage and re-engineering their use.
James S. McDonnell Foundation Grant-Studying Complex Systems
Modeling the structure and evolution of scholarly knowledge.
NSF IIS-0513650 NetWorkBench: A Large-Scale Network Analysis, Modeling and Visualization Toolkit for
Biomedical, Social Science and Physics Research.
The development, maintenance and extension of visualization techniques through a standard toolset for all
scientists to access robust data visualizations.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
Cole, Curtis L. Chief Information Officer
eRA COMMONS USER NAME (credential, e.g., agency login) Associate Professor of Medicine and Public Health
CLCOLE
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION (if a ) YEAR(s) FIELD OF STUDY
Bowdoin College, Brunswick, ME 1986 A.B. 1986 Psychology & History

Cornell University Medical College, New York, NY M.D. 1994 Medicine

The New York Hospital-Cornell Medical Center, New Primary Care Internal
Primary Care Internal
York, NY 1995
1995 Medicine Internship


The New York Hospital-Cornell Medical Center, New 1996 Primary Care Internal
York, NY Medicine Residency

The New York Hospital-Cornell Medical Center, New 1998 Me l
Yok,1998 Medical Informatics
York, NY


A. Positions and Honors.


2009-Present
2006-2009
2006-Present
2006-Present


Chief Information Officer, Weill Medical College of Cornell University, New York, NY
Chief Medical Information Officer, Weill Medical College of Cornell University, New York, NY
Associate Professor of Medicine, Weill Medical College of Cornell University, New York, NY
Associate Professor of Public Health, Weill Medical College of Cornell University, New York,
NY


2003-2006 Assistant Professor of Public Health, Weill Medical College of Cornell University, New York, NY
2000-2006 Assistant Professor of Medicine, Weill Medical College of Cornell University, New York, NY
1998-2006 Director of Information Services, Weill Cornell Physician Organization, Weill Medical College of
Cornell University, New York, NY.
1998-2006 University Overseer, Office of the Chief Information Officer, New York Presbyterian Hospital,
New York, NY
1997-2000 Clinical Instructor in Medicine, Cornell University, New York, NY
1996-1997 Project Coordinator, Ambulatory Clinical Information System Project, The New York and
Presbyterian Hospitals, Inc.
1995-1997 Clinical Associate in Medicine, Cornell University, New York, NY

B. Selected peer-reviewed publications.

Cole CL, Ambulatory Systems, Book Chapter in Ong, Medical Informatics: An Executive Primer, HIMSS
Books. 2007
Cole CL, Kanter AS, Cummens M, Vostinar S, Naeymi-Rad F. Using a terminology server and consumer
search phrases to help patients find physicians with particular expertise. Proc. of the 11th World Congress on
Medical Informatics: Medinfo 2004.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


C. Research Support.

5% in kind effort on grant # 5 R18 HS017029 entitled Electronic Prescribing and Electronic Transmission of
Discharge Medication Lists

UL1-RR024996 (Imperato-McGinley) 09/18/07-05/31/2012
NIH/NCRR
Clinical and Translational Science Award
The mission of the diverse trans-institutional, multi-disciplinary Clinical and Translational Science Center
(CTSC) is to move translational research seamlessly from bench to bedside and to the community. The CTSC
acts as a conduit through which essential resources, technological tools and education programs for all
partners can be efficiently shared and managed.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
Corson-Rikert, Jonathan W. Head of Information Technology Services
eRA COMMONS USER NAME (credential, e.g., agency login) Albert R. Mann Library
Cornell University, Ithaca, NY 14853
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DE EYEAR(s) FIELD OF STUDY
(if applicable)
Visual & Environmental
Harvard University B.A. 1973 su
Studies





Please refer to the application instructions in order to complete sections A, B, and C of the Biographical
Sketch.

A. Positions and Honors.

Positions and Emplovment


1978 1982
1983 1987
1987 1992

1992 2001
2001 -2006
2006-


Cartographer, Dane County Regional Planning Commission, Madison, WI
Research Analyst, Laboratory for Computer Graphics and Spatial Analysis, Harvard University
Programmer and Project Manager, Laboratory for Computer Graphics and Spatial Analysis,
Harvard University
Laboratory Manager, Program of Computer Graphics, Cornell University
Senior Programmer/Analyst, Albert R. Mann Library, Cornell University
Head of Information Technology Services, Albert R. Mann Library, Cornell University


Other Experience
1987 --1992 Principal developer of the ROOTS topological map digitization software, and PALMS, an
extended version of ROOTS with an OracleTM database interface to support integrated spatial
and text queries for applications in international development. With Denis White and Kelly
Chan.
1992 -2001 Cornell Site Coordinator, NSF Science and Technology Center for Computer Graphics and
Scientific Visualization (Brown University, California Institute of Technology, Cornell
University, University of North Carolina-Chapel Hill, and University of Utah)
2003 2009 Originator and lead developer of the VITRO software underlying the VIVO research networking
tool, combining a web-based ontology editor, content editor, and interface management tool to
structure knowledge and drive the dynamic, cross-indexed display of information.
http://vitro.mannlib.cornell.edu. With Brian Caruso, Brian Lowe, Nick Cappadona, and Miles
Worthington.


Honors
2003


Ans van Tienhoven Professional Development Award, Albert R. Mann Library


B. Selected peer-reviewed publications (in chronological order).

1. White, D., Corson-Rikert, J., and Maizel, M., 1987, 'WYSIWYG' map digitizing: Real time
geometric correction and topological encoding. In Proceedings from Auto-Carto 8
PHS 398 (Rev. 11/07) Page 55 Biographical Sketch Format Page






Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


(Bethesda, MD: American Congress on Surveying and Mapping), pp. 739 -743.
2. Jonathan Corson-Rikert. "Updating Multilayer Vector Databases," Seminar on Resources Planning
Management and Monitoring, IES Report 132, University of Wisconson-Madison, 147-159, 1988.
3. D. White, K. Chan, M. Maizel and J. Corson-Rikert. "Polygon Overlay to Support Point Sample Mapping:
The National Resources Inventory". In Auto-Carto 9. Edited by E. Anderson. 384-390. Baltimore, MD:
ASPRS & ACSM, 1989.
4. Waldemar Celes and Jonathan Corson-Rikert. "Act: An Easy-to-use and Dynamically Extensible 3D
Graphics Library" in Proceedings, Brazilian Symposium on Computer Graphics and Image Processing,
Campos do Jordao, SP -Brazil, October, 1997.
5. Jonathan Corson-Rikert. "Report of the Workshop on Rendering, Perception, and Measurement", ACM
SIGGRAPH Computer Graphics, Vol. 34, Issue 1, February, 2000.
6. B. Lust, S. Flynn, M. Blume, J. Corson-Rikert, B. Lowe. "Searching Interoperability Between Linguistic
Coding and Ontologies for Language Description", Proceedings of the E-MELD (Electronic
Metastructure for Endangered Languages Metadata) 2005 Workshop on Digital Language
Documentation, Cambridge, MA, July 1-3, 2005.
7. Brian Caruso, Brian J. Lowe, Jon Corson-Rikert, and Medha Devare. "VIVO: Case Study of an
Ontology-Based Website". Proceedings of the AAAI Fall Symposium on Semantic Web for Collaborative
Knowledge Acquisition (SWeCKa), 2006.
8. Brian Lowe, Brian Caruso, and Jonathan Corson-Rikert. "VIVO Development Roadmap: Enhancing an
Ontology-Based University Research Portal with OWL and Rules". Proceedings of the OWLED 2007
Workshop on OWL: Experiences and Directions, Innsbruck, Austria, June 6-7, 2007.
9. Medha Devare, Jon Corson-Rikert, Brian Caruso, Brian Lowe, Kathy Chiang, and Janet McCue. "VIVO:
Connecting People, Creating a Virtual Life Sciences Community", D-Lib Magazine, July/August 2007.

C. Research Support

Ongoing Research Support
NSF IIS-CXT 0712989 Steinhart (PI), McCue (Co-PI) 10/1/07 9/30/10
Promoting the curation of research data through library-laboratory collaboration
The proposed activity consists of two main parts: the design and deployment of a digital staging repository
and the design and deployment of a metadata management architecture. The first encompasses issues of
institutional policy, requirements analysis, and the selection and integration of existing software platforms
(e.g., Fedora). The second will deal with complex metadata issues such as web semantics, ontology
creation, and inter-domain cross-walking.
Role: Senior Investigator

Completed Research Support
NSF IIS 0437603 McCue (PI), Lust (Co-PI) 7/1/2004 12/31/2006
SGER: Planning Information Infrastructure Through a New Library-Research Partnership
This project examined the opportunities for partnership between the research community and the library to
ensure that research data are collected, preserved, and accessible to research communities; a prototype for
testing and demonstration was developed and protocols for inter-institutional library collaboration were
examined.
Role: Senior Investigator


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Principal Investigator/Program Director (Last, First, Middle): Conlon, Michael


BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
Davis, Valrie I. Outreach Librarian for Agricultural Sciences
eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DE EYEAR(s) FIELD OF STUDY
(if applicable)


University of South Florida B.S. 1998 English
Florida State University M.L.S. 2002 Library Science



NOTE: The Biographical Sketch may not exceed four pages. Follow the formats and instructions on the
attached sample.

A. Positions and Honors. List in chronological order previous positions, concluding with your present position. List
any honors. Include present membership on any Federal Government public advisory committee.

Positions and Employment


2000-2001
2002-2005
2005-2009


Marketing & Promotion Assistant, University Press of Florida
Collection & Research Services Librarian, Dickinson College, Waidner-Spahr Library
Assistant University Librarian, University of Florida Libraries, Marston Science Library


Other Experience and Professional Memberships
2005-2009 Institutional Representative, United States Agricultural Information Network (USAIN)
2005-2009 Institutional Representative, Agricultural Network Information Center (AGNIC)
2005-2009 Vendor Relations Committee, Special Libraries Association, Food Agriculture Nutrition Division
2005-2009 UF Distance Learning Council
2006-2009 UF Libraries Emerging Technologies Committee
2006-2009 Public Relations and Marketing Committee, University of Florida Libraries
2008-2009 Born Digital Initiative Working Group-Policy Development and Grant Writing Sub-Committee,
Agricultural Network Information Center (AGNIC)
2008-2009Secretary-Elect, Special Libraries Association, Food Agriculture Nutrition Division

B. Selected peer-reviewed publications (in chronological order). Do not include publications submitted or in
preparation.


1. Davis, V. (2007). Challenges of connecting off-campus agricultural science users with library services.
Journal of Agricultural and Food Information. Binghamton: Haworth Press. p. 39-47

2. Kennedy, K., Cataldo, T., Davis, V., Gonzalez, S., & Newsom, C. (2008). Evaluating continuing resources:
perspectives and methods from science librarians. Serials Librarian. 55 (3). p. 428-443

3. Russell-Gonzalez, S., Davis, V., Dinsmore, C., Frey, C., Newsom, C., Taylor, L. (2008). Bioactive: a game
for library instruction. Gaming in academic libraries: collections, marketing, and information literacy.
Association of College and Research Libraries. Chicago: IL.


PH S 398 (Rev. 11 /07)


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Principal Investigator/Program Director (Last, First, Middle): Conlon, Michael
4. Davis, V., Dinsmore, C. (2009). Serving a diverse and ever-changing agricultural sciences department:
Family, Youth & Community in perspective. Journal of Agricultural and Food Information. 10 (1) p. 17-26

5. Davis, V., Devare, M., Russell Gonzalez, S., Tennant, M. (2009) Implementation of a new research
discovery tool by the university libraries at Cornell University and the University of Florida. Proceedings
of the Contributed Papers Session. SLA Biomedical and Life Sciences Division.

6. Davis, V., Foss, M. (2009) Supporting the distance learning community with Interlibrary Loan and
Collection Management at the University of Florida Libraries. Journal of Library & Information Services
in Distance Learning. In press.


C. Research Support. List selected ongoing or completed (during the last three years) research projects (federal
and non-federal support). Begin with the projects that are most relevant to the research proposed in this
application. Briefly indicate the overall goals of the projects and your role (e.g. PI, Co-Investigator, Consultant) in
the research project. Do not list award amounts or percent effort in projects.


Completed Research Support
"Developing a Database to Foster Interdisciplinary Communication and Collaboration at UF", UF Libraries Mini-
Grant, co-PI, 10/2007-9/2008

Installed and populated test implementation of Cornell's VIVO database software at the University of
Florida. Test database presented to multiple UF campus groups to secure support for development of a
mature database to aid with research collaboration and communication of UF research to the campus
community and general public.


Biographical Sketch Format Page


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Program Director/Principal Investigator (Last, First, Middle):


BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
Devare, Medha Bioinformatics and Life Sciences Librarian
eRA COMMONS USER NAME (credential, e.g., agency login)

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DE EYEAR(s) FIELD OF STUDY
(if applicable)
Colby College, Waterville, Maine BA 1988 Biology
Cornell University, Ithaca, New York MS 1993 Environmental Toxicology
Cornell University, Ithaca, New York PhD 2000 Crop and Soil Sciences
Cornell University, Ithaca, New York Post-doc 2000-2004 Molecular Ecology



A. Positions and Honors

Positions and Experience
1996 2000: Graduate Research Assistant, Department of Crop and Soil Sciences, Cornell University
Investigated soil biological and physical constraints to productivity in the rice-wheat system of Nepal

2000 2004: Post Doctoral Associate, Department of Crop and Soil Sciences, Cornell University
Collected and analyzed soil samples to determine effects of Bt toxin from transgenic corn and of
insecticide on soil microbial populations and community structure using PCR, real-time PCR, T-RFLP,
and DGGE.

2004 present: Bioinformatics and Life Sciences Librarian, Albert R. Mann Library, Cornell University
Coordinate VIVO project; participate extensively in course and workshop instruction and development;
continued research and student advisement in Bt project; led diverse, multi-cultural group to consensus
agricultural technology and development in the Asia-Pacific region for global World Bank assessment.

Other Experience and Professional Memberships

2004 present: Member, Agronomy Society of America
2005 2008: Lead Author, International Assessment of Agricultural Knowledge, Science and Technology for
Development (IAASTD): East and South Asia and the Pacific
2006 2008: Member, Association of College and Research Libraries
2008 2009: Member, United States Agricultural Information Network



B. Selected peer-reviewed publications

Banu, S.P., M.A. Shaheed, A.A. Siddique, M.A. Nahar, H.U. Ahmed, M.H. Devare, J.M. Duxbury, J.G. Lauren,
G.S. Abawi, and C.A. Meisner. 2006. Soil biological health: a major factor in increasing the productivity of the
rice-wheat cropping system. International Rice Research Notes 30(1): 5-12.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael
Osterbur, D., K. Alpi, C. Canevari, P.M. Corley, M. Devare, N. Gaedeke, D.K. Jacobs, P. Kirlew, J.A. Ohles,
K.T.L. Vaughan, L. Wang, Y. Wu, and R. Geer. 2006. Vignettes: Diverse Library Staff Offering Diverse
Bioinformatics Services. Journal of the Medical Library Association 94(3): 306, E 188-191.

Devare, M., C.M. Jones, and J.E. Thies. 2007. Effects of transgenic Bt corn and tefluthrin on the soil microbial
community: diversity and activity. Journal of Environmental Quality 33(3): 837-843.

Thies, J.E. and M. H. Devare. 2007. An Ecological Assessment of Transgenic Crops. Journal of Development
Studies 43(1): 97-129.

Devare, M.H., J. Corson-Rikert, B. Caruso, B. Lowe, K. Chiang, and J. McCue. VIVO: Connecting People,
Creating a Virtual Life Sciences Community. D-Lib Magazine (July/August 2007).

Devare, M., L.M. Londoho-R, and J.E. Thies. 2007. Neither transgenic Bt maize (MON863) nor tefluthrin
insecticide adversely affect soil microbial activity or biomass: A 3-year field analysis. Soil Biology and
Biochemistry 39(8): 2038-2047.

Wang, Y., W. Wu, Y. Ding, W. Liu, A. Perera, Y. Chen, and M. Devare. 2008. Methane oxidation activity and
bacterial community composition in a simulated landfill cover soil is influenced by the growth of
Chenopodium album L. Soil Biology and Biochemistry 40 (9): 2452-2459.

Liu, W., W.X. Wu, H.H. Lu, Y.X. Chen, M. Devare, and J. Thies. 2008. Use of 13C labeling to assess C-
partitioning in transgenic and non-transgenic (parental) rice and their associated rhizosphere soil microbial
communities. FEMS Microbiology Ecology 67(1): 93-102.

Devare, M., C. Greenidge, G. Kelkar, E. Dano, W. Kabir, and R. Sulaiman. 2009. Development and
sustainability goals: AKST options. Chapter 5 in B. D. Mclntyre, H.R. Herren, J, Wakhungu, and R.T.
Watson (ed.) Agriculture at a Crossroads: the International Assessment of Agricultural Knowledge, Science
and Technology for Development (IAASTD), Volume II: East and South Asia and the Pacific. Island Press,
Washington DC.



C. Research Support

M. Devare, J. Corson-Rikert, J.A. Porciello, K. Chiang, S. Newberry, J. Powell, D. Schmidle, S. Whitaker, and
the Cornell University Library Management Team. Improving VIVO to Unify and Showcase Cornell
Research: Years 3-6. Three years.

M. Devare, J. Corson-Rikert, J. VanEe, S. Varvayanis, K. Chiang, J. McCue. VIVO: a Core Service to Sustain
a Unified Virtual Life Sciences Community at Cornell. Two years.

M. Devare, J. Thies, J.M. Duxbury, L. Allee, J. Losey, W. Wu, and E.Barrios. Assessing the Effects of Bt Crops
and Insecticides on Arbuscular Mycorrhizal Fungi and Plant Residue Carbon Turnover and Fate in Soil.
USAID #45010. Four years.

J. Thies, M. Devare (primary author), J.M. Duxbury, J. Esnard, L. Allee, and J. Losey. Assessing the
comparative risk of CRW transgenic corn and chlorpyrifos to the soil microbial community. USDA-CSREES
# 2001-03746. Three years.


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BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
Ding, Ying Assistant Professor of Information Science
eRA COMMONS USER NAME Core Faculty of Coginitive Science
dingying
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DEGREE YEAR(s) FIELD OF STUDY
(if applicable)
Xidian University, Xi'an, China B.S. 1993 Information Science
Graduate School of Chinese Academy of M.S. 1996 Library and Information Science
Science, Beijing, China
Nanyang Technological University, Ph.D. 2001 Information Science
Singapore


A. Positions and Honors.

Positions and Employment History


1996-1997
1997-2000

2000-2003

2003-2008
2008-

2009-


Database Designer, Library of Chinese Academy of Sciences, Beijing, China.
Research Assistant, School of Computer Engineering, Nanyang Technological University,
Singapore.
Senior Researcher, Department of Mathematics and Computer Science, Free University of
Amsterdam, the Netherlands.
Assistant Professor, Department of Computer Science, University of Innsbruck, Austria
Assistant Professor of Information Science, Indiana University School of Library and Information
Science, Bloomington, IN
Core Faculty of Cognitive Science, Indiana University School of Psychology, Bloomington, IN


Other Related Professional Experience (Since 2004)


2004
2004-
2004-2006
2004-2006
2004-2008

2004-2007
2004-2007
2004-2007
2004-2007
2006
2006-2007
2006-2008
2008-


Guest Editor, Austrian Artificial Intelligence Journal (OGAI) Special Issue on Semantic Web
Founding member of the Digital Enterprise Research Institute (DERI), Ireland and Austria
Co-founder, Co-chair of OntoWeb Foundation, Amsterdam, the Netherlands
Co-founder, Semantic Web Technology Amsterdam, the Netherlands
Member of Semantic Web Science Association (SWSA), Steering Committee Member for
International Semantic Web Conference
Steering Committee Member for European Semantic Web Conference
Research Director, NetDynamics, Austria
Senior Consultant, OntoText, Bulgaria
Co-founder, Electronic Services GmBH, Austria
Member of European Commission DG Information Society and Media (DG INFO)
Steering Committee Member for Asian Semantic Web Conference
Project management committee member, EASAIER Project (EU 6th FP)
Review board member for Wirtschaftsinformatik Journal


Selected Other Honors


Best Performance EU Project (EU 5th FP) OntoWeb


Biographical Sketch Format Page


2002


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


B. Selected peer-reviewed publications (since 2007).
(From more than 70 publications covering semantic web, web services, information retrieval, data mining,
social network and scientometrics)
E. Yan & Y. Ding (2009). The use of centrality measures in scientific evaluation: A coauthorship
network analysis. In Proceedings of the 12th International Conference on Scientometrics and
Informetrics, July 14-17, Rio de Janeiro, Brazil.
E. Yan, Y. Ding, & Q. Zhu (2009 forthcoming). Mapping Library and Information Science in China: A
Coauthorship Network Analysis. Scientometrics.
S. Kashoob, J. Caverlee and Y. Ding (2009). A Categorical Model for Discovering Latent Structure in
Social Annotations. In Proceedings of the Third International AAAI Conference on Weblogs and Social
Media (ICWSM2009). May 17-20, 2009, San Jose, California, USA.
Y. Ding, E. Jacob, J. Caverlee, M. Fried and Z. Zhang (2009). Profiling Social Networks: A Social
Tagging Perspective. D-Lib, March/April, 2009.
I. Toma, Y. Ding, K. Chalermsook, E. Simperl, D. Fensel (2009). Utilizing Web 2.0 in Web Service
Ranking. In Proceedings of the 3rd International Conference on Digital Society (ICDS'09), Cancun,
Mexico, February 1-7, 2009.
M. Hofmann and Y. Ding (2009). CitationBase: A Social Tagging Management Portal for References.
Poster at WebSci2009: Society On-Line, Athens, Greece, March 18-20, 2009.
Y. Ding, I. Toma, S. Kang, Z. Zhang and M. Fried (2008). Mediating and Analyzing Social Data.
Proceedings of The 7th International Conference on Ontologies, Databases, and Applications of
Semantics (ODBASE 2008), Lecture Notes in Computer Sciences, Nov 11-13, 2008, Monterrey,
Mexico, Springer-Verlag.
Y. Ding, S, Kang, I. Toma, M. Fried and Z. Yan (2008). Integrating Social Tagging Data. In
Proceedings of the 2008 IEEE International Conference on Systems, Man and Cybernetics, 12-15
October 2008, Singapore.
Y. Ding, C. Herzog, M. Luger, K. Prantner and Z. Yan (2008). OnTourism: Semantic eTourism Portal.
In Proceedings of 2nd International Scientific Conference of the e-Business Forum E-Business in
Travel, Tourism and Hospitality, March 14th, 2008, Athens, Greece.
J. M. Garcia, I. Toma, D. Ruiz, A. Ruiz-Cortes, Y. Ding and J. M. Gomez (2008). Ranking Semantic
Web Services Using Rules Evaluation and Constraint Programming. The Fourth Scientific Technical
Symposium on Web Services and SOA (JSWEB2008), Oct 29-30, 2008. Seville, Spain.
Y. Ding, I. Toma, S. Kang, M. Fried and Z. Yan (2008). Data Mediation and Interoperation in Social
Web: Modeling, Crawling and Integrating Social Tagging Data. WWW2008 Workshop on Social Web
Search and Mining (SWSM2008), 17th International World Wide Web Conference, April 21-25, 2008,
Beijing, China.
K. Prantner, Y. Ding, M. Luger, Z. Yan and C. Herzog (2007): Tourism Ontology and Semantic
Management System: State-of-the-arts Analysis. IADIS International Conference WWVW/Internet 2007,
Vila Real, Portugal, 5-8 Oct 2007.
D. Fensel, R. Krummenacher, O. Shafiq, E. Kuehn, J. Riemer, Y. Ding and B. Draxler (2007). TSC -
Triple Space Computing. Special Issue on ICT research in Austria. Journal of Electronics & Information
Technology, Jan/Feb, 31-38.
Z. Yan and Y. Ding (2007). Towards a Domain Oriented and Independent Semantic Search Model. In
Proceedings of the 11th International Conference on Knowledge-Based and Intelligent Information and
Engineering Systems (KES2007), Vietri sul Mare, Italy, September 2007, Springer.
Z. Yan, F. Scharffe and Y. Ding (2007). Semantic Search on Cross-Media Cultural Archive. In
Proceedings of the 5th Atlantic Web Intelligence Conference (AWIC2007), page: 220-225,
Fontainebleau, France, June 2007, Springer
Y. H. Ding, Y. Ding, D. Embley, O. Shafiq, and M. Hepp (2007). Making the Semantic Web a Reality
through Active Semantic Space. ESWC 2007 workshop on Bridging the Gap between Semantic Web
and Web 2.0, European Semantic Web Conference 2007, June 1-4, Innsbruck, Austria.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael
* M. Luger, Y. Ding, F. Scharffe, R. Duan and Z. Yan (2007). EASAIER Semantic Music Retrieval Portal.
Poster at the 2nd International Conference on Semantics And Digital Media Technologies (SAMT),
Genova, Italy, Dec 5-7, 2007.
* M. Luger, Y. Ding, Z. Yan, F. Scharffe, Y. Duan, Y. Raimond, L. Barthelemy and J. Reiss (2007).
EASAIER: Semantic Music Retrieval Portal. Poster and Demo at the 6th International Semantic Web
Conference (ISWC2007), Nov 11-15, 2007, Busan, Korea.
* F. Scharffe, Y. Ding and D. Fensel (2007). Towards Correspondence Patterns for Ontology Mediation.
Poster at Ontology Matching Workshop, the Sixth International Semantic Web Conference
(ISWC2007), Busan, Korea, Nov 11-15, 2007.
* F. Scharffe, Y. Raimond, L. Barthelemy, Y. Ding, and M. Luger (2007). Publishing and Accessing
Digital Archives using the EASAIER Framework. Poster and Demo at Workshop on cultural heritage
and the semantic web, the Sixth International Semantic Web Conference (ISWC2007), Busan, Korea,
Nov 11-15, 2007.
* Z. Yan, E. Cimpian, M. Zaremba, Y. Ding (2007). Business Process Modeling Ontology. Poster and
Demo at the 6th International Semantic Web Conference (ISWC2007), Nov 11-15, 2007, Busan, Korea.


Biographical Sketch Format Page


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
Hack, George O. Assistant Director and Lecturer
eRA COMMONS USER NAME (credential, e.g., agency login)

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DE EYEAR(s) FIELD OF STUDY
University of Florida Ph.D. 2004 Educational Technology
University of Florida Ph.D. 2004 Educational Technology


A. Positions and Honors.

Positions and Employment


1994-1996
1997-2002
2002-2004
2004-


Director of Education and Training, Wackenhut Educational Services, Miami, FL
Assistant In, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL
Instructor, University of Florida College of Education, Gainesville, FL
Assistant Director and Lecturer, University of Florida HSC Libraries, Gainesville, FL


Other Experience and Professional Memberships


1996-1997
2008-2009
2000-


Instructional Design Consultant, University of Florida, Gainesville, FL
Instructional Design Consultant, Compendium for Children's Health, Jacksonville, FL
Association for Educational Communications and Technology


B. Selected peer-reviewed publications (in chronological order).
None

C. Research Support
None


Biographical Sketch Format Page


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
Holmes, Kristi L. Bioinformaticist
eRA COMMONS USER NAME (credential, e.g., agency login) Bernard Becker Medical Library

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION (if a ) YEAR(s) FIELD OF STUDY
Chadron State College, Chadron, NE 1996-1998 Biology
University of Nebraska, Kearney, NE BS 1998-2000 Biology
Iowa State University, Ames, IA PhD 2000-2005 Biochemistry

A. Positions and Honors.
Positions and Employment
1998-2000 Research Assistant, Department of Chemistry, University of Nebraska, Kearney, NE (Design,
synthesis, and structure-activity relationship of 9-(pyridinyl)aminoacridines)
1998-2000 Research Assistant, Department of Chemistry, University of Nebraska, Kearney, NE (Ligand
structural effects on palladium(ll) charge-transfer complex solvatochromism)
1999 Instructor, Department of Chemistry, University of Nebraska, Kearney, NE (summer session)
2000-2005 Graduate Research Assistant, Department of Biochemistry, Biophysics, and Molecular Biology,
Iowa State University, Ames, IA (Understanding 16S ribosomal RNA conformational changes
during 30S subunit assembly)
2005-2006 Lecturer and Course Developer, Department of Biochemistry, Biophysics, and Molecular
Biology, Iowa State University, Ames, IA
2006-present Bioinformaticist, Bernard Becker Medical Library Washington University in St. Louis School of
Medicine, St. Louis, MO
2006 Consultant, National Center for Biotechnology information. Course Developer and Instructor,
National Center for Biotechnology Information (NCBI) Advanced Workshop for Bioinformatics
Information Specialists (NAWBIS) National Library of Medicine, Bethesda, MD
2007 Adjunct Assistant Professor, Department of Biology, University of Missouri-St. Louis, St. Louis,
MO

Other Experience and Professional Memberships


2004-2005

2006-2007

2006-present

2007-present

2007-present
Louis, MO
2007-present
2007-present
2007-present
2007-present
2009-present


Graduate and Professional Student Senate Representative, University Library Committee, Iowa
State University, Ames, IA
Member, Bernard Becker Medical Library Strategic Planning Committee, Washington University
School of Medicine, St. Louis, MO
Member, Young Scientists Program Steering Committee, Washington University School of
Medicine, St. Louis, MO
Coordinator, Faculty Profiling and Collaboration Project Working Group Washington University
School of Medicine, St. Louis, MO
Member, Genomics Curriculum Working Group, Washington University School of Medicine, St.

Member, American Medical Informatics Association
Member, Medical Library Association (MLA)
Member, MLA Medical Informatics Section
Member, MLA Molecular Biology Special Interest Group
Course Developer and Instructor: Clinical Genomics: from bench to bedside. Medical Library
Association Continuing Education (CE) contact hours series.
http://www.cech.mlanet.org/node/414


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Honors
2000 lota Sigma Pi National Honor Society for Women in Chemistry
2004 Iowa State University Teaching Excellence Award (Office of the Vice Provost for Research and
Advanced Studies), Iowa State University, Ames, IA
2007 Medical Informatics MBL/NLM Course Fellowship Marine Biological Laboratory, Woods Hole,
MA. Sponsored by the National Library of Medicine.


B. Selected peer-reviewed publications (in chronological order).

Mosher, MD, Holmes, KL, and Frost, KS. "Structure-Activity Relationships for the 9-(Pyridin-2'-yl)-
aminoacridines" Molecules (Special Issue: Biologically Relevant Heterocyclic Compounds) 2004, 2, 102-108.

Holmes, KL and Culver, GM. Mapping structural differences between 30S ribosomal subunit assembly
intermediates. Nat Struct Mol Biol. 2004 Feb; 11(2):179-86.

Holmes, KL and Culver, GM. Analysis of conformational changes in 16S rRNA during the course of 30S
subunit assembly. J. Mol. Biol. 2005 Nov 25;354(2):340-57.

Gaedeke, N, Holmes, KL, Messersmith, D, and Morris, RC. RNA Analysis Tools Module. National Center for
Biotechnology Information. Course developer and instructor National Center for Biotechnology Information
(NCBI) Advanced Workshop for Bioinformatics Information Specialists (NAWBIS) National Library of
Medicine, Bethesda, MD [Online] http://www.ncbi.nlm.nih.gov/Class/NAWBIS/. [date revised August 8, 2007;
date cited June 2, 2009]

Sarli, CC, Dubinsky, EK, and Holmes, KL. Beyond Citation Analysis: A Model for Assessment of Research
Impact. J Med LibrAssoc., (in press)


Biographical Sketch Format Page


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
Joyce, Gerald F. Professor of Chemistry and Molecular Biology
eRA COMMONS USER NAME
gjoyce
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DE EYEAR(s) FIELD OF STUDY
(if applicable)

University of Chicago B.A. 1978 Biological Sciences
University of California, San Diego M.D. 1984 Medicine
University of California, San Diego Ph.D. 1984 Chemistry
The Salk Institute, La Jolla, CA- 1985-1989 Biochemistry
A. Positions and Honors


Positions
1982-1984
1984-1985
1985-
1985-1989
1989-1992

1989-
1992-1996
1996-
1996-
2006-
2008-


Doctoral Student; Research Advisor Professor Leslie E. Orgel, The Salk Institute
Internship, Mercy Hospital and Medical Center, San Diego, CA
Medical Licensure, State of California
Postdoctoral Fellow; Research Advisor Professor Tan Inoue, The Salk Institute
Assistant Professor, Departments of Chemistry and Molecular Biology, The Scripps Research
Institute (TSRI)
Faculty, Graduate Program in Biology and Graduate Program in Chemistry, TSRI
Associate Professor, Departments of Chemistry and Molecular Biology, TSRI
Investigator, The Skaggs Institute for Chemical Biology, TSRI
Professor, Departments of Chemistry and Molecular Biology, TSRI
Dean of the Faculty, TSRI
Co-Program Director and Director for Translational Science, Scripps Translational Science
Institute, NIH Clinical and Translational Science Award (CTSA) Consortium


Professional Activities


1992-1998
1993-1999
1996-
2000-
2003-
2003-
2005-
2005-
2008-
2009-


Co-Founder, Scientific Advisory Board, Darwin Molecular Corp., Bothell, WA
Founding Associate Editor, Chemistry & Biology
JASON, Scientific Advisory Panel for U.S. National Security
Head of Faculty in Chemical Biology, Faculty 1000, Biology Reports Ltd.
Editorial Board, PLoS Biology, Public Library of Science
Board of Scientific Advisors, The Beckman Institute, Caltech
Scientific Advisory Board, Ensemble Discovery Corp., Cambridge, MA
U.S. National Academy of Sciences Committee on International Security and Arms Control
Editorial Board, Quarterly Review of Biophysics
Technology Advisory Council, BP plc, London, UK


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Honors
1994 National Academy of Sciences Award in Molecular Biology
1995 Pfizer Award in Enzyme Chemistry, American Chemical Society
1997 Herbert W. Dickerman Award, State of New York Department of Health
1997 Hans Sigrist Prize, University of Bern, Switzerland
1998 Plenary Lecture, Pontifical Academy of Sciences, Vatican City
1999 Invited Lecture, Royal Swedish Academy of Sciences, Stockholm
2001 Linnaeus Lecturer, Uppsala University, Sweden
2001- Member, U.S. National Academy of Sciences
2005 H.C. Urey Award of the International Society for the Study of the Origin of Life
2006 T.Y. Shen Lectureship, Department of Chemistry, University of Manchester, UK
2006 Plenary Lecture, Nobel Workshop on "The Origin of Life", Royal Swedish Academy of Sciences
2007 Invited Lecture, Linnaeus Symposium, Royal Swedish Academy of Sciences, Stockholm
2008 Inaugural Leslie E. Orgel Memorial Lectureship, The Salk Institute, La Jolla, CA
2008 Commencement Address, City of Hope Graduate School of Biological Sciences, Duarte, CA
2009 Public Lecture, Royal Swedish Academy of Sciences, Stockholm

B. Selected Peer-Reviewed Publications
Joyce, G.F. (1989) RNA evolution and the origins of life. Nature 338, 217-224.
Joyce, G.F. (1989) Amplification, mutation, and selection of catalytic RNA. Gene 82, 83-87.
Robertson, D.L. & Joyce, G.F. (1990) Selection in vitro of an RNA enzyme that specifically cleaves single-
stranded DNA. Nature 344, 467-468.
Beaudry, A.A. & Joyce, G.F. (1992) Directed evolution of an RNA enzyme. Science 257, 635-641.
Joyce, G.F. (1992) Directed molecular evolution. Sci. Am. 267(6), 90-97.
Lehman, N. & Joyce, G.F. (1993) Evolution in vitro of an RNA enzyme with altered metal dependence.
Nature 361, 182-185.
Breaker, R.R. & Joyce, G.F. (1994) Emergence of a replicating species from an in vitro RNA evolution
reaction. Proc. Natl. Acad. Sci. USA 91, 6093-6097.
Breaker, R.R. & Joyce, G.F. (1994) A DNA enzyme that cleaves RNA. Chem. Biol. 1, 223-229.
Dai, X., De Mesmaeker, A. & Joyce, G.F. (1995) Cleavage of an amide bond by a ribozyme. Science 267,
237-240.
Wright, M.C. & Joyce, G.F. (1997) Continuous in vitro evolution of catalytic function. Science 276, 614-617.
Santoro, S.W. & Joyce, G.F. (1997) A general-purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci.
USA 94, 4262-4266.
Nowakowski, J., Shim, P.J., Prasad, G.S., Stout, C.D. & Joyce, G. F. (1999) Crystal structure of an 82-
nucleotide RNA-DNA complex formed by the 10-23 DNA enzyme. Nature Struct. Biol. 6, 151-156.
Rogers, J. & Joyce, G.F. (1999) A ribozyme that lacks cytidine. Nature 402, 323-325.
Jaeger, L., Wright, M.C. & Joyce, G.F. (1999) A complex ligase ribozyme evolved in vitro from a group I
ribozyme domain. Proc. Natl. Acad. Sci. USA 96, 14712-14717.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Ordoukhanian, P. & Joyce, G.F. (1999) A molecular description of the evolution of resistance. Chem. Biol. 6,
881-889.
Joyce, G.F. (2000) Employing DNAzymes to target bcr-abl mRNA in chronic myelogenous leukemia. Blood
Cells, Molecules and Diseases 26, 60-61.
Nowakowski, J., Shim, P.J., Stout, C.D. & Joyce, G.F. (2000) Alternative conformations of a nucleic acid
four-way junction. J. Mol. Biol. 300, 93-102.
Sheppard, T.L., Ordoukhanian, P. & Joyce, G.F. (2000) A DNA enzyme with N-glycosylase activity. Proc.
Natl. Acad. Sci. USA 97, 7802-7807.
Sheppard, T.L., Wong, C.-H. & Joyce, G.F. (2000) Nucleoglycoconjugates: design and synthesis of a new
class of DNA-carbohydrate conjugates. Angew. Chemie 39, 3660-3663.
Joyce, G.F. (2001) RNA cleavage by the 10-23 DNA enzyme. Methods Enzymol. 341, 503-517.
Joyce, G.F. (2002) The antiquity of RNA-based evolution. Nature 418, 214-221.
McGinness, K.E. & Joyce, G.F. (2002) RNA-catalyzed RNA ligation on an external RNA template. Chem.
Biol. 9, 297-307.
McGinness, K.E. & Joyce, G.F. (2002) Continuous in vitro evolution of a ribozyme that catalyzes three
successive nucleotidyl addition reactions. Chem. Biol. 9, 585-596.
Paul, N. & Joyce, G.F. (2002) A self-replicating ligase ribozyme. Proc. Natl. Acad. Sci. USA 99,12733-12740.
Ordoukhanian, P. & Joyce, G.F. (2002) RNA-cleaving DNA enzymes with altered regio- or enantioselectivity.
J. Am. Chem. Soc. 124, 12499-12506.
Reader, J.S. & Joyce, G.F. (2002) A ribozyme composed of only two different nucleotides. Nature 420, 841-844.
Kumar, R.M. & Joyce, G.F. (2003) A modular, bifunctional RNA that integrates itself into a target RNA. Proc.
Natl. Acad. Sci. USA 100, 9738-9743.
Kuhne, H. & Joyce, G.F. (2003) Continuous in vitro evolution of ribozymes that operate under conditions of
extreme pH. J. Mol. Evol. 57, 292-298.
Joyce, G.F. (2004) Directed evolution of nucleic acid enzymes. Annu. Rev. Biochem. 73, 791-836.
Shih, W.M., Quispe, J.D. & Joyce, G.F. (2004) A 1.7-kilobase single-stranded DNA that folds into a
nanoscale octahedron. Nature 427, 619-622.
Springsteen, G. & Joyce, G.F. (2004) Selective derivatization and sequestration of ribose from a prebiotic
mix. J. Am. Chem. Soc. 126, 9578-9583.
Kim, D.-E. & Joyce, G.F. (2004) Cross-catalytic replication of an RNA ligase ribozyme. Chem. Biol. 11, 1005-1512.
Oberhuber, M. & Joyce, G.F. (2005) A DNA-templated aldol reaction as a model for the formation of pentose
sugars in the RNA world. Angew. Chemie 44, 7580-7583.
Paul, N., Springsteen, G. & Joyce, G.F. (2006) Conversion of a ribozyme to a deoxyribozyme through in vitro
evolution. Chem. Biol. 13, 329-338.
Paegel, B.M., Grover, W.H., Skelley, A.M., Mathies, R.A. & Joyce, G.F. (2006) Microfluidic serial dilution
circuit. Anal. Chem., 78, 7522-7527.
Joyce, G.F. (2007) Forty years of in vitro evolution. Angew. Chemie 46, 6420-6436.
Voytek, S.B. & Joyce, G.F. (2007) Emergence of a fast-reacting ribozyme that is capable of undergoing
continuous evolution. Proc. Natl. Acad. Sci. USA 104, 15288-15293.
Paegel, B.P. & Joyce, G.F. (2008) Darwinian evolution on a chip. PLoS Biol. 6, 900-906.
Lincoln, T.A. & Joyce, G.F. (2009) Self-sustained replication of an RNA enzyme. Science 323, 1229-1232.


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Lam, B.J. & Joyce, G.F. (2009) Autocatalytic aptazymes enable ligand-dependent exponential amplification
of RNA. Nature Biotechnol. 27, 288-292.
Voytek, S.B. & Joyce, G.F. (2009) Niche partitioning in the coevolution of 2 distinct RNA enzymes. Proc.
Natl. Acad. Sci. USA 106, 7780-7785.


C. Research Support


None.


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BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
King, Paula Director, Kresge Library
eRA COMMONS USER NAME (credential, e.g., agency login)

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DEGREEYEAR(s) FIELD OF STUDY
(if applicable) YAs OSTD
University of Wisconsin-Madison MA 1978 Library Science
University of Wisconsin-Madison BA 1979 Cultural Anthropology


A. Positions and Honors.


1979-1981
1981-1987
1987-1991
1991-


Assistant Librarian, NASA Dryden Flight Research Center
Manager, Technical Library, U.S.A.F. Western Space & Missle Center
Manager, Library, Children's Hospital & Health Center, San Diego
Director, Kresge Library, The Scripps Research Institute


B. Selected peer-reviewed publications (in chronological order).

None



C. Research Support.

None


PHS 398/2590 (Rev. 11/07) Page 71 Biographical Sketch Format Page


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
Krafft, Dean B. Chief Technology Strategist
eRA COMMONS USER NAME (credential, e.g., agency login)

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DE EYEAR(s) FIELD OF STUDY
(if applicable)
Carleton College, Northfield, MN B.A. 1976 Mathematics
Cornell University, Ithaca, NY M.S. 1979 Computer Science
Cornell University, Ithaca, NY Ph.D. 1981 Computer Science



Please refer to the application instructions in order to complete sections A, B, and C of the Biographical
Sketch.

A. Positions.

1974-1976 Programmer/Analyst, Carleton College
1981-1987 Research Associate, Computer Science Department, Cornell University
1987-2005 Director of Computing Facilities, Computer Science Department, Cornell University
2005-2008 Principal Investigator, National Science Digital Library Core Integration Project (http://nsdl.org)
2005-2008 Director of Information Technology, Computing and Information Science, Cornell University
2008-present Chief Technology Strategist, Cornell University Library
2008-present Senior Research Associate, Information Science, Cornell University


B. Selected peer-reviewed publications (in chronological order).

1. James R. Davis, Carl Lagoze, Dean B. Krafft, "Dienst: Building a production technical report server", in
Digital Libraries Research and Technology Advances: ADL'95 Forum McLean, Virginia, USA, May 15-
17, 1995 Selected Papers, Lecture Notes in Computer Science, Volume 1082, Jun 1996, Pages 259 -
271, DOI 10.1007/BFb0024616, URL http://dx.doi.org/10.1007/BFb0024616

2. Carl Lagoze, William Arms, Stoney Gan, Diane Hillmann, Christopher Ingram, Dean Krafft, Richard
Marisa, Jon Phipps, John Saylor, Carol Terrizzi, Walter Hoehn, David Millman, James Allan, Sergio
Guzman-Lara, Tom Kalt, "Core Services in the Architecture of the National Digital Library for Science
Education (NSDL)". In Proceedings of the Second ACM/IEEE-CS Joint Conference on Digital Libraries
(July, 2002). http://arxiv.org/abs/cs.DL/0201025

3. Carl Lagoze, Dean Krafft, Tim Cornwell, Naomi Dushay, Dean Eckstrom, and John Saylor, "Metadata
aggregation and 'automated digital libraries': A retrospective on the NSDL experience," in Joint
Conference on Digital Libraries, (Chapel Hill, NC, 2006), ACM. http://arxiv.org/abs/cs.DL/0601125

4. Carl Lagoze, Dean Krafft, Tim Cornwell, Dean Eckstrom, Susan Jesuroga, and Chris Wilper,
Representing Contextualized Information in the NSDL. in ECDL2006, (Alicante, Spain, 2006), Springer.
http://arxiv.org/abs/cs. DL/0603024


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


5. Laura Bartolo, Cathy Lowe, Dean Krafft, and Robert Tandy, "NSDL MatDL: Adding Context to Bridge
Materials e-Research and e-Education", in ECDL 2007, (Budapest, Hungary, 2007), Springer, 499-500.
http://dx.doi.org/10.1007/978-3-540-74851-9 51

6. Dean B. Krafft, "The NCore Platform: An Open-Source Suite of Tools and Services for Implementing
Digital Libraries", in OR2008, Third International Conference on Open Repositories (Southampton,
England, 2008). http://pubs.or08.ecs.soton.ac.uk/11/

7. Dean B. Krafft, Aaron Birkland and Ellen J. Cramer, "NCore: Architecture and Implementation of a
Flexible, Collaborative Digital Library," in Joint Conference on Digital Libraries, (Pittsburgh, PA, 2008),
ACM. http://arxiv.org/abs/0803.1500

C. Research Support

Ongoing Research Support

11/1/07-10/31/09 Principal Investigator, Moore Foundation/Fedora Commons, Fedora Commons Durable
Platform for Collections, Collaboration, and Publications. Ongoing development of the open-source Flexible,
Extensible Digital Object Repository Architecture (Fedora).

Completed Research Support

10/1/07-9/30/08 Principal Investigator, NSF DUE/UCAR, NSDL Core Integration Increasing Capacity and
Engagement. Developed and operated in production the technical infrastructure for the National Science
Digital Library (http://nsdl.org).

6/1/05-12/31/07 Principal Investigator, NSF DUE, Collaborative Project: Core Integration Leading NSDL
Toward Long-Term Success. Initial development of the Fedora-based repository, architecture, tools, and
services for the National Science Digital Library.


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BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
McDonald, Robert H. Associate Dean for Library Technologies and
eRA COMMONS USER NAME Digital Library Programs;Associate Director, Data to
Insiaht Center. Pervasive Technoloav Institute
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DE EYEAR(s) FIELD OF STUDY
(if applicable)


University of South Carolina MLIS 1998 Information Science
University of Georgia M. Mus. 1996 Music Composition



A. Positions and Honors

Assistant Librarian, Auburn University, Auburn, AL 03/1999 05/2002
Associate University Librarian and Head Media Center Florida State University, Tallahassee, FL 05/2002 -
9/2002
Associate University Librarian and Associate Director for Library Technology Florida State University,
Tallahassee, FL- 09/2002 6/2003
University Librarian and Associate Director for Library Technology, Florida State University, Tallahassee, FL -
7/2003 12/2005
Chronopolis Project Manager San Diego Supercomputer Center, La Jolla, CA 12/2005 6/2006
Director, Strategic Data Initiatives San Diego Supercomputer Center, La Jolla, CA 7/2006 08/2008
Associate Librarian and Associate Dean for Library Technologies, Indiana University, Bloomington, IN -
08/2008 present
Associate Director Data to Insight Center, Pervasive Technology Institute, Indiana University, Bloomington, IN
- 05/2009 present

Track Chair, Educause Western Regional Conference Program Committee 2009
Program Planning Committee, Open Repositories Conference 2009
Library Information Technology Association Monographs Editor 2008-210
Frye Institute Fellow 2009

B. Selected peer-reviewed publications (in chronological order)

McDonald, R.H., T.O. Walter, (2009). "Restoring Trust Relationships within Collaborative Digital Preservation
Federations." Proceedings of the 4th International Conference on Open Repositories. May 18, Atlanta, GA.
Jordan, C., R.H. McDonald, D. Minor, and A. Kozbial. (2008). "Cyberinfrastructure Collaboration for Distributed
Digital Preservation." Proceedings of the 4th IEEE International Conference on eScience. Dec. 10-12,
Indianapolis, IN.
Hutt, A., B. Westbrook, A. Kozbial, R.H. McDonald, & D. Sutton, (2008). "Developing Preservation Metadata for
Use in Grid-based Preservation Systems." Proceedings of the 5th International Conference on the
Preservation of Digital Objects, Sept. 30, London, UK.
Walters, T.O., R.H. McDonald, (2008). "Creating Trust Relationships for Distributed Digital Preservation
Federations." Proceedings of the 5th International Conference on the Preservation of Digital Objects, Sept.
30, London, UK.


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Principal Investigator/Program Director (Last, First, Middle): Conlon, Michael
Moore, R.L., J. D'Aoust, R.H. McDonald, and D. Minor (2007). "Disk and Tape Storage Costs Models."
Proceedings of the 2007 IS&T Archiving Conference, May 21-24, 2007, Arlington, VA.
Berman, F., R.H. McDonald, B.E.C. Schottlaender, and A. Kozbial (2007). "The Need to Formalize Trust
Relationships in Digital Repositories." Educause Review 43(3) (May/June 2008): 10-11.
Thomas, Chuck, and Robert H. McDonald. (2007) "Measuring and Comparing Participation Patterns in Digital
Repositories: Repositories by the Numbers Part 1." D-Lib Magazine 13(9/10).
McDonald, R.H. and C. Jordan (2007). "Replication Policies for Distributed Digital Preservation Repositories."
Proceedings of NASA Symposium Science Archives in the 21st Century, April 25-26, 2006, College Park,
MD.
Thomas, Chuck and R.H. McDonald (2006). "A Performance Support Systems Approach to Digital Publishing
in Libraries." JCDL'06: Proceedings of the 6th ACM/IEEE-CS Joint Conference on Digital Libraries, 2006
p.336.
Thomas, C.F., R.H. McDonald, A.D. Smith, and T.O. Walters (2005). "The New Frontier of Institutional
Repositories: A Common Destination with Different Paths," New Review of Information Networking 11:1
(May): 65-82.

C. Research Support

IMLS NLG: Alabama Cornerstone Project
IMLS funded grant to provide a collaborative statewide initiative to make historical treasures from
Alabama's archives, libraries, museums, and other repositories electronically accessible.
Library of Congress NDIIPP Funding: MetaArchive of Southern Digital Culture
Partnership of six southeastern academic libraries to preserve one-of-a-kind born digital materials using the
Lots of Copies Keep Stuff Safe (LOCKSS) virtual private network preservation system.
Library of Congress NDIIPP Funding: Chronopolis Demonstration Testbed
Library of Congress funded proposal to provide long-term preservation for NDIIPP partner data within the
Chronopolis Federated Digital Preservation Framework. Partners included SDSC, UCSD Libraries,
National Center for Atmospheric Research, and the University of Maryland.


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BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
Mclntosh, Leslie D. Research Instructor,
eRA COMMONS USER NAME (credential, e.g., agency login) Ophthalmology and Visual Sciences

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DE EYEAR(s) FIELD OF STUDY
(if applicable)
Texas A&M University, College Station, TX B.A. 1990-1993 Biology
Biostatistics &
Saint Louis University, St. Louis, MO M.P.H. 2004-2006 Biot &
Epidemiology
Saint Louis University, St. Louis, MO Ph.D. 2006-2008 Epidemiology



A. Positions and Honors. List in chronological order previous positions, concluding with your present
position. List any honors. Include present membership on any Federal Government public advisory
committee.


1997 -2001:

2000 2008:
2001 -2003:
2004 2006:
2006 Summer:

2006 2007:
2007 2008:
2008 Present


Institutional Researcher, Adjunct Instructor, and Tutor, Mineral Area College, Park Hills,
MO
President, Jasmine Properties, Farmington, MO
Consultant in computer information technology, Farmington, MO
Course Coordinator and Website Developer, Saint Louis University, St. Louis, MO
Internship in Network Analysis, Center for Computational Analysis of Social and
Organizational Systems (CASOS), Carnegie Mellon University, Pittsburgh, PA
Evaluation Analyst, Saint Louis University, St. Louis, MO
Research Assistant, Washington University, St. Louis, MO
Research Instructor, Washington University, St. Louis, MO


Professional Memberships:


2005
2005
2007
2007
2008
2008
Louis


Member, American Statistical Association
Member, International Network for Social Network Analysis
Member, Association for Research in Vision and Ophthalmology
Member, Society for Medical Decision Making
Member, American Medical Informatics Association
Member, Institute of Clinical and Translational Sciences (ICTS) at Washington University in St.


B. Selected peer-reviewed publications (in chronological order). Do not include publications
submitted or in preparation.

Mariah Dreisinger, Ajlina Karamehic-Muratovic, Leslie Mclntosh, Ross Brownson, Elizabeth Baker.
Examining the role of training in evidence-based public health: A qualitative study. Health Promotion
Practice. 2009 (in press)

Mclntosh L. Internet Data Collection. In: Boslaugh S., editor. Encyclopedia of epidemiology. Thousand
Oaks, California: Sage Publishing, 2007.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


C. Research Support.

Current support:
Development of a Vision Specific Utilities Elicitation Method
Principal Investigator: Steven Kymes, PhD
1 R03 EY017862-01
NIH/NEI
Role: Psychometrician Collaborator

Previous support:
Collaborative Longitudinal Evaluation of Keratoconus (CLEK)
Principal Investigator: Mae Gordon, PhD
5 U10 EY10077-10S1
NIH/NEI
Role: Psychometrician Research Assistant

E-learning Networks Project: Tracking Youth Attitudes, Opinions, & Beliefs with Network Text Analysis
Co-Principal Investigators: Santosh Vijaykumar, M.S and Leslie Mclntosh, PhD
Impact Alliance (USAID sub-contract grant)
Role: Investigator and Quantitative Analyst


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BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
Nagarajan, Rakesh Assistant Professor of Pathology & Immunology
eRA COMMONS USER NAME (credential, e.g., agency login)
RAKESH
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DE EYEAR(s) FIELD OF STUDY
(if applicable)
University of Virginia B.A. 1994 Interdisciplinary
Washington University School of Medicine Ph.D. 2003 Neuroscience
Washington University School of Medicine M.D. 2003 Medicine


A. Positions and Employment


2003-June 2005

June 2005-Present
January 2003-Present
September 2006-Present
September 2007-Present


Instructor, Pathology & Immunology, Washington University School of Medicine
(WUSM)
Assistant Professor, Pathology & Immunology, WUSM
Co-Director, Alvin J. Siteman Cancer Center Bioinformatics Core
Director, Neuroscience Blueprint Biomedical Informatics Core
Co-Director, George M. O'Brien Center for Kidney Disease Research
Translational Research Core; Director, Clinical and Translational Science Award
Biomedical Informatics Program


Honors
1990-1994 Echols Scholar Program, University of Virginia
1992-1994 Barry M. Goldwater Scholarship, University of Virginia
1992-1994 Howard Hughes Undergraduate Research Apprenticeship Program, University of Virginia
2002 Spencer T. & Ann W. Olin Medical Scientist Fellow Award, WUSM
2006 caBIGTM Outstanding Team Contribution Award, Siteman Cancer Center
2006 caBIGTM, Integrative Cancer Research Workspace Team Mentoring Award
2006 caBIGTM, Tissue Banks and Pathology Tools Workspace Team Award

B. Selected peer-reviewed publications (in chronological order).
1. Nagarajan R, Svaren, J., Le, N., Araki, T., Watson, M., and Milbrandt, J. (2001). EGR2 mutations in
inherited neuropathies dominant-negatively inhibit myelin gene expression. Neuron 30, 355-68.

2. Nagarajan R, Le, N., Mahoney, H., Araki, T., and Milbrandt, J. (2002). Deciphering peripheral nerve
myelination by using Schwann cell expression profiling. Proc Natl Acad Sci U S A 99, 8998-9003

3. Young AP, Nagarajan R, Longmore GD. (2003). Mechanisms of transcriptional regulation by Rb-E2F
segregate by biological pathway. Oncogene. 22, 7209-17.

4. Le, N., Nagarajan, R., Wang, J. Y., Araki, T., Schmidt, R. E., and Milbrandt, J. (2005). Analysis of
congenital hypomyelinating Egr2Lo/Lo nerves identifies Sox2 as an inhibitor of Schwann cell
differentiation and myelination. Proc Natl Acad Sci U S A.

5. Le, N., Nagarajan, R., Wang, J. Y., Svaren, J., LaPash, C., Araki, T., Schmidt, R. E., and Milbrandt, J.
(2005). Nab proteins are essential for peripheral nervous system myelination. Nat Neurosci 8, 932-940.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


6. Chang, L. W., Nagarajan, R., Magee, J. A., Milbrandt, J., and Stormo, G. D. (2006). A systematic model
to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor
binding profiles. Genome Res 16(3), 405-413.

7. Sharma MK, Mansur DB, Reifenberger G, Perry A, Leonard JR, Aldape KD, Albin MG, Emnett RJ,
Loeser S, Watson MA, Nagarajan R., Gutmann DH (2007). Distinct genetic signatures among pilocytic
astrocytomas relate to their brain region origin. Cancer Res 67(3), 890-900.

8. Chang LW, Fontaine BR, Stormo GD, and Nagarajan R. (2007). PAP: a comprehensive workbench for
mammalian transcriptional regulatory sequence analysis. Nucleic Acids Res 35, W238-244.

9. Chang, L.W., Payton, J.E., Yuan, W., Ley, T.J., Nagarajan, R., and Stormo, G.D., Computational
identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute
promyelocytic leukemia. Genome Biol, 2008. 9(2): p. R38.

10. Deshmukh, H, Yeh, TH, Yu, J, Sharma, MK, Perry, A, Leonard, JR, Watson, MA, Gutmann, DH, and
Nagarajan, R., High-resolution, dual-platform aCGH analysis reveals frequent HIPK2 amplification and
increased expression in pilocytic astrocytomas. 2008. Oncogene, Apr 14 (Epub ahead of print).

C. Research Support
P30 CA91842 (Eberlein) 7/1/04-6/30/09
NIH/NCI
Cancer Center Support Grant
The Siteman Cancer Center is an interdisciplinary, integrated NCI-designated Clinical Cancer
Center
Role: Co-Director of Bioinformatics Core

#26XS185 (Nagarajan) 6/2/06-6/1/09
NCI subcontract with SAIC-Frederick, Inc.
A caGRID-enabled Microarray Analysis Application
The major goals of this project are to develop a caGrid Client termed caBench-to-Bedside (caB2B) that
will be able to leverage any caGrid data or analytical service to facilitate clinical and translational
research.

UL1 RR024992 (Polonsky) 9/17/07-5/31/12
NIH/NCRR
Washington University Institute of Clinical and Translational Sciences (CTSA)
Program 2.03 Biomedical Informatics (Nagarajan)
Role: Program Director
The overarching goals of our CTSA Biomedical Informatics Program is to facilitate clinical and translational
research through the creation of a new Center for Biomedical Informatics, development of a
comprehensive electronic Clinical and Translational Research Environment (eCATRE) that will integrate
the research, collaboration, and educational activities of the ICTS, providing services and tools for data
management and integration of clinical and molecular data sets, and develop a broad range of training
resources.

P30 NS057105 (Holtzman) 9/25/06-8/31/11
NIH/NINDS
WU Center for Translational Neuroscience
Core G: Informatics and Data Integration (Nagarajan)
Role: Director
The aims of these cores are to coordinate biospecimen management for neuroscience-based protocols, to


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


migrate legacy data from neuroscience biospecimen repositories into a comprehensive biospecimen
informatics system, termed Tissue Suite, and to develop informatics tools to facilitate curation, query,
analysis, and visualization of complex data sets across other Neuroscience Blueprint cores.

P30 DK079333 (Hammerman) 8/3/07-5/31/12
NIH/NIDDK
Washington University Center for Kidney Disease Research
Core D: Kidney Translational Research Core
Role: Co-Director
The Washington University Kidney Translational Research Core will serve at a state-of-the-art
accessible repository for clinical information and biological specimens. Services will be provided for
collecting, storing, de-identifying, and curating data. In addition, the KTRC will integrate storage of
biospecimens from several pre-existing repositories, assist in new collection efforts, and serve as a
centralized storage facility for kidney disease related biospecimens.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BIOGRAPHICAL SKETCH
NAME POSITION TITLE
Noel Jr., Richard J. Associate Professor
eRA COMMONS USER NAME
rjnoeljr
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DEGREEYEAR(s) FIELD OF STUDY
(if applicable) YA( OSTD
Boston College, Chestnut Hill, MA BS 1993 Biology
University of Wisconsin, Madison, WI PhD 1998 Biochemistry
Ponce School of Medicine, Ponce, PR post doc 2001 Pharmacology


A. Positions and Honors.


Positions
1993-1998
1998-2001
1999-
1999-
2001-
2001-2006
2001-2003
2002-
2003-2006
2007-
2007-
2008-
2008-


Research Assistant, University of Wisconsin Madison
Research Associate, Ponce School of Medicine, Department of Pharmacology
Graduate Admissions Committee, Ponce School of Medicine, Ponce, PR
Graduate Advisory and Curriculum Committee, Ponce School of Medicine, Ponce, PR
Assistant Professor, Department of Biochemistry, Ponce School of Medicine, Ponce, PR
Assistant Professor, Department of Microbiology, Ponce School of Medicine, Ponce, PR
Supervisor of DNA Core, AIDS Research Program, Ponce School of Medicine, Ponce, PR
Medical Student Admissions Committee
Molecular Biology Core Facility, Co-Director, Ponce School of Medicine, Ponce, PR
Molecular Biology Core Facility, Director, Ponce School of Medicine, Ponce, PR
Associate Professor, Department of Biochemistry, Ponce School of Medicine, Ponce, PR
Internal Advisor for PSM-RISE training program
Internal Advisor for PSM-Moffitt Partnership


Professional Memberships and Honors
Travel Award Recipient: 2006 Society on Neuroimmune Pharmacology, Santa Fe, NM, 2005 International
Meeting of the Institute of Human Virology. Baltimore, MD, 2004 International
Meeting of the Institute of Human Virology. Baltimore, MD
Member, Society on Neuroimmune Pharmacology, 2005-present
Member, American Society of Microbiology, 2006-present
Member, American Society for Biochemistry & Molecular Biology, 1999-present
Member, American Association for the Advancement of Science, 1999-present
NIH-sponsored Molecular Biosciences Training Grant trainee, 5T32GM007215 (1994-1997)
NSF Fellowship honorable mention (1993)
Phi Beta Kappa (elected May 1993)

B. Peer-reviewed publications (in chronological order).
1. D. Czarniecki, R.J. Noel Jr., and W.S. Reznikoff. (1997) The -45 Region of the E. coli lac Promoter: CAP-
Dependent and CAP-Independent Transcription. J. Bacteriol. 179 (2), pp. 423-429.
2. R.J. Noel Jr. and W.S. Reznikoff. (1998) CAP, the -45 region, and RNA polymerase: three partners in
transcription initiation at lacP1 in Escherichia coli. J. Mol. Biol. 282, pp.495-504.
3. R.J. Noel Jr. and W.S. Reznikoff. (2000) Structural studies of the lacUV5-RNA polymerase interactions in
vitro: phosphate ethylation and the missing nucleoside effects. J.Biol.Chem. 275 (11), pp.7708-7712.
4. R.J. Noel Jr.*, Chaudhary, S., Rodriguez, N., Kumar, A., and Y. Yamamura. (2003) Phylogenetic
Relationships Between Puerto Rico and Continental U.S.A. HIV-1 pol Sequences: A shared HIV-1
infection. Cell. Mol. Biol. 49 (8), pp.1193-1198.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael
5. G. Tirado, G. Jove, R. Kumar, R. J. Noel, E. Reyes, G. Sepulveda, Y. Yamamura and A. Kumar (2004).
Differential HIV-1 evolution in blood and genital tract of HIV-infected females: Evidence for the involvement
of drug resistant and immunological variant of the virus. Virology 324(2), pp. 577-86.
6. G. Tirado, G. Jove, R. Kumar, R. J. Noel, E. Reyes, G. Sepulveda, Y. Yamamura and A. Kumar (2004).
Compartmentalization of Drug Resistant-Associated Mutations in Treatment Naive HIV-infected Female.
AIDS Research and Human Retroviruses 20(6), pp. 684-6.
7. R. Kumar, A. Perez-Casanova, G. Tirado, R. J. Noel, C. Torres, I. Rodriguez, M. Martinez, S. Staprans, E.
Kraiselburd, Y. Yamamura, J. D. Higley, A. Kumar. (2005) Increased viral replication in SIV/SHIV-infected
macaques with self-administering model of chronic alcohol consumption. J. Acquir.lmmune Defic. Syndr.
39 (4), pp.386-90.
8. R. J. Noel Jr.* and A. Kumar (2006) Virus Replication and Disease Progression Inversely Correlate with
SIV Tat Evolution in Morphine-Dependent and SIV/SHIV-infected Indian Rhesus Macaques. Virology.
346(1), pp.127-38.
9. R. J. Noel Jr.*, A. Toro-Bahamonde, Z. Marrero-Otero, S. Orsini, A. Verma, R. Kumar, and A. Kumar
(2006) Lack of Correlation Between SIV-Nef Evolution and Rapid Disease Progression in Morphine-
dependent Non-Human Primate model of AIDS. AIDS Res. Hum. Retrovir. 22(8), pp. 817-23.
10. R. J. Noel Jr.*, Z. Marrero-Otero, R. Kumar, G.S. Chompre-Gonzalez, A.S. Verma, and A. Kumar. (2006)
Correlation between SIVTat Evolution and AIDS progression in Cerebrospinal Fluid of Morphine-dependent
and Control Macaques Infected with SIV and SHIV. Virology. 349(2), pp.440-452.
11. V. Rivera-Amill, R.J. Noel Jr., S. Orsini, G. Tirado, J.M.Garcia, S.Buch, and A. Kumar (2007) Variable
Region 4 of SIV Envelope Correlates with Rapid Disease Progression in Morphine-exposed Macaques
Infected with SIV/SHIV. Virology. 358(2), pp. 373-383.
12. R.J. Noel Jr.* and A. Kumar. (2007) SIV vpr evolution is inversely related to disease progression in a
morphine-dependent rhesus macaque model of AIDS. Virology. 359(1), pp.397-404.
13. A. Perez-Casanova, R.J. Noel Jr., V. Rivera-Amill, K. Husain, and A. Kumar. (2007) Morphine mediated
deterioration of oxidative stress leads to rapid disease progression in SIV/SHIV-infected macaques. AIDS
Res. Hum. Retrovir. 23(8), pp.1004-7.
14. A.Perez-Casanova, K. Husain, R.J. Noel Jr., V. Rivera-Amill and A. Kumar. (2008) Interaction of SIV/SHIV
Infection and Morphine on Plasma Oxidant/Antioxidant Balance in Macaque. Mol. Cell. Biochem.308(1-2),
pp. 169-175.
15. R. Noel, V. Rivera-Amill, S. Buch, and A. Kumar. (2008). Opiates, immune system, AIDS and non-human
primate model. J. Neurovirol. 14, 1-7.
16. V. Rivera-Amill, R. Noel, S. Buch, and A. Kumar. (2009). Analysis of the V1V2 region of SIV envelope in
the brains of morphine-dependent and control SIV/SHIV-infected macaques. AIDS Res. Hum. Retrovir. In
press.
*Corresponding Author.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
Russell Gonzalez, Sara A. Physical Sciences Librarian
eRA COMMONS USER NAME (credential, e.g., agency login)

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION DE EYEAR(s) FIELD OF STUDY
(if applicable)
California Institute of Technology B.S. 1996 Geophysics
University of California, Santa Cruz Ph.D. 2001 Geophysics/Seismology
Florida State University M.L.I.S. 2005 Library Science




A. Positions and Honors. List in chronological order previous positions, concluding with your present position.
List any honors. Include present membership on any Federal Government public advisory committee.

Positions and Employment

2001-2005 Research Scientist, Weston Geophysical Corporation, Lexington, MA
2005-2009 Assistant University Librarian, University of Florida Libraries, Marston Science Library

Other Experience and Professional Memberships

Special Library Association 2005-2009

Science & Technology Division, 2005-2009
2006-2009 Awards Committee
2007-2009 Communications Committee
2008-2009 Website Administrator

Physics, Astronomy, Mathematics Division, 2005-2009

2006-2007 Assistant Bulletin Editor
2007-2008 Bulletin Editor

Florida-Caribbean Chapter, 2005-2009

2008-2009 Ethics Ambassador
2007-2009 North-central Florida Representative

Honors
1.University of California Regents Fellowship, 1996
2.Graduate Assistance in Areas of National Need (GAANN) Fellow, UC Santa Cruz, 1998
3.Outstanding Teaching Assistant, UC Santa Cruz Department of Earth Sciences, 2000
4.Institute of Geophysics and Planetary Physics Fellow, 2001
5.Science-Technology Division, Special Library Association S. Kirk Cabeen Award, 2006

B. Selected peer-reviewed publications (in chronological order). Do not include publications submitted or in
preparation.
PHS 398/2590 (Rev. 11/07) Page 83 Biographical Sketch Format Page






Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


1.S.A. Russell, T. Lay, and E.J. Garnero, "Seismic evidence for small-scale dynamics in the lowermost mantle
at the root of the Hawaiian hotspot", Nature, 396, 255-258, 1998.
2.S.A. Russell, T. Lay, and E. Garnero, "Small scale lateral shear velocity and anisotropy heterogeneity near
the core-mantle boundary beneath the central Pacific imaged using broadband ScS waves", J. Geophys. Res.,
104, 13183-13199, 1999.
3.S.A. Russell, C. Reasoner, T. Lay, and J. Revenaugh, "Coexisting shear- and compressional-wave seismic
velocity discontinuities near the base of the mantle beneath the central Pacific", Geophys. Res. Lett., 28, 2281-
2284, 2001.
4.J. Bonner, D.G. Harkrider, E.T. Herrin, S.A. Russell, R.H. Shumway, and I. Tibuleac, "Evaluation of short-
period, near-regional Ms scales for the Nevada Test Site", Bull. Seism. Soc. Am., 93, 1773-1791, 2003.
5.J.M. Rokosky, T. Lay, E.J. Garnero, and S.A. Russell, "High-resolution investigation of shear wave
anisotropy in D" beneath the Cocos Plate", Geophys. Res. Lett., 31, 411-425, doi:10.1029/2003GL018902,
2004.
6.T. Lay, E.J. Garnero, and S.A. Russell, "Lateral variation of the D" discontinuity beneath the Cocos Plate",
Geophys. Res. Lett., 31(15), 2004.
7.M. Avants, T. Lay, S. Russell, and E.J. Garnero, "Shear-velocity variation within the D" region beneath the
central Pacific", J. Geophys. Res., 111, B05305, doi:10.1029/2004JB003270, 2006.
8.S.A. Russell Gonzalez, K. Kennedy, and P. Cenzer, "E-Education: Does an online degree make a difference
to academic library employers?", Association of College and Research Libraries 13th National Conference
Proceedings, Baltimore, MD, 2007.
9.K. Kennedy, S. Russell Gonzalez, and P. Cenzer, "Student Perspectives on Library School Degrees and the
Hiring Process". Journal of Education for Library and Information Science. 48 (4), 2007.
10.K. Kennedy, T. Cataldo, V. Davis, C. Newsom, and S. Russell Gonzalez, "Evaluating Continuing
Resources: Perspectives and Methods from Science Librarians. Serials Librarian. 55 (3), 2008.
11.S. Russell Gonzalez, V. Davis, C. Dinsmore, C. Frey, C. Newsom, and L. Taylor, "Bioactive: a game for
library instruction". Gaming in academic libraries: collections, marketing, and information literacy. Association
of College and Research Libraries. Chicago: IL, 2008.
12.V. Davis, M. Devare, S. Russell Gonzalez, and M. Tennant, "Implementation of a new research discovery
tool at two University libraries". Proceedings of the Contributed Papers Session. SLA Biomedical and Life
Sciences Division, 2009.

C. Research Support. List selected ongoing or completed (during the last three years) research projects
(federal and non-federal support). Begin with the projects that are most relevant to the research proposed in
this application. Briefly indicate the overall goals of the projects and your role (e.g. PI, Co-Investigator,
Consultant) in the research project. Do not list award amounts or percent effort in projects.

"Developing a Database to Foster Interdisciplinary Communication and Collaboration at UF", UF Libraries Mini-
Grant, co-PI, 10/2007-9/2008

Installed and populated test implementation of Cornell's VIVO database software at the University of
Florida. Test database presented to multiple UF campus groups to secure support for development of a
mature database to aid with research collaboration and communication of UF research to the campus
community and general public.

"Science Education for Teachers and Students Throughout Florida", NASA Hubble Space Telescope
Education and Public Outreach, consultant, 2/2008-1/2010

Procured and set up a system with software for 3-D display of astronomical and planetary datasets.
System was designed to be mobile to transport to K-12 institutions throughout Florida to teach students
about astronomy.


Biographical Sketch Format Page


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael

BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE
Tennant, Michele R. Bioinformatics Librarian
eRA COMMONS USER NAME (credential, e.g., agency
login)

TENNANTM

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and
include postdoctoral training.)
DEGREE
INSTITUTION AND LOCATION (if ai ) YEAR(s) FIELD OF STUDY
(if applicable)
University of Southern California, Los Angeles, CA BS 1982 Biological Sciences

Wayne State University, Detroit, MI Ph.D. 1991 Biology

University of California, Los Angeles, CA M.L.I.S. 1994 Library & Information
Science
A. Positions and Honors.
Positions and Employment
Intern, Information Services, Amgen, Inc., Thousand Oaks, CA, June-Sept. 1994

University Librarian, Health Science Center Libraries, University of Florida, Gainesville, FL, July 2006-; (Visiting
Librarian, Aug. 1995-Aug. 1996; Assistant University Librarian; Aug. 1996-June 2002; Associate University
Librarian, July 2002-June 2006)

Joint Appointment, Department of Molecular Genetics and Microbiology, College of Medicine, University of
Florida, Gainesville, FL, 2003-

Other Experience and Professional Memberships
Medical Library Association (MLA), member, 1995-

Special Libraries Association (SLA), member, 1995-

Fellow (competitive program), Medical informatics: a course for health professionals", sponsored by the
National Library of Medicine, held at Woods Hole, MA, 29 May-5 June 1996

Visiting Scholar, Medical Sciences Library, University of Puerto Rico, 9-10 Mar. 1998

Visiting Instructor, Denison Memorial Library, University of Colorado Health Sciences Center, 26-27 Apr. 1999

Convener, Medical Library Association's Molecular Biology and Genomics Special Interest Group, Aug.1999-
May 2001

Invited Participant, initial planning meeting, "Scientists' needs, library roles, and future directions." National
Center for Biotechnology Information, Bethesda, MD, 10-12 Jan. 2001

Chair, SLA's Biomedical and Life Sciences Division, June 2001-June 2002 (Chair-elect, June 2000-June 2001,
Past-chair, June 2002-June 2003)


Biographical Sketch Format Page


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PH S 398/2590 (Rev. 11 /07)






Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


University of Florida, Genetics Institute, Executive Committee, member, Aug. 2001-

Planning meeting, development of advanced course and enhancement of basic course in use of NCBI
resources. Invited participant/consultant. National Center for Biotechnology Information, Bethesda, MD, 9-10
Aug. 2001 and 26-29 Mar. 2002

"Bioinformationist", invited presentation at "The informationist", invitation-only conference, National Library of
Medicine, Bethesda, MD, 4 Apr. 2002

"NCBI advanced workshop for bioinformatics information specialists (NAWBIS)." Continuing Education
Course, module developer and course instructor, Bethesda, MD, 6, 8 Aug. 2002, 5, 7 Aug. 2003, 3-4 Aug.
2004, 2-3 Aug. 2005, 8-9 Aug. 2006, 7-8 Aug. 2007

Task Force on Information Specialists in Context, Medical Library Association, member, May 2003-Dec. 2005

"Advanced workshop for bioinformatics information specialists: an educational collaboration" (poster with N.
Gaedeke [presenter], K. Alpi, J. Lyon, J. Ohles, D. Osterbur, and R. Geer). World Library and Information
Congress: 69th IFLA General Conference and Council, Berlin, Germany, 5-6 Aug. 2003

Attendee (competitive program), "Bio21: teaching biology with bioinformatics" conference, University of North
Carolina, Chapel Hill, NC, 17-18 Oct. 2003

"Introduction to molecular biology information resources." Continuing Education Course, regional instructor,
taught for the National Center for Biotechnology Information (NCBI). U.C.L.A., Los Angeles, CA, 17-19 Nov.
2003, University of Florida, Gainesville, FL, 24-26 Mar. 2004, Vanderbilt University, Nashville, TN, 4-6 Apr.
2005, University of California, Davis, 28-30 Mar. 2006, Emory University, Atlanta, GA, 14-16 Mar. 2007,
Washington University, St. Louis, MI, 14-16 Apr. 2008

National Library of Medicine, Proposed Changes to the NLM Classification in the Areas of Cells and Genetics,
reviewer (with C. Botero), Jan. 2005

Journal of the Medical Library Association, Editorial Board, member, July 2005 June 2008

Planning panel on National Library of Medicine support for genomic science in the 21st century. Invited
panelist, National Library of Medicine, Bethesda, MD, 21-22 Nov. 2005 and 14-15 Mar. 2006.

National Library of Medicine, proposed changes to the NLM classification in the areas of bacteria and proteins,
reviewer (with C. Botero) Dec. 2005

University of Florida, Future of the Libraries Task Force, member, June-Dec. 2006 (provost-appointed task
force)

"Strategies for library support for research", invited presentation, Association of Research Libraries
Membership Meeting, St. Louis, MO, 23 May 2007 (videotaped)

'How (and how well) do researchers use bioinformatics resources? A preliminary analysis." Medical Library
Association Annual Conference, Chicago, IL, 19 May 2008

"The Institutional Review Board and library research: memoirs of a multi-site project." Biomedical and Life
Sciences Division, Special Libraries Association Annual Conference, Seattle, WA, 16 June 2008

"Library-based bioinformatics support: changing perceptions, changing roles." Biomedical and Life Sciences
Division, Special Libraries Association Annual Conference, Seattle, WA, 17 June 2008


PH S 398 (Rev. 11 /07)


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Biographical Sketch Format Page






Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


"Library-based bioinformatics support: who and how? An exploration of librarian and scientist perspectives."
STS Forum for Science & Technology Library Research, American Library Association Annual Conference,
Anaheim, CA, 29 June 2008

National Library of Medicine, Biomedical Library and Informatics Review Committee, member, Nov. 2008 -
June 2012

"Bioinformatics librarian." Invited presentation, E-science Symposium, sponsored by the Regional Medical
Library of New England and the Boston Library Consortium, and the Lamar Soutter Library, Worcester, MA, 7
Apr. 2009

Medical Library Association, Continuing Education Committee, member, May 2009 Apr. 2012.

"Implementation of a new research discovery tool by the university libraries at Cornell University and the
University of Florida." Biomedical and Life Sciences Division, Special Libraries Association Annual
Conference, Washington, D.C., 16 June 2009 (with V. Davis, M. Devare, and S.R. Gonzalez)

Honors
Top 20 Library Instructional Paper of the Year, American Library Association, Library Instructional Round Table
(LIRT), 2003, "The role of medical libraries in undergraduate education: a case study in genetics" (J. Med. Libr.
Assoc., 90(2):180-193)
Distinguished Member Status, Academy of Health Information Professionals, 2005-2010
Distinguished Member Award, Recipient, SLA, Biomedical and Life Sciences Division, 2005
Estelle Brodman Academic Medical Librarian of the Year Award, Recipient, MLA, 2005

B. Selected peer-reviewed publications (in chronological order).
Miyamoto, M.M., B.F. Koop, J.L. Slightom, M. Goodman and M.R. Tennant. 1988. Molecular systematics
of higher Primates: genealogical relations and classification. Proc. Natl. Acad. Sci. USA, 85:7627-31

Allard, M.W., M.M. Miyamoto, L. Jarecki, F. Kraus, and M.R. Tennant. 1992. DNA systematics and evolution
of the Artiodactyl family Bovidae. Proc. Natl. Acad. Sci. USA, 89:3972-6

Tennant, M.R. and B.W. Francis. 1999. Course-integrated instruction in an academic health science library: a
comparison of basic science and clinical strategies. p.45-63 in "Getting the Message Across: Innovation in
Library Instruction and Training in Biomedical and Life Sciences Libraries: Proceedings of the Contributed
Paper Session, Biomedical and Life Sciences Division, Special Libraries Association, 90th Annual Conference"
(Eleanor MacLean and Peggy Jones, conveners)

Tobin, T.M., and M.R. Tennant. 2000. TAILor made: the enhancing of a liaison program to meet the needs of
veterinary clinicians and researchers. Proceedings of the 8th International Congress on Medical Librarianship,
http://www.icml.org/monday/icahis2/tobin.htm

Tennant, M.R., M.E. Rezeau, P. Tucker, L.C. Butson, M. Boyle, and G. Clayton. 2001. Customizing for
clients: developing a library liaison program from need to plan. Bull. Med. Libr. Assoc., Jan;89(1):8-20

Liu, R.F.G., M.M. Miyamoto, N.P. Freire, P. Ong, M.R. Tennant, T.S. Young, and K.F. Gugel. 2001. Molecular
and morphological supertrees for Eutherian (Placental) mammals. Science, Mar 2;291(5509):1786-9

Tennant, M.R., and T.T. Cataldo. 2002. Development and assessment of specialized liaison services: clinical
vs. basic science in a veterinary medicine setting. Med. Ref. Serv. Q., 21(2):21-37


Biographical Sketch Format Page


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Tennant, M.R., and M.M. Miyamoto. 2002. The role of medical libraries in undergraduate education: a case
study in genetics. J. Med. Libr. Assoc., 90(2):180-93

Tennant, M.R. 2005. Bioinformatics librarian: meeting the information needs of genetics and bioinformatics
researchers. Ref. Serv. Rev., 33(1):12-9

Tennant, M.R., and J.A. Lyon. 2006. Online resources for genetics researchers, clinicians, and the public:
Online Mendelian Inheritance in Man and GeneTests. J. Elec. Res. Med. Libr.; 3(2):1-23

Lyon, J.A, M.R. Tennant, K. Messner, and D.L Osterbur. 2006. Carving a niche: establishing bioinformatics
collaborations. J. Med. Libr. Assoc., 94(3):330-5

Tennant, M.R., T.T. Cataldo, P. Sherwill-Navarro, and R. Jesano. 2006. Evaluation of a liaison librarian
program: client and liaison perspectives. J. Med. Libr. Assoc., 94(4):402-9, e201-4

Lyon, J.A., M.R. Tennant, and B. Danielson. 2006. Introducing Protein Data Bank, Molecular Modeling
Database, and Cn3D. J. Elec. Res. Med. Libr., 3(3):1-20

Cataldo, T.T., M.R. Tennant, P. Sherwill-Navarro, and R. Jesano. 2006. Subject specialization in a liaison
librarian program. J. Med. Libr. Assoc., 94(4):446-8

Tennant, M.R., and J.A. Lyon. 2007. Entrez Gene: a Gene-centered "Information Hub". J. Electron. Res.
Med. Libs., 4(3):53-78

Botero, C., S. Carrico, and M.R. Tennant. 2008. Using comparative online journal usage studies to assess the
big deal. Libr. Res. & Tech. Serv. 52(2):61-8

Tennant, M.R., and M.M. Miyamoto. 2008. The role of the medical librarian in the basic biological sciences: a
case study in virology and evolution. J. Med. Libr. Assoc., 96(4):290-8

Ferree N, N. Schaefer, L.C. Butson, and M.R. Tennant. 2009. Liaison librarian tiers: a tool for change. J. Med.
Libr. Assoc. 97(2):145-8

(Publications selected from 27 peer-reviewed publications)

C. Research Support
Ongoing Research Support
Medical Library Association 7/1/07-6/30/09
Assessment of user skills and efficiency in the application of bioinformatics resources to answer biological
questions
The major goal of this project is to understand how researchers search the resources available from the
National Center for Biotechnology Information in an effort to inform instruction, marketing, and design of
resources
Role: Principal Investigator

Completed Research Support
Medical Library Association 7/1/07-6/30/08
Exploring models of library-based bioinformatics support programs: services, staffing, training and funding
The major goal of this project is to explore models of library-based bioinformatics support programs at
institutions that provide successful services
Role: Principal Investigator

National Science Foundation, Improvement to Dissertation Grant, 1988-91
PHS 398 (Rev. 11/07) Page 88 Biographical Sketch Format Page








Principal Investigator/Program Director (Last, First, Middle):


RESOURCES
FACILITIES: Specify the facilities to be used for the conduct of the proposed research. Indicate the performance sites and describe capacities,
pertinent capabilities, relative proximity, and extent of availability to the project. If research involving Select Agent(s) will occur at any performance
site(s), the biocontainment resources available at each site should be described. Under "Other," identify support services such as machine shop,
electronics shop, and specify the extent to which they will be available to the project. Use continuation pages if necessary.

Laboratory:




Clinical:





Biocontainment Resources Available: Complete if research involving Select Agent(s) will occur at any performance site(s), otherwise indicate N/A.




Animal:


Computer:
Cornell: The Albert R. Mann Library maintains a temperature-controlled, secure server room with
approximately 30 production UNIX, Linux and Windows 2000 Servers, and maintains 24 hour, 7 day a week,
on-call staff support. Servers have battery backup for uninterrupted service in the event of power outages
and are on a tape backup schedule with offsite storage. Internet access, data security, system operation,
data interchange, client and server applications and other computation resources necessary to implement
and operate the development effort under this project will be provided by Mann ITS.





Office:
Cornell: The Albert R. Mann Library is a state-of-the-art Agriculture, Life Sciences and Human Ecology library
located on the Cornell University Ithaca Campus in upstate New York. The ITS office suite is a modern
facility with bright, open spaces, a designated project room for staff collaboration, and reconfigurable
furniture to meet the changing needs of the department. The space is large enough to accommodate the
additional staff needed to support the project.


Other:


Resources Format Page


MAJOR EQUIPMENT: List the most important equipment items already available for this project, noting the location and pertinent capabilities of each.


Conlon, Michael


PH S 398 (Rev. 11 /07)


Page 89








Principal Investigator/Program Director (Last, First, Middle):


RESOURCES
FACILITIES: Specify the facilities to be used for the conduct of the proposed research. Indicate the performance sites and describe capacities,
pertinent capabilities, relative proximity, and extent of availability to the project. If research involving Select Agent(s) will occur at any performance
site(s), the biocontainment resources available at each site should be described. Under "Other," identify support services such as machine shop,
electronics shop, and specify the extent to which they will be available to the project. Use continuation pages if necessary.

Laboratory:




Clinical:





Biocontainment Resources Available: Complete if research involving Select Agent(s) will occur at any performance site(s), otherwise indicate N/A.




Animal:


Computer:
Indiana: The infrastructure servers that will run the VIVO software are part of the DLP infrastructure that is
managed at IUB by UITS.


Office:
Indiana: Offices will be provided by the Indiana University Libraries in Bloomington.



Other:


MAJOR EQUIPMENT: List the most important equipment items already available for this project, noting the location and pertinent capabilities of each.


Resources Format Page


Conlon, Michael


PH S 398 (Rev. 11 /07)


Page 90








Principal Investigator/Program Director (Last, First, Middle):


RESOURCES
FACILITIES: Specify the facilities to be used for the conduct of the proposed research. Indicate the performance sites and describe capacities,
pertinent capabilities, relative proximity, and extent of availability to the project. If research involving Select Agent(s) will occur at any performance
site(s), the biocontainment resources available at each site should be described. Under "Other," identify support services such as machine shop,
electronics shop, and specify the extent to which they will be available to the project. Use continuation pages if necessary.

Laboratory:




Clinical:





Biocontainment Resources Available: Complete if research involving Select Agent(s) will occur at any performance site(s), otherwise indicate N/A.




Animal:




Computer:

Ponce: The Ponce School of Medicine (PSM) Management Information Systems (MIS) Department provides
service and support to the four degree programs and thus serves all constituents within the institution. A
campus wide network, supported by both physical and wireless infrastructure, links all PSM units and
divisions. External web log-on is fully supported to facilitate access by off-site clinical faculty as well as to
provide service for 'out-of office' faculty, staff and students. The MIS Department has a Director who
operates under the oversight of the Executive Dean for Administration and Finance and coordinates closely
with the Facilities and General Services division and other informatics-based support (library, audiovisual,
etc.) The MIS Department has adequate resources to fully support the Ponce School of Medicine as an early
implementer of the VIVO system, including the required web access, security, system operation, data
management, as well as computational resources (including client and server support).

Office:

Ponce: Sufficient office space exists to fully support the activities contemplated under this grant agreement.


Other:

Ponce: Resources of the Fundaci6n Angel Ramos Library, particularly the Learning Resources Center and
linked computerized teaching laboratories will provide support for VIVO instruction to the PSM research
community.

MAJOR EQUIPMENT: List the most important equipment items already available for this project, noting the location and pertinent capabilities of each.


Resources Format Page


Conlon, Michael


PHS 398 (Rev. 11/07)


Page 91








Principal Investigator/Program Director (Last, First, Middle):


Conlon, Michael


RESOURCES
FACILITIES: Specify the facilities to be used for the conduct of the proposed research. Indicate the performance sites and describe capacities,
pertinent capabilities, relative proximity, and extent of availability to the project. If research involving Select Agent(s) will occur at any performance
site(s), the biocontainment resources available at each site should be described. Under "Other," identify support services such as machine shop,
electronics shop, and specify the extent to which they will be available to the project. Use continuation pages if necessary.

Laboratory:




Clinical:





Biocontainment Resources Available: Complete if research involving Select Agent(s) will occur at any performance site(s), otherwise indicate N/A.




Animal:




Computer:


SCRIPPS: The Scripps Research Institute (TSRI) provides multi-campus institute-wide computing
infrastructure resources through a Senior Vice President who has oversight of institutional assets and system
resources of the Information Technology Services (ITS) organization at each of its two campuses: la Jolla
California and Jupiter, Florida. ITS will provide the core resources necessary for TSRI to participate fully as
an "early implementer" of the VIVO system. Internet access, data security, system operation, data
interchange, client and server applications and other computation resources necessary to implement and
operate the system will be provided by ITS.


Office:


SCRIPPS: Sufficient office space exists to fully support the activities contemplated under this grant
agreement.


Other:


SCRIPPS: The resources of the Kresge Library, in particular the expertise of its Director and staff, will be a
valuable asset as TSRI plays its part in the implementation, operation, and refinement of VIVO.


MAJOR EQUIPMENT: List the most important equipment items already available for this project, noting the location and pertinent capabilities of each.


Resources Format Page


PHS 398 (Rev. 11/07)


Page 92







Principal Investigator/Program Director (Last, First, Middle):


RESOURCES
FACILITIES: Specify the facilities to be used for the conduct of the proposed research. Indicate the performance sites and describe capacities,
pertinent capabilities, relative proximity, and extent of availability to the project. If research involving Select Agent(s) will occur at any performance
site(s), the biocontainment resources available at each site should be described. Under "Other," identify support services such as machine shop,
electronics shop, and specify the extent to which they will be available to the project. Use continuation pages if necessary.

Laboratory:
WUSTL: One Nagarajan lab occupies approximately 1,700 square feet of modern research biomedical
informatics space in the Cortex Building (4320 Forest Park Avenue, Suite 211). The second Nagarajan lab
located in Building 4444 (4444 Forest Park Avenue, Suite 6300) occupies 1,000 square feet. This includes
ten carrels, each capable of being occupied by up to four programmer analysts, a dedicated server room,
and two dedicated conference rooms where face to face, voice, web, and video conferences take place.

Clinical:


Biocontainment Resources Available: Complete if research involving Select Agent(s) will occur at any performance site(s), otherwise indicate N/A.


Animal:


Computer:
WUSTL: The Nagarajan Labs house forty-two high-end Windows XP workstations, which have dual multi-
core processors, 2-4 GB RAM, at least 146GB hard drive, and a DVD-RW drive. Programming IDEs
installed on these machines include Borland Builder 6.0 Enterprise Edition, Microsoft Visual Studio.NET
Architect, Kylix 3.0 Enterprise Edition, Borland JBuilder Enterprise Edition, Eclipse 3.4, and ActivePerl 5.8.
All machines also have Oracle 10g Client installed. Xerox Phaser 8400 DP and 8550 DP color printers are
networked and present in the lab for printing purposes. Multiple servers (-60) are available to store, serve,
and back up clinical, genomic, and annotation data. The major ones are as follows:
Purpose Processor RAM Disk Space
Clinical Data (CLINDB) 2 x 3.6 GHx Xeon 4 Gb 3.2 TB
Database Backup Management 2 x 3.6 GHx Xeon 6 Gb 146 GB
Workstation Backup 2 x 3.0 GHx Xeon 6 GB 3.8 TB
Database and Server Backup 2 x 3.0 GHx Xeon 6 Gb 9.7 TB
Genome Annotation Database Server 2 x 3.0 GHx Xeon 8 Gb 5.1 TB
Web Application Server 2 x 3.0 GHx Xeon 4 Gb 146 Gb

Office:
WUSTL: Sufficient office space exists to fully support the activities contemplated under this grant
agreement.

Other:
WUSTL: The Bernard Becker Medical Library serves as an information services hub for the Medical Center
and extends its services and resources to the global health science community. The biomedical resource
collection includes 32 databases, over 4,000 full-text e-journals, 1,500 e-books and numerous selected web
sites. The library also holds 4,500 print journals, 101,000 print books and 1,200 audiovisual items.

WUSTL: The library's Translational Research Support Division supports the broader goals of translational
biomedicine by providing information resources and expertise that support basic research, health information
outreach to consumers and the community, and the publication and dissemination of scientific information.


Resources Format Page


Conlon, Michael


P HS 398 (Rev. 11 /07)


Page 93







Principal Investigator/Program Director (Last, First, Middle):


WUSTL: The Division includes two bioinformaticists who provide instruction, consultation services, and
support for specialized software and databases. The Division also includes a Scholarly Communications
Specialist to increase awareness among faculty of the issues and options for disseminating and storing
scientific information as the digital age redefines standard publishing models.

WUSTL: The Health Information Resources Division provides a broad range of biomedical information
resources and training services covering clinical point of care, evidence-based medicine and information
management. Through this division the library focuses on integrating information management into the
curricula of the various educational programs and promoting the effective use of information resources in the
school's clinical mission. It also oversees the library's Liaison Program, which assigns a librarian to each of
the school's divisions, departments or programs to focus on their specific information needs. Circulation
services, interlibrary lending and document delivery also fall within the scope of services managed by the
Health Information Resources Division.


MAJOR EQUIPMENT: List the most important equipment items already available for this project, noting the location and pertinent capabilities of each.


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Principal Investigator/Program Director (Last, First, Middle):


RESOURCES
FACILITIES: Specify the facilities to be used for the conduct of the proposed research. Indicate the performance sites and describe capacities,
pertinent capabilities, relative proximity, and extent of availability to the project. If research involving Select Agent(s) will occur at any performance
site(s), the biocontainment resources available at each site should be described. Under "Other," identify support services such as machine shop,
electronics shop, and specify the extent to which they will be available to the project. Use continuation pages if necessary.

Laboratory:





Clinical:





Biocontainment Resources Available: Complete if research involving Select Agent(s) will occur at any performance site(s), otherwise indicate N/A.





Animal:


Computer:
WCMC: Weill Cornell Medicine College Information Technology and Services, along with the Clinical and
Translational Science Center Bioinformatics Core provides enterprise wide computing infrastructure to
WCMC as well as a subset of these services to its core partner institutions. Both ITS and the CTSC core are
overseen by Dr. Curtis Cole, the CIO and Bioinformatics Core Director. ITS already supports VIVO and will
provide the additional core resources necessary for WCMC to participate fully as an "early implementer" of
the VIVOweb system. Internet access, data security, system operation, data interchange, client and server
applications and other computation resources necessary to implement and operate the system will be
provided by ITS. Distribution on the CTSC Portal will be done as a collaboration between the CTSC Core
and ITS.

Office:
WCMC: Sufficient office space exists to fully support the activities contemplated under this grant agreement.


Other:
WCMC: The resources of the Wood Library, in particular the expertise of its Digital Services Librarian, will be
a valuable asset as WCMC plays its part in the implementation, operation, and refinement of VIVOweb.


Resources Format Page


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Principal Investigator/Program Director (Last, First, Middle):


RESOURCES
FACILITIES: Specify the facilities to be used for the conduct of the proposed research. Indicate the performance sites and describe capacities,
pertinent capabilities, relative proximity, and extent of availability to the project. If research involving Select Agent(s) will occur at any performance
site(s), the biocontainment resources available at each site should be described. Under "Other," identify support services such as machine shop,
electronics shop, and specify the extent to which they will be available to the project. Use continuation pages if necessary.

Laboratory:




Clinical:




Biocontainment Resources Available: Complete if research involving Select Agent(s) will occur at any performance site(s), otherwise indicate N/A.




Animal:


Computer:
UF: The University of Florida (UF) provides shared information technology resources including high speed
networking, data center services, administrative systems and academic technology support through its office
of information technology led by Dr. Charles Frazier, interim CIO. UF serves at the Network Operations
Center for the state-wide Florida Lambda Rail, a consortium of 11 schools in Florida to provide high speed
research networking across the state. The Florida Center for Library Automation is headquartered at UF and
provides library cataloguing services to the state university system. VIVO will be hosted by Smathers Library
IT Services.


Office:

UF: The university has sufficient office space in the departments participating in this proposal to fully support
the staff of this proposal.


Other:


UF: The University of Florida Libraries, including the Smathers Library, the Marston Science Library and the
Health Science Center Library have established liaison programs with University of Florida programs and
their researchers. Their expertise and existing relationships are a valuable asset in the development of
support and continuity for VIVO.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael
CHECKLIST
TYPE OF APPLICATION (Check all that apply.)
M NEW application. (This application is being submitted to the PHS for the first time.)
D RESUBMISSION of application number:
(This application replaces a prior unfunded version of a new, renewal, or revision application.)


RENEWAL of grant number:
(This application is to extend a funded grant beyond its current project period.)


D REVISION to grant number:
(This application is for additional funds to supplement a currently funded grant.)
D CHANGE of program director/principal investigator.
Name of former program director/principal investigator:
D CHANGE of Grantee Institution. Name of former institution:
E FOREIGN application E Domestic Grant with foreign involvement List Country(ies)
Involved:
INVENTIONS AND PATENTS (Renewal appl. only) [ No O Yes
If "Yes," E Previously reported O Not previously reported
1. PROGRAM INCOME (See instructions.)
All applications must indicate whether program income is anticipated during the periods) for which grant support is request. If program income is
anticipated, use the format below to reflect the amount and sourcess.
Budget Period Anticipated Amount Source(s)
$0.00
$0.00
2. ASSURANCES/CERTIFICATIONS (See instructions.)
In signing the application Face Page, the authorized organizational representative agrees to comply with the policies, assurances and/or certifications
listed in the application instructions when applicable. Descriptions of individual assurances/certifications are provided in Part III and listed in Part I, 4.1
under Item 14. If unable to certify compliance, where applicable, provide an explanation and place it after this page.
3. FACILITIES AND ADMINISTRATIVE COSTS (F&A)/ INDIRECT COSTS. See specific instructions.
M DHHS Agreement dated: 7/6/2006 No Facilities And Administrative Costs Requested.
D DHHS Agreement being negotiated with Regional Office.
D No DHHS Agreement, but rate established with Date
CALCULATION* (The entire grant application, including the Checklist, will be reproduced and provided to peer reviewers as confidential information.)
a. Initial budget period: Amount of base $ 1,534,194 x Rate applied 46.50 % = F&A costs $ 713,400
b. 02 year Amount of base $ 1,423,596 x Rate applied 46.50 % = F&A costs $ 661,972
c. 03 year Amount of base $ x Rate applied % = F&A costs $
d. 04 year Amount of base $ x Rate applied % = F&A costs $
e. 05 year Amount of base $ x Rate applied % = F&A costs $
TOTAL F&A Costs $ 1,375,372
*Check appropriate box(es):
D Salary and wages base X Modified total direct cost base l Other base (Explain)
D Off-site, other special rate, or more than one rate involved (Explain)
Explanation (Attach separate sheet, if necessary.):






4. DISCLOSURE PERMISSION STATEMENT: If this application does not result in an award, is the Government permitted to disclose the title of
your proposed project, and the name, address, telephone number and e-mail address of the official signing for the applicant organization, to
organizations that may be interested in contacting you for further information (e.g., possible collaborations, investment)? I Yes I No
PHS 398 (Rev. 11/07) Page 97 Checklist Form Page








Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


VIVO: Enabling National Networking of Scientists

A. A Semantic Approach to Research Networking
This application proposes a solution to facilitate research networking and collaboration of basic,
clinical, and translational researchers including investigators, students, technical staff and others. The
Semantic Web/Linked Data approach we envision confers the ability to implement locally controlled
researcher network installations that interoperate to create a flexible and scalable multi-institutional
network. Although we focus solely on the researcher network for this project, our platform has the
capacity to transparently include and interrelate resource listings and other relevant information. Our
technology choice allows us to easily consume, integrate and expose data hosted by partners who
have other research network or resource discovery platforms in place.

B. Rationale and Approach
B.1. Rationale
We propose an open, Semantic Web-
based network of local ontology- ----
driven databases called VIVO to
enable national networking via ..
information sharing about researchers
and their activities. VIVO will draw on
as well as contribute to, other web- VIVOis a ach-focusedds cery ool toot
accessible services and tools.
The Semantic Web' enables e.. .
automated and human navigation to
represent and mine digital data, and it r
supports interoperability and By
integration of data from a variety of
sources2. Recently, many of the larger
goals of the Semantic Web are
starting to be realized, particularly in
the new Linked Data3 effort. We have
5 years of experience with VIVO (see
Figure 1), a real-world Semantic Web Figure 1 Discover Cornell VIV Interface
application developed at Cornell
University in Ithaca (Cornell), and currently in use at Cornell and as GatorScholar4 at the University of
Florida (UF). VIVO facilitates research discovery and networking and demonstrates that Semantic
Web technology is ready to serve as the foundation for enabling national networking of scientists,
providing significant benefits for describing inter-linked data in flexible and openly accessible ways.
A significant portion of ongoing and proposed technical innovation related to biomedical research
revolves around the goal of facilitating the sharing of data and other sorts of information and
resources while enhancing collaboration among researchers across a variety of disciplines. For many
researchers the geographical and organizational confines of a department, college, or even a single
university bear very little relevance to the scope of their research or the pool of colleagues they may
seek for collaboration. Researchers are often left to find their own paths to discover current activities
and active researchers in their field and beyond, usually by a combination of personal connection,
disciplinary knowledge, and fortuitous discovery through search engines, leaving those who have yet
to develop their own network of personal contacts at a significant disadvantage.


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


A number of social networking tools attempt to facilitate interpersonal connection by providing a local,
national or even global platform to post and link profiles, pictures, ideas and comments. Most of these
platforms are closed worlds that often do not support direct interaction with other systems.
Technology and marketplace transitions dictate that services and data available today may no longer
be freely available tomorrow; no single tool or service is likely to successfully maintain a consistent
leadership position, resulting in collective information investment risks being lost in favor of the next
popular interface or feature set.
Biomedical and translational institutions and programs face similar challenges as do researchers, in
presenting a clear picture of their biomedical teaching and research capabilities internally and to the
outside world. These institutions seek to encourage cross-disciplinary collaborations but rarely provide
any venue to support discovery and nurture person-to-person connections. There is often disconnect
between functional areas, with most resources allocated to defining administrative, instructional and
research
computing needs,
rather than the
evolving nature of
research. "*
apd
The problem is
even more VIVOweb
severe when pubi c~
looking beyond "0. rm "Y
one institution to ,
understand" i .
patterns or trends ,un.roi
or identify I ,.. k, C re ,nI
specific o-.. Ih 'd -O f" pr-"
expertise. ,
:. VIVOweb
Scientific .., Ur i .- V VOwebN
information is .- f pW"U
rarely provided -""
with consistency .-- wp
except within ,
narrow
disciplinary I.u ch-.n. VIVOweb
confines. We
must be able to
communicate Figure 2 Local VIVOweb instances interlinked with each other and the
Semantic Web
diverse activities, Semantic Web
expertise, outcomes, and resources in ways that can be understood nationally and even globally, not
just in a local context. In this fluid landscape, the key element is how to combine authoritative
information from its most local context into a coherent, large-scale picture that will meet the needs of
research teams, institutions, and cross-institutional views. VIVO enables a web (VIVOweb) of
researcher data that will catalyze and accelerate the creation of connections between researchers to
meet these needs. VIVOweb will empower researchers to find information about people of
professional interest and extend their research communities not just via prior knowledge or
serendipity, but through recommendation or suggestion networks based on commonalities in the
profile data.
The most fruitful way of promoting researcher networking and discovery at the individual/personal,
institutional and national level is to provide authoritative data from and about researchers themselves
and about other related institutional resources in an open and consistent format. This is what we
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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


currently support with VIVO, and are proposing for VIVOweb. These data will be described using
explicit semantic relationships, and published on the Semantic Web according to accepted Linked
Data standards. We will also make these data available on the human web through locally-managed
institutional portals that allow researchers to directly browse and search this data within or across
institutions (see Figure 2). VIVOweb does not attempt to re-invent collaborative tools such as wikis
and blogs or impose that any one tool be globally accepted, acknowledging the plethora of
established and emerging popular platforms. Instead, it focuses on enabling users to discover each
other via networks based on common interests and other direct or indirect connections, incorporating
and sharing structured data with other tools as appropriate.
As of May 2009 the Linked Open Data initiative offers nearly five billion data element links
represented as "triples" of the form (object, relationship, object), for example (person, co-authored
with, person) or (person, published, paper). Many of these triples represent biomedically-relevant
genome, gene expression, protein and pathway data5. This number continues to grow, and
VIVOweb's semantic approach allows it to easily consume these data to enrich researcher profiles,
while also interoperating with these and other data sources and making content available for
immediate consumption. A number of publications also suggest that there has been great innovation
and interest in Semantic Web applications to facilitate research in a variety of areas within the
biomedical and life sciences communities, including genetic and drug efficacy analyses and clinical
and molecular dataset management, particularly from the perspective of strengthening translational
research-a key goal of the National Institute of Health Roadmap for Medical Research6'7'8'9'10. The
richness of the literature on the utility of Semantic Web technologies to further biomedical research
leaves little doubt that the application we propose here to enable research networking is not only
timely, but the most assured path to long-term utility and participation by individuals and institutions.
A recent PricewaterhouseCoopers Technology Forecast1 examines the forces and technologies
behind global data discovery and integration and forecasts "a transformation of the enterprise data
management function driven by explicit engagement with data semantics." While relational database
approaches to enterprise-level data management problems have been optimized and work effectively
within single organizations, locally-specific database system implementations do not lend themselves
to reuse at the level of Web-scale data federation. Table 1 below, from the report, contrasts traditional
data integration with the Linked Data approach.
Table 1 Benefits of the Linked Data Approach to Data integration


Data structure

Data integration method


Data integration
scalability

Contextual richness


Information source bias
Business unit
involvement
Standardization method


PHS 398/2590 (Rev. 11/07)


Traditional data integration
Predominately relational: focus
is on sets of similar data
Extract from original source,
transform to local data
definitions, load on own servers
Each new data source expands
costs exponentially

Constrained by costs and central
staff workloads

Internal
Report requestors

One standard, no exceptions,
loss of valuable information
context


Linked Data approach
More flexible: focus is on relationships
between things regardless of similarity
Link to source of data using data
definitions in shared ontology

New data sources are accessible at
minimal cost, and business domains
share the federation cost
Benefits from the network effect:
context gets added with new data and
linkages
Internal and external
Managers of their own ontology and
external data-linking activities
Explicitly allows both standard data
and contextual information


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Interoperable enhanced VIVO installations
managed locally, but offering cross- .- ; - .- a-
institutional searching, browsing, and other
capabilities will form VIVOweb, which will
grow as a natural extension of Cornell's
VIVO application from a single, multi-
campus research discovery tool to a
distributed network. Proof of concept for- 2 -
VIVO's value in a variety of settings and :.
languages is provided by active ,a, .
installations at UF (GatorScholar12), the .
University of Melbourne (Find an Expert13), .. .-
and the Chinese Academy of Sciences
(Southwest China Biodiversity portal14).
VIVO was initially developed to enable the
discovery of researchers and resources in
the life sciences across Cornell's
complicated administrative landscape of
disciplines, departments, centers, colleges -
and campuses. VIVO integrates public Figure 3 Drupal test portal driven by VIVO content
content about researchers from a variety of
authoritative databases at the university and also allows individuals to log in using their Cornell net ID
and password to modify their own profiles. VIVO also promotes resource discovery across Cornell-
including facilities, equipment and research-related services, such as databases and sample
collections, workshops and seminars. All data in VIVO are available for easy consumption by other
web pages or services.
To ensure adoption, usage, maintenance, and post-funding sustenance of VIVOweb at the individual,
institutional, and national levels we propose technical innovation and support coupled with a
community-focused approach that provides a high-value product to institutions through local
installation and control of each VIVO platform. The involvement of appropriately skilled information
management specialists from libraries, as well as researchers, administrators and IT personnel from
all partner institutions, including recipients of Clinical and Translational Science Awards, also
contribute to the success of VIVOweb. Finally, the governance structure we envision will contribute
further oversight and direction, and includes Scientific, Technical, and Executive Advisory Boards, the
last consisting of personnel and researchers from the NIH, as well as other major research
universities.
B.2. Approach
The VIVO research networking platform currently installed at Cornell and UF will be extended and
enhanced to address needs at the individual, institutional, and national levels-with modifications to
create a more complete institutional research discovery tool with a variety of new capabilities,
including the creation of active personal and team networks through the application of social
networking tools, and the production of semantically-rich data to integrate, analyze, visualize and
distribute at the national level.
B.2.a. VIVO Platform at Cornell and Florida
VIVO was developed by the Cornell University Library beginning in 2003 to meet individual and
institutional research discovery needs and already addresses many areas of importance to
researchers. VIVO supports ontology as well as content editing, and is also a simple content
management system that enables the representation of the resulting structured information in web
pages. It uses the standard Resource Description Framework (RDF) Semantic Web data model and


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Web Ontology Language (OWL) schemas that identify distinct types of data and defines properties to
connect these data with consistent, bi-directional relationships. For example, the profile of a person
includes simple text attributes including name, title and statements of research or teaching interests,
but extends much farther to include affiliation, activity and outcome relationships to departments,
research grants, publications, talks, courses, research areas and geographic areas. Each of these
entities is a defined type in its own right that may in turn have its own relationships to other people or
to a funding agency, event sponsor, research center or topic.
The VIVO installations at Cornell and UF aim not only to automate the harvesting of information from
a variety of authoritative sources into a common institutional resource, but also to make data or
profiles available for consumption or display by web sites and services across the university. While
the accumulation of content, both entities and the relationships between them, initially depended
largely on manual entry of information by librarian and staff editors, currency and accuracy concerns
have prompted integration into information technology framework via automated data ingest
procedures that are already utilized at Cornell, and soon to be implemented at UF. Data currently
ingested at Cornell include: active personnel, titles, affiliations, and courses from PeopleSoft
databases, grants from a custom Oracle database, publications from PubMed and public information
reported by faculty via a reporting system called Activity Insight newly adopted by the majority of
Cornell's colleges. The Cornell and UF installations also feature an editing component that ties in with
local authentication systems to enable personnel very easily to manage and update their own pre-
populated VIVO profiles. This "self-editing" service has been utilized successfully by researchers at
Cornell for over a year. Two additional portals illustrate VIVO's ability to deliver filtered semantic data
for the realm of data sharing: a test portal developed in the Drupal content management system15
(see Figure 3) and one showcasing Graduate Programs in the Life Sciences for prospective graduate
students, and powered by life sciences content queried dynamically from VIVO16 (see Figure 4).
B.2.b. Proposed Multi-Institutional Researcher Network
This project will extend VIVO from a single institutional installation to a multi-institutional, distributed
model that is VIVOweb. No central portal will be created; local installations will facilitate access to
both local and national-level information in
all installations. VIVOweb will offer the C,
functionality already provided by VIVO, as --- -.
well as new features and services tailored
to the local context, including but not limited
to analysis and visualization tools to
promote new paths to discovery, improved
data ingest, streamlined ontology editing,
an increased number of authentication
options, and a decentralized indexing
capability to enable cross-institutional
browsing and searching. VIVOweb will also
include the ability to provide data as email
lists or in a variety of formats for social
networking tools, for the automatic
generation of NIH and other biosketches,
and for faculty reporting purposes.
VIVOweb's flexible and extensible data
model will allow it to present a simple ---.. ..
structure of people and their activities within Figure 4 Graduate Programs in the Life Sciences
and across institutions, featuring links Powered by dynamic queries from VIVO
among them and connections to other
people as well as their professional
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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


information.
There are many ways a person's expertise may be discovered, through grants, presentations, courses
and news releases, as well as through research statements or publications listed on their profile-
resulting in the creation of implicit groups or networks of people based on a number of pre-identified,
shared characteristics. We will extend the VIVO ontology to support personal work groups and
associated properties to represent the informal relationships evolving around collaboration, and allow
individuals and groups the option to limit the visibility of these more informal and dynamic
relationships, or "active groups". New types and properties can be added without writing additional
code or altering the database structure of the application, and selected portions of a personal network
can be managed as an independent graph for export to social networking tools. New plug-ins already
in development within Dr. Katy Borner's group at Indiana University will also allow easy and effective
visualization of the various relationships possible at the institutional or national level.
Cornell's VIVO currently spans the Ithaca campus and the Weill Cornell Medical College within a
single software installation. Rather than combining multiple institutions into a single, large, central
database, we propose to install separate versions capable of supporting direct cross-institutional
references using Linked Data standards. Each entry in VIVOweb will have a stable URI from which its
constituent and immediately related data can be requested. RDF can be requested for data
harvesters and HTML can be requested for web browsers. This allows seamless linking between one
installation and another across VIVOweb. If researchers move from one institution to the next, their
persistent URLs can be 'forwarded'. Linking one VIVO to another where a connection is known to
exist addresses one component of the need for a national network. VIVO's distributed indexing
capability will enable individuals to search across institutions and find collaborators where they have
no known connections, and to discover the existence and patterns of collaboration across multiple
institutions and ultimately at the national level.
Development effort will support indexing distributed content at all participating institutions from the
beginning. Cornell and UF will host indexing services. Additional participating institutions can choose
to replicate the index to optimize local performance for cross-institutional searching. Indexing sites will
harvest data from each independent VIVOweb site based on the common core ontology that identifies
a level of granularity for harvesting people, expertise, topics, research activities, and other data across
all the sites. The development and refinement of this ontology will be the subject of investigation by
Dr. Ying Ding at Indiana University, in close collaboration with the core development and facilitation
teams. Searches initiated from any local VIVO node will then have the option of extending to the multi-
site index. The first step towards this is the local installation of the VIVO platform at partner
institutions. Our technology is capable of integrating seamlessly with other researcher networking
platforms via workflows that first convert data from these systems into semantic form using templates
to be provided with the VIVO installation package or commercially licensed tools (see Section C.2 for
details).
VIVOweb's Semantic Web principles and open, flexible structure represent a research networking
solution that will appropriately and efficiently allow integration of the application with varied
institutional infrastructures. They will allow VIVOweb to scale in size and scope while adapting to new
purposes and unforeseen content, providing an evolving, dynamic, virtual community for the
biomedical sciences-and beyond at every institution. Data from local systems-whether based on
the VIVO platform or not-will be linked and shared across institutional platforms, but visible locally
through institutional portals such as VIVO and GatorScholar to facilitate the networking and discovery
of people. The visibility and unique functionality of these portals will stimulate the further evolution of
this virtual community across institutional boundaries. Specific functionalities and services proposed
for VIVOweb may be summarized as follow:


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Ability to search and browse locally and nationally to "find people like me", most
searched, or topic-related expertise: By keyword or MeSH term, location, department or
institution, grants, geographic area, publication, authorship, types of papers or journals
commonly published in, and more.
Profile modification using institutional authentication system: Add to or change
information ingested from institutional authoritative sources; display or hide sections from
national view.
Ability to ingest data from authoritative sources: Including human resources, grants, and
course databases, faculty reporting systems, personal citation management tools and web
pages.
Easy modification of core ontology: Using improved ontology editor capabilities to more
accurately reflect local needs that might deviate from the Semantic Web for Research
Communities ontology bundled with each local VIVO installation.
Delivery of data to consuming services and mobile devices: Including specialized topical
or unit portals, web social networking or collaborative tool APIs, reporting tools and
biosketches.
Networking: Create and share public and private groups, adding or removing investigators to
and from designated groups or contact lists, suggest useful additions to others, navigate
across successive connection paths.
Communication: Dynamically create and manage email lists through external list
management tools, such as. Lyris Listmanager17, query based on affiliation or topical affiliation
to create email lists for a variety of purposes.
Analytical capabilities and spatial mapping: Using multi-dimensional network analysis tools
and visualization techniques to analyze small team, departmental, institutional, or national
groupings by publications, grants, funding agencies, and expertise as determined by keywords
and concepts conveyed in publications, grants, self-designation and more.
B.2.c. Sustainability through Building Community
The primary goal of our approach to enable national networking of researchers is to offer a wide-
ranging perspective on multiple aspects of biomedical and translational research across multiple
institutions not just to researchers, but also to students, administrative and service officials,
prospective faculty and students, donors, funding agencies, and the public and to empower them to
contribute each in their own way.
We are advocating for the creation of asset-based, rather than need-based virtual communities, at the
individual, institutional, and national level with the focus on making previously "invisible" human assets
visible at all levels. According to research conducted at Northwestern University, while a need-based
community focuses on "needs, deficiencies and problems", an asset-based community begins with a
commitment to uncovering the community's capabilities and assets18. This and other work has
demonstrated that investment in asset-based models is the most effective way of solving problems, as
long as a need can be rapidly and accurately linked to an asset19'20
It is critical to recognize that any technology or tool designed to create a network of human assets
within and between academic institutions will be adopted, used and maintained only if the individuals
- the assets in this case and the institutions perceive value in it.
Value to the individual is most likely to be assessed by responses to questions such as:
What does this tool do to advance my research and academic standing?


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Can I use it to reliably find potential collaborators and other people of interest to me within my
institution and beyond?
Can I use it to create inter-institutional groups or networks based on common areas of
research or interest?
Is it current, accurate, immediate?
Will it expedite the reporting and communication of my work?
How much effort will it take to maintain my information-how easy is it to use and update?
Value to the institution is likely to be assessed primarily by administrators, based on responses to
questions such as:
What does this tool do to advance the standing of my institution?
Does it enhance recruitment and retention of top-notch faculty and students?
Does it foster collaboration, particularly across traditional boundaries?
Does it help improve the fraction of successfully funded grant proposals?
Can it increase efficiencies associated with the management and dissemination of information
about people and resources?
What does it cost to sustain and improve?
How easily does the technology or platform interoperate with others and how agile is it?

Finally, value to NIH and other federal agencies, professional biomedical societies and organizations
can be evaluated by such factors as easier identification of experts and potential reviewers, more
effective use of grant dollars through improved collaboration, and possible synergies with services
already offered by NIH-such as eraCommons, PubMed and others.
The technical sections of this proposal will make it clear that the capabilities suggested by these
questions are indeed functionalities that the VIVO platform will enable for individuals and the
institution. However, our work with the platform at Cornell and UF also demonstrates that delivering
technical capability alone is not sufficient to ensure adoption, usage and maintenance by either the
individual or the institution. Technical innovation for a networking tool such as this must be
backstopped by human facilitation-in this instance, by information specialists from institutional
libraries, or by other informatics professionals, wherever possible. We anticipate that researcher
engagement and outreach by information specialists will promote adoption, usage, and maintenance
of VIVOweb by the research communities in their institutions, thereby fostering the creation of virtual
communities of biomedical researchers at all three levels above, accessible through local VIVO
installations.
That the asset-based community approach employed for the initial development of VIVO at Cornell
and UF, and the library-based outreach efforts associated with it are valued and successful, is
evidenced by this small sample of feedback from researchers and administrators at both institutions:
"VIVO provides unparalleled access to information about the life sciences at Cornell
in a user-friendly way. This will be of particular benefit not only to those researchers
and students already at Cornell, but potential faculty and students as well, by
offering a much-needed, integrated view of the life sciences community at Cornell."
"VIVO saved my life as a new faculty member at Cornell; I used it all the time to find
facilities and people I might work with."
"First, allows individuals...to quickly find faculty with specific
research interest. Undoubtedly, this raises the visibility of the life sciences faculty
among potential granting agencies, students, and policymakers. Second, it
facilitates interactions between life science faculty with divergent backgrounds. This


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facilitation increases the likelihood of grant funding by drawing on synergisms
within the college."
" up-to-date awareness is vital for researchers
to make timely contacts, find potential collaborative partners, access literature
searches, and locate other resources necessary for their work. It will be particularly
useful because of the growing interdisciplinary among the sciences."
B.2.d. Support through the Libraries
Our proposal posits that the engagement of a neutral and trusted campus entity with information
management expertise will greatly facilitate adoption, usage, and maintenance of such a tool.
Evidence from Cornell and UF suggests that the academic library-in its capacity as a generally
impartial and trustworthy organization with a clear understanding of the needs of the research
community and the proven capability of engaging with it, expertise in information management and
dissemination, and an established liaison function-admirably performs this role. Further, medical and
science and engineering libraries have traditionally provided information resources and technology in
support of educational, research, and patient care objectives, and are taking on an increasing role in
fostering and supporting collaborative efforts on campus to shorten the gap between bench and
bedside. Recent advancements in translational medicine have prompted libraries to develop
information solutions which support dissemination and facilitate a fluid exchange of data in the
increasingly cross-disciplinary research setting. Over the last few years, a number of medical libraries
have responded to changing information needs by expanding their services to offer visionary
programs which enhance the flow of information and promote collaborative opportunities in the
translational research environment. The stalwart engagement and stewardship provided by the NIH's
National Library of Medicine (NLM) in support of biomedical research has provided a valuable model,
and many programs and services offered by these libraries are frequently developed and coordinated
by PhD-level specialists trained and certified by the NIH.
That libraries have successfully met these needs provides a foundation for a library-based community
support network for VIVO. While support of both user and development communities will be
challenging, a library-based model best addresses many of the issues which may arise during this
process. Librarians, including several with PhDs and/or bioinformatics expertise and NIH training with
expertise as NCBI course developers and instructors have been included to facilitate intra-and inter-
institutional adoptions, usage, and maintenance of VIVOweb. Through technology advancements
mentioned in this proposal, as well as evaluation and further development by the seven adoption
partners, VIVOweb will grow a community based support network. As adopters become developers,
the support network will work to develop the critical components for building a community-based
support network. Based on the Cornell and UF experience, librarians and domain specialists will be
particularly valuable in:
Establishing virtual environments which facilitate communication and collaborations-such as
wikis-for both the outreach and development teams which will serve all members of the
VIVOweb consortium. This includes, but is not limited to a listserv, development and outreach
wikis, news items and publications.
Providing in-person and e-mail "help desk" support in the use of VIVOweb.
Developing support documentation, including an FAQ, quick-start guide and manuals on the
VIVO application, suggested and proven outreach and support strategies, and guidelines for
development of new modules.
Creating and supporting a comprehensive suite of educational materials for VIVO users and
implementation and support teams, including both text-based and video tutorials which range
in complexity from basic needs to more complicated or innovative uses of the application.


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Facilitating inter-institutional collaboration on the development of a common ontology.
Engaging with researchers and administrators in the local setting to educate and engender
buy-in and ensure institutional support
Serving as link between researchers and central technology teams by regularly providing
feedback on usability problems encountered, what works well and what is missing but
essential for a successful product.

Training materials and support documentation will be modeled after widely used materials provided by
the NLM for applications, databases and services such as PubMed, NCBI, MyNCBI and others21.
We anticipate that personnel outside the Library will increasingly assist with this task as VIVOweb
becomes accepted and increasingly integrated into the administrative and communications
mainstream. However, it represents a considerable technological and cultural shift from current
practice for most institutions, just as any new campus-wide initiative faces many challenges in
achieving clarity in mission and consistency in execution. For an ambitious e-community building
endeavor such as this to truly succeed-that is, to be adopted, used, and maintained- technical
innovation as well as careful and engaged stewardship by institutional libraries will be essential.
B.2.e. Engagement of Recipients of Clinical and Translational Science Awards (CTSAs)
Any project to support biomedical researchers will clearly need support from recipients of CTSAs,
which represent a primary community of practice. The CTSA institutions22 have considerable interest
in national networking and have formed a workgroup to facilitate consortium-wide collaboration. One
of the functions of the consortium is to support researcher networking across institutions. VIVO is
designed specifically to address this need. Members of the CTSA consortium will be asked to serve
on VIVO governance bodies Executive, Scientific and Technical and actively participate in
facilitated discussions of the needs of this important group of research institutions.
B.2.f. Support for all Institutions
It is important to note that many other National Center for Research Resources (NCRR) and NIH-
funded centers and programs also include researchers making very significant contributions to
advance biomedical research. Our consortium of institutions therefore includes CTSA recipients as
well as other NCRR awardees to ensure the broadest possible interpretation of biomedical
researchers. This approach will ensure that our ontology is scalable across a wide variety of
disciplinary types and therefore more easily scalable and extensible beyond the funding cycle of this
grant.
As schools choose to adopt VIVO, the community-based mechanisms for support scale to national
levels and are sustainable in supporting networking of researchers.
It is important to note that many other National Center for Research Resources (NCRR) and NIH-
funded centers and programs also include researchers making very significant contributions to
advance biomedical research. Our consortium of institutions therefore includes CTSA recipients as
well as other NCRR awardees to ensure the broadest possible interpretation of biomedical
researchers. This approach will ensure that our ontology is scalable across a wide variety of
disciplinary types and therefore more easily scalable and extensible beyond the funding cycle of this
grant.
The creation and distribution of support materials, both educational and promotional, will be an
essential means of facilitating institutional awareness and adoption of VIVO. Materials will be
designed and created for the institutional and national audiences at the University of Florida, under
the direction of Dr. George Hack.


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Among the materials to be developed is a comprehensive suite of educational resources for VIVO
users and implementation and support teams. These resources will include a variety of tools help
facilitate integration of VIVO at the institutional and national level. Educational support is an important
component in the library-based support model. For successful implementation of VIVO to occur,
researchers at implementation sites need to feel comfortable navigating VIVO, allowing the resource
to promote serendipitous discovery of collaborative opportunities. Informative web-based support
materials will be available from the VIVO project website such as a FAQ, a "quick-start" guide, links to
documentation and published papers about the application. A robust collection of online tutorials will
be developed, offering just-in-time support to researchers who wish to utilize the power of VIVO. This
immediate response will be further supported by providing access to podcasts and videocasts of
VIVO-related events. Strong educational support of VIVO is best served by combining this rich online
VIVO presence with a strong in-person support component at implementation sites. To accomplish
this, a robust series of instructional materials, including PowerPoint slides and handouts, will be
developed for use to deliver in-person instruction and presentations. These instructional materials will
be developed in a series of stand-alone modules, such as: a basic VIVO overview and training;
institutional discovery: using VIVO for new investigators, students, and staff; managing VIVO profiles
by proxy: support for administrative support staff; VIVO for the institutional administrator, and
advanced VIVO applications. The modules will be easily interchangeable and present an ala carte
approach to standardized instructional design.
A comprehensive suite of marketing materials to be used on a national basis will also be created by
the University of Florida. Such materials will be created in a variety of formats including web, print,
graphics, audio, video, and animation technologies to support curriculum offerings and promote VIVO.
The marketing/communications coordinator at UF will work closely with institutional outreach teams
during adoption, use best practices to identify change agents, promote and market the characteristics
of VIVO as a new innovation, and establish the key elements of a change process that will facilitate
adoption.
Both educational and promotional materials will offer a standardized look and feel, but still offer
institutions opportunities for customization with their own logos. The VIVO logo and color scheme will
be featured prominently to build the VIVO presence in materials related to the application to ensure
that VIVO is a brand that becomes recognized nationwide from locally-hosted resource workshops
to national-level scientific meetings. Support materials will include images and logos, PowerPoint
templates, and code for incorporation on implantation site websites all for use by the VIVO
consortium members
While these support materials will be designed and created at the University of Florida, all modules
could be easily customized with institutional logos and further customized with real-world examples
from any specific institution, with the assistance of a librarian. This approach will be convenient and
can be scaled up or back, depending upon the institutional needs. As schools choose to adopt VIVO,
the community-based mechanisms for support scale up to a national and sustainable activity in
support of networking researchers.
B.2.g. Support through Professional Societies
Professional societies of researchers will be engaged to adopt VIVO. Professional societies have a
natural role to play in facilitating the networking of their members. By adopting VIVO, they make
themselves visible in the national network. By participating in community-based support, they provide
increased visibility for their services as well as additional support for their members. By ensuring that
the Semantic Web recognizes and facilitates the identification of members, the societies leverage
VIVO in support of their goals, helping to build the national network. Professional societies can
promote VIVO through their own communication channels, reaching large numbers of researchers.
Researchers who are members of professional societies can highlight this membership in a rich
manner through their own VIVO profile as well.
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Implementation of VIVO for a professional society is a straightforward process. The VIVO software is
designed to be easy to host. Creating profiles for professional society staff members is simple and
allows these people to be found through the Semantic Web and support research activities.
Our approach builds on five years of experience with VIVO -- a semantic web platform for
representing researcher information, a national library-based support program for researchers
with specific expertise in biomedical research, significant strength in social networking and
ontology development, and an open approach for creating community and technical
development and support.

C. Project Plan
C.1. Governance
The development and support of VIVOweb will be governed by three national advisories an
Executive Advisory Board, a Scientific Advisory Board and a Technical Advisory Board. These
groups ensure that VIVOweb meets the needs of researchers, institutions and the NIH.
C.l.a. Executive Advisory Board
The Executive Advisory Board (EAB) sets the direction for VIVOweb development and support
activities and ensures full coordination with the implementation of resource discovery resulting in a
seamless Semantic Web of both scientists and resources. Constituted from a cross-section of the
research community, with NCRR representation, and with representation by the implementers of the
network for resource discovery, the EAB advises the Principal Investigator and the project teams on
all matters related to the creation of national networking of researchers. See Table 2. Quarterly
evaluation reports are provided to EAB members. Additional members will be added in consultation
with NCRR to ensure appropriate representation.
The group will meet twice per year. Members will receive travel support. One meeting per year will
be held at NIH in Bethesda. One meeting per year will be held in conjunction with a national meeting
such as the CTSA Consortium meeting.
Table 2 VIVOweb Executive Advisory Board
Member Affiliation
TBA PI Resource Discovery
Julianne Imperato-McGinley, MD Weill Cornell Medical College, PI CTSA
TBA CTSA Consortium Representative
TBA NCRR Representative
Gloria Thomas, PhD Xavier University
Peter Stacpoole, MD, PhD University of Florida, PI CTSA
Michael Conlon, PhD University of Florida, Ex officio, PI Research Networking
TBA TBA
TBA TBA

C.1.b. Scientific Advisory Board
The Scientific Advisory Board will consist of a spectrum of biomedical researchers who will provide
direct input regarding the support activities and the needs for features and ontology components to
support their work. Members will be recruited nationally by the EAB members, by members of the
project team and with the recommendation of NCRR. Support systems will include a web site and wiki
to facilitate the gathering of input from the Scientific Advisory Board. Bi-monthly conference calls and
gatherings at national meetings will be used to solicit further input.


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C.1.c. Technical Advisory Board
The Technical Advisory Board (TAB) will guide all aspects of the technical development of VIVOweb,
including ensuring that: 1) content from local installations can be picked up by any national network;
2) the VIVOweb installations can use community-sourced data such as Linked Open Data; 3)
VIVOweb is fully interoperable with the resource discovery network; and 4) interfaces to and from
VIVOweb to other tools meet the needs of the research community. See Table 3. Additional
members will be added in consultation with NCRR to ensure representation of all technical matters
regarding VIVO and the VIVOweb.
Table 3 VIVOweb Technical Advisory Board


Member
John Wilbanks
York Sure

Neil Smalheiser
Barand Mons
Kei Cheung
Chris Bizer
Steffen Staab
Abel L. Packer
Stefan Decker
Carole Goble
Dean Krafft


Affiliation
Creative Commons
University of Koblenz, Germany. Scientific Director of the Liebniz
Institute for Social Science
University of Illinois, Chicago
University of Rotterdam, The Netherlands
Yale University
Free University of Berlin, Linked Open Data
University of Koblenz, Germany
BIREME/OPS/OMS, Director, Brazil
Director of DERI Galway, Ireland
University of Manchester, UK, co-director of e-Science NorthWest
Cornell University


C.1.d. Project Organization
Figure 5 shows the project organization.
The EAB oversees the project. Evaluation
cyann), Project Operations (orange) and
Project Governance bodies (blue) report to
the EAB. Project Operations is organized
into three activities Development,
coordinated by Jonathan Corson-Rikert,
National Activities, coordinated be Medha
Devare and Site Implementations,
coordinated by Valrie Davis.
C.1.e. Development Teams
The project will support three development
clusters, at Cornell, UF and Indiana
University.

The Cornell group will focus on extensions
to the current core VIVO functionality and
access controls to better support individual
and team networking, improve scalability,
and support workflow for data ingest and
export. This group will also develop the
distributed search indexing capability and
Linked Data functionality. Any architectural
changes necessary to support a more
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Figure 5 VIVOweb project organization


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modular architecture for ingest, export, or to allow plug-in extensions for visualization or other
purposes will be coordinated with UF and Indiana University teams.
The Indiana University developers will work in two teams under the leadership of Katy Borner and
Ying Ding. Borner's Cyberinfrastructure for Network Science Center will implement advanced data
mining and visualization in support of social networking, metrics, and presentation. Ding will lead
efforts pertaining to the development and maintenance of ontologies used by the Semantic Web to
represent scientists and investigators.
UF developers, under the direction of Christopher Barnes, will focus on interfaces to software in the
institutional setting, and packaging of VIVO for deployment. Interfaces will be built for 1) PeopleSoft23,
to provide authoritative data to VIVO regarding people in the institution; 2) Drupal24, to enable the use
of VIVOweb from within research team Drupal implementations; 3) Shibboleth, to provide federated
identity management, and 4) Sakai25, to provide access to research networking from within the
popular open source course and content management platform. We anticipate the need for additional
interfaces as determined by the VIVOweb governance processes.
C.1.f. Media Support Team
Dr. Devare will direct the efforts of the team at UF lead by Dr. George Hack in the development of
instructional support and other media materials for VIVOweb. Instructional videos, promotional
material, web sites, conference materials, collateral for exhibits and other material will be developed
by Dr. Hack's team.
C.1.g. Adoption Support
Dr. Devare will coordinate effort related to the national adoption of VIVOweb. This includes
development of promotional materials and web sites, presentations at professional societies and
conferences. In this effort she will be supported by all members of the project team.
C.1.h. Implementation Teams
Each of the seven participating institutions has an implementation team that will deploy VIVO during
the first year of the project and then implement VIVOweb during the second year. Table 4 lists
implementation leads for each of the schools. Each implementation team participates in the
evaluation led by Dr. Leslie Mclntosh of Washington University.
Table 4 Implementation Team Leads at each of the participating institutions
Participating Institution Implementation Lead
Cornell University Medha Devare
University of Florida Sara Gonzalez
Indiana University Robert McDonald
Scripps Research Institute Gerald Joyce
Ponce Medical School Richard Noel
Washington University Rakesh Nagarajan
Weill Cornell Medical College Curtis Cole

Valrie Davis at UF will coordinate the implementations and provide support to the implementation
teams. Implementation teams provide input to the evaluation team. The evaluation team prepares
quarterly summaries regarding the implementation for the advisory boards.
C.1.i. Researcher Support Teams
The libraries of each institution will provide support for researchers using VIVOweb. Librarian
contributions to creating support for the adoption, usage and maintenance of VIVOweb may be
summarized as follows:


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Organizational/Workflow and Training Responsibilities. The information specialists in the
institutional libraries will facilitate growth and maintenance of local VIVO instances by:
Hiring, training, coordinating and supervising staff who will initially enter data for individual
profiles and related pages in VIVO,
Ensuring that relevant content and content types related to biomedical research are entered in
VIVO and the relationships between individuals and pieces of information-the entities-are
accurately and consistently represented,
Integrating project support resources into the institutional culture, including in-person training
events and just-in-time online instructional and support resources, and
Organizing and implementing usability testing for both self-editing of individual profiles and
those of related academic units.
Outreach Responsibilities. As academic appointees, the information specialists provide outreach to
departments, programs, centers and individual researchers, with whom they have enduring
professional relationships and to whom they provide assistance to facilitate research. Through their
liaison roles, these information specialists:
Bring to the project an understanding of both news-worthy and day-to-day activities and issues
of importance that inform data element and design decisions. Examples of these might include
research areas, collaborative initiatives and committees that are used to pre-populate pick lists
that researchers can use while editing their profiles,
Collaborate with groups across departments and administrative units to add content streams
and improve efficiency,
Demonstrate VIVO and its self- and proxy-editing capability at departments, institutes, centers
and researcher's offices to inform individuals, provide feedback from users and increase
support for the VIVOweb initiative. Their experience as instructors of digital information
resources endows them with a unique awareness of user behavior in a digital climate.
Have developed strong and trusted professional relationships with their research clients, and
will be able to use these connections to facilitate all tasks performed in relation to this project.
Navigating VIVOweb's Technological Underpinnings. VIVO is an ontology-based tool to integrate
diverse information through simple, consistent categorization by types and relationships. Librarians
are trained to understand, develop and encode ontological relationships and apply them pragmatically
to keep VIVO straightforward and simple to use.
Membership in the Institutional Research Community. Research is the primary subject of a
librarian's work. Information specialists are well positioned, trusted arbiters within an institution's
research community, capable of efficiently clustering information for VIVOweb that reflects important
nuances at a level appropriate for a general higher-education audience.
C.1.j. Evaluation Team
Dr. Leslie Mclntosh of Washington University will lead the evaluation efforts related to the project. Dr.
Mclntosh will be assisted by a biomedical informatics specialist to conduct assessment tasks, acquire
data, and analyze these data sets in collaboration with Dr. Mclntosh. Quarterly reports will be
prepared and made available to the advisory boards.
C.2. Technical Design
VIVOweb is based solidly on Semantic Web technologies recommended by the World Wide Web
Consortium (W3C). The core is the RDF26 where items being described are assigned globally unique
identifiers (URIs, or Uniform Resource Identifiers) and their relationships and attributes are described
in discrete pieces called "triples" or "statements." A collection of triples forms a graph of data that may
be stored in a single file or distributed across the entire web. Another W3C standard, SPARQL
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(Sparql Protocol and RDF Query Language27) makes it possible to query Semantic Web data using
SQL-like syntax. RDF relationships may also be embedded into standard web pages using RDFa
(Resource Description Framework in Attributes), which allows browsers or search engines to extract
structured data. Google recently announced that it would begin harvesting RDFa data28, following on
the heels of other search engines such as Yahoo29.
Semantic Web standards, such as RDF Schema (RDFS30) and the Web Ontology Language (OWL31),
make it possible to exchange ontologies, which specify the semantics of the terminology and
relationships used in RDF descriptions. Ontologies also enable reasoning, or inference of new triples
based on existing data. VIVO takes advantage of RDF's triple-based structure and OWL's constructs
for defining types of resources and their relationships to build a flexible, extensible knowledge base
describing academic researchers and their activities.
VIVO takes an additional step beyond the use of Semantic Web technologies at the local application
level by embracing the principles of Linked Data, which is a concept articulated by World Wide Web
inventor Tim Berners-Lee in a 2006 design note32. Linked Data promotes a web of data on the scale
of today's human-readable web, where interconnections between datasets are created as easily as
HTML hyperlinks. With Linked Data, RDF resources are assigned URIs that are dereferenceable, that
is, a request for the URI will direct humans or machines to useful data describing the resource. These
data should include additional URIs to allow the web of data to be browsed or crawled seamlessly.
The Linked Data community estimates that 142 million links between Semantic Web datasets have
been created.33 Links between institutional VIVO datasets will allow seamless browsing across
institutions. VIVOweb does not require coordination between installations when describing new
people, organizations, topics, or other entities. Different URIs representing the same resource can be
cross-referenced through OWL sameAs properties. In the cases where this approach is not possible
due to differences in ontology semantics between datasets, we will follow best practices emerging
from ongoing research in the field (Glaser et al., 2009).
C.2.a. The VIVO Platform
VIVO is unique in offering three major functional components in one package: ontology editing to
create or modify a data model, intuitive user editing for data and relationships and a simple content
management system to present an attractive web presence. This integration was designed and
developed from the ground up to support a researcher networking application in the institutional
environment. Unlike relational database-driven systems, VIVO requires no fixed data model with
tables and fields internally defining the data elements supported in the system. VIVO instead provides
an administrative editing interface to define types of data and relationships among these data types; a
common core ontology data structure (see Figure 6) will be supplied with the VIVO installation
package, but institutions will be free to extend the model further as required for local needs without
additional coding.
Institutions may choose the extent to which they integrate VIVO into local IT infrastructure for
authentication to allow modification of profiles by individual researchers or their proxies and for data
ingest. This integration generates additional startup cost but lowers ongoing operational costs data
is only entered once into the appropriate system of record and is pushed to VIVO through interfaces.
Data quality is improved through use of normal university data management processes and changes
to core institutional data can continue to happen in the appropriate database of record.
VIVO is also capable of disseminating data to other institutional web sites as well as harvesting from
them. VIVO provides generic RDF/XML output that can be customized or filtered within VIVO or
transformed into desired reports outside of VIVO according to local requirements. By providing
incoming and outgoing data paths through both human interaction and machine processes, VIVO is
capable of integrating well into institutional enterprise architectures.


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Under the hood, VIVO is a Java servlet application using Java Server Pages for page rendering;
existing installations use the open-source Apache Tomcat servlet container and the Apache web
server. VIVO's search function employs the Lucene library34. RDF data are managed through HP's
Jena Semantic Web library,35 which allows direct access to a variety of triple store implementations,
including those based on familiar relation database systems. Existing VIVO installations use
MySQL36, which, like all of the libraries used by VIVO, is freely available and open source. VIVO's
default configuration caches RDF data in memory to support very fast queries and web page
rendering. This technique scales to an institution the size of Cornell or Florida; in cases where much
larger RDF data sets are involved, VIVO may use any RDF triple store that implements Jena's graph
service provider interface and supports the SPARQL query language. These include third-party
commercial RDF stores such as AllegroGraph37 and OpenLink Virtuoso38, as well as a number of
open-source stores provided by HP. Several of these systems have been demonstrated to store more
than one billion RDF triples successfully.39 The VIVOweb technical development process will include
further testing and optimization in order to deploy highly scalable triple stores for large data sets,
including modification if necessary to integrate triple stores that do not provide a direct Jena interface,
such as the Sesame40 native store. A cluster of Sesame stores is used in SemaPlorer,41 which took
first prize in the Billion Triples Track of the 2008 Semantic Web Challenge.42
C.2.b. Ontologies
VIVO's flexible and extensible data model will allow it to present a simple structure of people and their
activities
across a
university, w- a] / s ---
featuring -M / Entity
links among o -p --
them and --
connections '- [_\
to other "....I -\ d-.
people as
well as their Figure 6 Sample entity structure for a faculty member showing common internal
professional data properties as well as object property relationships with other entities
information -
using a network graph structure to most naturally represent a real-world network of relationships (see
Figure 6). There are many ways a person's expertise may be discoverable, including talks, courses,
and news releases as well as through research statements or publications listed on their profile-
resulting in the creation of implicit groups or networks of people based on a number of pre-identified,
shared characteristics. 43
Ontology is an important approach to model knowledge so as to improve information organization,
sharing and understanding. It has a crucial role to enable content-based access, interoperability,
communications and provide qualitatively new levels of services on the next generation web. VIVO is
powered by ontological approaches to digest main assets of information and knowledge derived from
and requested by research networks44. It re-organizes the current existing authorized information from
faculty annual reports, institutional scholarly databases, funding records, teaching materials in an
ontological manner so that this information can be re-packaged and re-presented to the researchers
to facilitate their networking.45'46
The ontology work to date at Cornell and UF informs, but does not wholly determine, the course of
ontology development for this project, to be conducted as a close collaboration between the
community and technical teams under the overall direction of Professor Ying Ding of Indiana
University. Goals include optimal alignment with existing ontologies in wide use, extensibility for local
needs and provision for ontology-level local controls over what information is shared nationally.


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Mapping different localized VIVO ontologies for VIVOweb's multi-institutional scope can be realized
through the community efforts to achieve the agreement for specific mappings. Extending and
maintaining VIVO ontologies should reflect biomedical community needs and facilitate visualization,
semantic analysis and networking, developed by Borner, also at Indiana University.
Ontology documentation will include information about the ontology's design principles and guidelines
for local extensions. The ontology team will prepare a set of best practices for training potential users
and facilitating adoption of our technologies and approaches.
Maintaining a modular ontology structure facilitates ontology re-use, ontology mapping and data
integration. The core ontology for VIVO installations will be based on the Semantic Web Research
Community (SWRC) ontology developed by the large European Funded Network of Excellence
KnowledgeWeb47. The SWRC ontology models major entities of research communities about
persons, organizations, publications and their relationships.
We will also implement mappings where possible to enable VIVOweb data to be queried locally and
nationally using a number of different widely-adopted social ontologies including FOAF (Friend of a
Friend)48, SKOS (Simple Knowledge Organization System)49, DOAP (Description of a Project)50, SIOC
(Semantically-Interlinked Online Communities)51, Dublin Core52, and GEO (Geographic Names)53.
These will ensure interoperability with other data and systems publishing data to the Semantic Web.54
Throughout this project we aim to further enhance this ontology to better reflect the requirements
coming from research networks in the biomedical domain, especially through the testing of VIVO in
our partners' institutions and universities. We will extend the VIVO ontology to support personal work
groups and associated properties to represent the informal relationships evolving around
collaboration, and to allow individuals and groups the option to limit the visibility of these more
informal and dynamic networks and manage them as an independent graph for export to social
networking or collaborative tool APIs.
C.2.c. VIVO in the Institutional Context
Scalability through multiple independently administered installations is a major strength of this
proposal. During the scope of this project, VIVO can provide a customized and extensible presence at
the diverse participating institutions and provide convincing and varied models for propagation under
full local institutional control in the national context. Institutions without broad IT support services will
be able to utilize a more basic version, while larger institutions with more technologically integrated
resources will be able to add additional content modules and more fully integrate the application to
consume existing data sources at that institution and serve as an integrated source of data for other
applications. The VIVO approach as demonstrated at Cornell is designed to transcend the
administrative and organizational constraints of any one institution.
If Cornell and UF are at all typical of research institutions, an integrated view of people, affiliations,
grants, publications, courses, talks, research interests and international activities across internal
organizational units fills a rather glaring void in university data federation and data presentation for
internal and external communications, especially at the level of detail the VIVO platform affords. VIVO
offers a solution to appropriately and efficiently integrate with varied institutional infrastructures.
For most institutions there will be tangible benefits to justify the initial overhead of closer integration of
VIVO into Systems of Record (SOR). VIVO offers ample potential for synergies deriving from its data
integration capabilities, effectiveness as a public web application, and ability to disseminate filtered
data to other services and web sites. The investment required for an institution to interface VIVO's
authentication framework or to adapt VIVO's tools to integrate core data will be repaid by improved
data consistency and a higher public visibility for researchers, students and staff; individual buy-in will
be improved by reducing data entry time, and through the VIVOweb network, authoritative and
consistent data will be propagated to the national level.


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In the institutional setting, the VIVO installation is interfaced to SOR that indicate who is a faculty
member or researcher and provide basic authoritative information regarding department affiliations,
previous positions, degrees earned and administrative roles. At Cornell, these SOR currently include
human resources, grants, courses, annual faculty reports and the LDAP directory. As the SOR
update, interfaces keep VIVO up-to-date. Established university processes are used to maintain data
in the SOR, while faculty and their proxies continue to maintain data local only to VIVO, such as
research interests, international focus, and professional or service activities. Cornell has also
successfully addressed issues of data stewardship through a clear separation between "faculty as
employee" data (often private) from "faculty as academic" data (largely public) in its faculty annual
reporting. VIVO provides a coherent public outlet for academic and research-focused data that
individual faculty have marked as publicly visible in their annual reporting.
Authentication to VIVO is required in the local setting to gain authorized access to edit information for
a researcher. Researchers or their designated proxies may update information in the researcher's
profile. Local authentication (a VIVO username and password) is supported, as well as use of
institutional authentication methods such as LDAP/Active Directory and Kerberos. For use cases
involving cross-institutional access to privileged information, federated authentication via Shibboleth55
will be supported. Shibboleth enables researchers to access privileged information in VIVOweb
implementations other than the one at their home institution using credentials from their home
institution, provided they are authorized to access the information.
The VIVO platform will run independently at each institution and offer a local search as currently
configured at Cornell (Ithaca and Weill) and UF; any changes in local content are automatically
reflected in the local index as they are saved. Local installations can, through annotations on the
ontology, limit the range of data elements considered for public viewing or export, in concert with
appropriate administrative staff and institutional policy. The VIVOweb ontology team will focus cross-
site data indexing at a level appropriate for cross-institutional and national discovery, exposing data
through common vocabularies such as FOAF56 as well as the native SWRC-derived internal ontology.
Institutional VIVO portals will make researchers and their multiple interconnections more visible on the
web through standard search indexing, shortly to be enhanced through Google and Yahoo's recent
announcement that special tags embedded in web pages will be harvested to improve relevance
ranking algorithms and enhance search results. VIVO will support RDFa57, an extensible vocabulary
for referencing relationships via published ontologies within HTML tags on standard web pages.
C.2.d. VIVO in the Internet Context
VIVO is ideally positioned to ingest data from Internet sources such as PubMed and other publications
databases. While some institutions such as North Carolina State University, maintain an institution-
wide citation database in connection with an institutional repository58, or have licensed special access
to bibliometric tools through commercial databases, publications are perhaps the leading data source
for research networking, but are poorly exploited by institutional data sources.
The distributed technical and content development teams working across partners during the grant
period will collaborate to streamline the acquisition of each institution's publications citations from
national and international database, focusing initially on PubMed. The teams will develop an
improved workflow using web service APIs when available, concentrating on known challenges such
as author disambiguation, where some combination of automated processing and interactive review
will be required. Initiatives for unique identifiers such as the ID.LOC.GOV project (currently limited to
addressing Library of Congress subject headings) and PubMed Unique Identifiers (PMIDs) offer
promise that this problem may become less burdensome in the future. Although several proprietary
systems for unique author identifiers are also being developed, we do not expect these private
systems will be openly available at the scale of entire institutions. VIVO can easily store any number
of identifiers to help disambiguate authors and investigators, but it will use an institution-based URI as


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the primary identifier for any individual entry following Linked Data standards that rely only on
standard HTTP request and responses and institutional domain name registration rather than any
special resolution services. If a person moves from one institution to another, a standard HTTP
redirect can be returned and the redirect accomplished without a user's intervention or even
knowledge.
Initiatives such as the Indiana University Scholarly Database59 with 23 million paper, patent, and grant
records, as well as the growing datasets available as Linked Data, offer largely untapped sources of
additional information to enhance local institutional data about researchers. The Bio2RDF project60
provides Linked Data for dozens of data sets, including microarray, pathway analysis, human genome
and protein data. The ability to make RDF connections as appropriate to biomedical data and to
reuse existing efforts ranging from RDF versions of MeSH to authoritative databases for referencing
species and geographic places, makes it possible for VIVO to augment researcher social networks
with rich descriptions of the content of their research.
C.2.e. VIVO in the Semantic Web
While Cornell's VIVO links researchers across four physical campuses and numerous disciplines and
departments within one software installation, multiple independent instances of VIVO will be
interlinked as VIVOweb to support cross-institutional discovery and networking. This active networking
across a national body of diverse institutions will be promoted by a cross-site search engine as well as
through exploration tools employing network analysis and visualization. Knowledge and expertise
navigation, management and utilization will be supported through network analysis and visualization
services.
The cross institutional search will allow a VIVO system at one institution to query across all
relationships in the national network. An example of this would be a researcher querying a local VIVO
system with a question such as, "Who are all the people in New York who are working on astroviridae
infections?" VIVO will run independently at each institution and offer local search and editing services,
but many times there will be information relevant to a search at a VIVO system at a non-local
institution. To provide results to queries across institutions the data from institutions will be
aggregated by a distributed system which will operate as part of VIVOweb. Each institutional system
will be able to query against the distributed system containing the aggregated data indexes.
The VIVO instance at each institution will not only provide a web-based front end for querying and
browsing, but it will also contribute a node to a clustered system for the support of a distributed
national search index. This clustered system will aggregate all of the information from the local VIVO
systems and process it into a full text index and a RDF index. The RDF index will service queries
based on the relations between entities in the system and the full text index will allow unstructured
term based searching.
The clustered component of the system will be built using Apache Hadoop61 and Hbase62. The
Hadoop framework transparently provides the execution of parallelized jobs such as aggregation of
data from local VIVO systems, construction of indexes and processing intensive visualization jobs.
Hadoop also provides for transparent distributed data storage; which will be critical to scaling when
managing aggregated datasets. Hbase, a database built on top of Hadoop, will be used to store the
aggregated RDF and for servicing relation based queries.
The national index will be updated daily with changes from the local VIVO systems by a job which
runs on the cluster and pulls data from the local systems. Running a separate index for the national
network will enable local control over what is exposed for indexing and allow the national index to filter
content based at the level of the ontology appropriate for national-level discovery and networking.


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The analysis and visualization tools developed by the Indiana University team will also access the
distributed VIVO instances for source data in the form of RDF triples. If computationally intensive
processing is required by the analysis tools it will be executed using the Hadoop cluster.
No central hub will be needed to support national indexing, nor will the full content of any local
installation be pulled into a central index or database. The VIVO software will be modified to allow
local users to extend searches to the national index, when so desired. Initiation of queries and display
of search results will be supported through REST style web services returning common data formats
such as HTML, JSON, or XML.
C.2.f. Network Analysis and Visualization
Many cross-institutional relationships can be mapped directly through co-authorships, shared service
on professional committees, joint grant projects, and similar direct linkages, more extensive
relationships can be discovered or prospectively suggested through network-enabled analysis of text
content, linkages to common keywords and evolving patterns of relationships that indicate common
experience or research interests63. The Indiana University development team will investigate analysis-
driven enhancements, query tools, and visualization tools to build pathways for discovery across

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multiple VIVO instances and evaluate the potential of such techniques at the scale of a national
network.
At all three levels-the individual, institutional, and national-multiple techniques can be applied to
identify trends, patterns and outliers in support of insight and easy interpretation, including temporal,
geospatial, topical (semantic text mining), and network analysis techniques64. Exactly what analysis
and visualization techniques are most appropriate depend very much on the final set of supported
user needs, the available data and the delivery mechanism. In many ways, the most directly
communicable forms of analysis based on transparent linkages will be most effective.
Burner's team at Indiana University has developed scholarly knowledge management tools over the
past four years and has actively been using them for three years65. Samples are available.66,67
Diverse approaches to analyze and visualize scholarly data have been developed and tested. Among
them are tools for the visualization of evolving co-authorship networks68 such as those shown at
geospatial visualization of conference attendances, co-investigator networks (Figure 7, left) or
advisor-funding-student networks (Figure 7, right).


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Figure 8 Interactive on-line browser interface to neuroscience jobs in the United States (left) and co-
authorship linkages by the Chinese Academy of Sciences overlaid on a geospatial world map (right)

To reduce the cognitive load associated with the learning of new network layouts or 'reference
systems', static base maps such as geospatial maps or maps of science can be used. An exemplary
visual interface to neuroscience jobs in the U.S. is given in Figure 8, left. Co-authorship patterns or



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Figure 9 UCSD Map of Science with sample data overlays of expertise profiles

other linkages can be overlaid over geospatial or topical reference systems as well (see Figure 8,
right).

Figure 9 shows the UCSD Map of Science69 covering all sciences as well as the arts and humanities -
23,748 journals indexed by Scopus and Reuters/Thomson Scientific (ISI SCI, SSCI, and A&H
Indexes). Each of the 13 main scientific disciplines is labeled and color coded in a metaphorical way,
e.g., Medicine is blood red and Earth Sciences are brown as soil. Circle size denotes the number of
papers and multiple graphs can be prepared and animated over time. In this manner, VIVO usage
per science area can be identified based on the journals in which researchers in VIVO publish. Circle
size denotes the number of papers and multiple graphs can be prepared and animated over time.


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The map can be used to communicate the 'intellectual footprint' or 'trajectory' over the landscape of
science for one individual researcher based on papers s/he cites and/or publishes. It has also been
used to communicate the (evolving) 'expertise profiles' of institutions and even countries. The map
can also be used to communicate the very different temporal dynamics of scientific disciplines, bursts
of activity, or emergent research frontiers.
This part of the project will benefit from the interdisciplinary, multi-institution Network Workbench70,71
(NWB) tool development project lead by Borner. The NWB tool supports the large-scale analysis of
scholarly data including publication, citation and joint investigator relationships. It provides access to
more than 110 algorithms relevant for the study of social networks, and can be used to quickly test
and refine analysis workflows and visualizations in support of effective research networking.
C.2.g. VIVO Networking for Researchers and Groups
The root object of interest in a research networking infrastructure is the individual researcher node.
Researchers, whether in the role of author, investigator, faculty member, inventor or trainee, can have
multiple attributes and linkages depending on these roles as reflected in the ontology structure. We
anticipate there might be upwards 1,000,000 researcher nodes in the distributed VIVOweb system.
Researchers form themselves into groups, formally constituted research teams, institutes and centers,
informal project staff and networks of common interest. A researcher might be a member of several
dozen groups. Groups will vary in size from a few people to hundreds of researchers, and we expect
to support the tasks of group formation, management and productivity. We envision that creating a
group or research network proceeds in a very similar manner to friending people in FaceBook: simply
find a person, ask him/her if she wants to join a group and upon confirmation, both researchers are
connected to a 'group' node. Formal groups will be populated by systems of record and authorized
individuals.
Team formation typically requires understanding the expertise, resources and network connections of
each participating researcher. It also benefits from seeing what a new member adds to an existing
team through new connections based on subject area, research activities, affiliations and other forms
of linkages.
Group management benefits from a local view of the triples (person, member of, team) that make up
the researchers/students in a group.
Group productivity requires effective exploitation of strong and weak linkages of researchers, effective
communication of intermediate and final results and evaluation of researchers' contributions as input
to future group formation. VIVOweb will provide bi-lateral data exchange that can be used to interface
VIVOweb installations to group productivity tools.
Support for groups will be a key area of new development in the ontology, so that groups can be
linked not only to multiple investigators, but also to publications, grants and facilities. Access controls
leveraging the ontology structure will provide fine-grained, contextual control over viewing and editing,
an important feature for individuals wishing to use VIVOweb for personal and team-based networking,
where some connections may be speculative or private, especially when just forming.
C.3. Implementation
Each of the seven schools will implement VIVOweb and join a prototype national research network.
Implementing VIVOweb involves hosting the VIVO platform, populating VIVOweb with information
regarding the researchers at the institution, and creating a community of practice around support and
maintenance of the platform and its data.


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C.3.a. Release 1 Implementation
To achieve the goal of prototyping a national network for research networking, we propose to deploy a
local VIVO application at each partner institution. VIVO will be installed and configured by the local
institution based on the availability of institutional data sources and configured for interactive editing in
accordance with the institution's authentication systems.
VIVO can provide a self-contained, local research networking solution featuring a public web display
portal for researcher interests and accomplishments (see Figure 1). VIVO can consume RDF from
any source and ontologies created using any standard editor such as Protege.72 Phase 1 will prioritize
connections with local authentication systems to ensure that data can also be modified by researchers
who log in with their institutional credentials to use the self-editing component in VIVO. Local
modifications to the VIVOweb ontology will also be possible through interactive editing screens.
Administrative editing roles will typically be assigned to librarians or research support professionals,
with student labor to capture data from CVs or existing web sites. This model enables small
biomedical research institutes or any institution without assured central IT support to provide an
attractive research networking system "out of the box," capable of serving as a proof of concept to
elicit commitments of scarce institutional IT resources for localized authentication and tapping into
data sources of record.
Local VIVO installations will be sustainable only if data are current and accurate. Researchers have
little time to maintain information in their profiles. As a result, data ingest will be a critical part of the
technical innovation for institutional adopters of the VIVO platform. The early focus will be on
implementing an accepted common ontology (such as the Semantic Web for Research Communities
ontology adopted by UF's instance, GatorScholar), and on setting up data feeds from institutional
sources for authoritative human resource information (active personnel, titles, affiliations), grants and
publications from PubMed and other databases such as Web of Science or Scopus, depending on
local licenses. Ingest procedures will be implemented in year 2 to harvest information from faculty
reporting systems in use at partner institutions.
VIVO at Cornell is populated primarily by data feeds from the PeopleSoft human resources database,
from an Oracle grants database and from a PeopleSoft student records system that provides course
information. XML web services from a new, externally-hosted faculty reporting system will provide
very granular information directly from annual updates by faculty from several Cornell colleges, using
workflow tools that identify both additions and deletions. The campus LDAP server provides updates
to contact information, and feeds to a new university events calendar and news service are underway,
following the model of leveraging any and all appropriate existing institutional data sources to assure
information currency and to allow maintenance for each data element to happen in the database of
record.
Development at UF will improve the data ingest workflow from SOR, which most frequently involves
converting data from relational databases into the statement-based Semantic Web data model
through the vehicles of CSV or tab-delimited text files, direct database views, XML data files or web
services. Workflow templates to keep VIVO updated from SOR will be included in the distribution
package for implementation as automated or semi-automated processes depending on local
situations, allowing VIVO to be updated using established institutional policies and procedures.
Each institution's VIVO will become part of a distributed computing cluster that will harvest data from
each local node for a cross-institutional search index and for network analysis and visualization. The
local VIVO application will be used to edit and display profiles of researchers at an institution in the full
context of their affiliations, activities and accomplishments. VIVO has already been independently
installed at UF and at two international locations. The partners in this proposal have committed to
begin working with local VIVO installations from the beginning of the grant period to allow maximum
opportunity for formative evaluation and feedback within the first year.


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Phase 1 will include providing a level of documentation and quick start guides to allow installation of
"VIVO in a box" by information technology professionals with no previous experience with the
constituent open source tools. The VIVO platform will be further documented and installation
packages developed during phase 1 to facilitate deployment at additional institutions (Section C.2.a).
The ontology group will also enhance the core VIVO ontology to improve direct interoperability with
ontologies in the research project, temporal, geographic, publication and biomedical domains.
C.3.b. Release 2 Implementation
Research and development at Indiana University initiated during phase 1 will add more direct support
for personal and institutional-level networking and for reporting and query tools designed to support
prospective discovery of collaborators to complement relationships discoverable through co-
authorship and other more direct common affiliations presently visible in VIVO (Section C.2.c). These
features are also discussed in more detail as use cases in Section B.1 above. Cornell and UF will add
features previously described. The resulting release will fully implement networking of researchers
among the seven schools. Each school will upgrade their VIVO release 1 system to release 2.
Upgrades are intended to be straightforward. Initial seeding of the databases and maintenance of
data will have taken place during the implementation of the first release implementation of release 2
is intended to demonstrate the long-term viability of locally support VIVOweb maintenance.
During release 2, data from these institutionally-hosted VIVO systems will be made available for local
harvesting and repurposing using standard RDF syntaxes such as RDF/XML73. National networking
capability will be fully realized during this phase, and enable more institutions to join the network.
Institutions will be encouraged to join the network as the first seven complete their release 2
implementations.
C.3.c. Release 3 Implementation
Release 3 will be developed over the last six months of the two year grant period. Features and
improvements will be drive by the evaluation of the first two releases and the governance process.
Release 3 will be available prior to the end of the grant period and marks the transition of VIVOweb to
community-supported open source. The seven participating schools are not expected to implement
the system as part of their work on this proposal. A positive outcome would be for schools to accept
responsibility for the care and maintenance of their VIVOweb systems based on the utility they have
observed during the grant period.
By release 3 we anticipate and welcome adoption by schools outside the initial group of seven. By
broadening the community we begin the path to true research networking.
C.4. Dissemination
The dissemination and adoption of VIVOweb by institutions will be fueled by outreach efforts coupled
with a strong technical and community support model. A researcher network platform may be
technically very sound, but will only be used and maintained if it is of value at multiple levels as has
already been mentioned-and if the stakeholders are well-supported, and completely understand and
appreciate the value of participating in the network. While a large part of this value is provided by
technical innovation, experience with the VIVO platform at Cornell and UF has indicated that
sustained outreach efforts targeted at administrators and researchers alike to publicize the tool and its
value can have immense and lasting positive ramifications. Dissemination efforts will also have to take
into account the likelihood that national dissemination will differ from adoption by participating
institutions-the "early adopters"-characterized by author Geoffrey Moore74 as those "...who have
the insight to match an emerging technology to a strategic opportunity...". Although Moore's book,
relates primarily to commercial products, many of its principles apply, and will be employed in the
VIVOweb dissemination plan.


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C.4.a. Dissemination within Participating Institutions
Proactive and "apolitical" service and support, and "marketing" VIVO to researchers and
administrators has been a key to dissemination and adoption of the VIVO platform at Cornell and UF,
and will be heavily relied upon as VIVOweb is disseminated within participating institutions. Based on
experience accumulated through these implementations, support for participating institutions will
primarily focus on short one-on-one or group presentations that highlight the benefits to researchers
and the institution of participating in VIVOweb, and inform users and administrators of the ease in
maintaining personal information. Technical backstopping by personnel on local and national
development teams, and building collaborations with institutional information technology will be a key
support element. However, the most effective provision of the liaison and outreach activities that these
goals presuppose will require community support, which will be provided by information specialist
facilitators in the institutional library system.
Personnel with important roles in this effort will ideally exhibit good understanding of individual and
institutional research programs, activities, and needs, have the ability to effectively navigate the
administrative and political landscape, be able to communicate confidently and knowledgably with
their stakeholders, and be capable of conveying essential information about VIVOweb without resort
to technical jargon and details. They will liaise not only with institutional stakeholders, but also with
personnel within the national coordination and implementation teams, to implement a locally viable
process and workflow to promote dissemination. They will also work with the metadata and other
librarians on the project team (such as those with expertise in MeSH, CTSC activities, metadata, and
ontologies) to ensure that the project is responsive to the need for local modifications-to the core
ontology, for instance. Responsiveness to user feedback is critical to ensuring the successful
dissemination of VIVOweb.
A well-conceived and implemented dissemination effort for participating institutions will earn a good
reputation for VIVOweb, an essential feature of the national dissemination endeavor.
C.4.b. National Dissemination
The national dissemination effort will concentrate on promoting adoption of VIVOweb by new
institutions who are not early adopters. Moore classifies this group into two: early majority-or
"pragmatists", and the late majority, and identifies the major barrier to successful dissemination of a
technology product being the pragmatists. According to Moore:
"Overall, to market to pragmatists, you must be patient. You need to be conversant
with the issues that dominate their particular business. You need to show up at the
industry-specific conferences and trade shows they attend. You need to be
mentioned in articles that run in magazines they read. You need to be installed in
other companies in their industry. You need to have developed applications that are
specific to their industry. You need to have partnerships and alliances with the
other vendors who serve their industry. You need to have earned a reputation for
quality and service."
Based on this analogy, our pragmatists are likely to be encountered when the national dissemination
effort begins, and success at fostering adoption of VIVOweb at this scale will likely require patience,
familiarity with current issues in biomedical research, and a presence at biomedical events, venues-
and literature, if possible. That VIVOweb will be an application that services needs in biomedical
research is a given, as is the fact that it will collaborate with and draw information from other
biomedical service providers such as PubMed and other data and resource discovery sources as
much as possible.
Movement towards national marketing and dissemination will begin immediately after funding begins,
even though the early dissemination focus will be on participating institutions. It is clear that with the


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essential role that these early adopters will play in the development and implementation of VIVOweb,
libraries are a constituency to which to market VIVOweb as one way to promote adoption. The
Medical Library Association (MLA) is the primary library association for librarians who serve
biomedical researchers, and its annual conference would be a logical place to introduce
VIVOweb. However, with funding beginning in September, and MLA not meeting on a national basis
until May 2010, initial marketing to this audience will begin at the regional level with presentation
and/or exhibition at MLA chapter conferences. In 2009, 8 chapter meetings will be held between 21
September and 1 November (with a ninth meeting in January 2010) covering all regions of the United
States.
Some other appropriate scientific, library, and informatics related conferences that will be covered
include the American Association for the Advancement of Science Annual Meeting (February 2010 in
San Diego); the American Society for Microbiology Annual Meeting (May 2010 in San Diego); the
American Medical Informatics Associations Annual Symposium (AMIA; November 2009 in San
Francisco, November 2010 in Washington, D.C.); AMIAs Summit on Translational Bioinformatics
(Spring 2010 in San Francisco); AMIAs Spring Conference (May 2010 in Phoenix); the Special Library
Association Annual Conference (June 2010 in New Orleans); and the Association of Research
Libraries, that meets as part of the American Library Association's annual conference (June 2010 in
Washington, D.C.)
Another way to introduce VIVOweb to library decision-makers is to present at the Association of
Academic Health Libraries, a group made up of library directors and associate directors that will meet
in Boston in November of 2009. It is imperative that VIVOweb also be introduced to potential end-
users (researchers) through presentation and exhibition at their conferences as well. The American
Association for the Advancement of Science Annual Meeting is a natural choice for exhibition. Other
ways to advertise VIVOweb to potential end-users is through correspondence with associations such
as the National Academy of Sciences, the Institute of Medicine, and the National Academy of
Engineering. An obvious group to whom to advertise is the CTSA Consortium. Additional methods of
dissemination will include the use of association email lists, demonstrations on YouTube, and an
advertising webpage dedicated to VIVOweb.
C.5. Evaluation
The end goal of this project is to have a tool for researchers to facilitate research networking,
collaborations, and data sharing to improve scientific dissemination. To provide evidence that the
VIVO project meets this goal, we will employ various evaluation techniques to assess a minimum of
six objectives related to VIVO support, implementation, dissemination (see Table 5). The Washington
University (WU) team will lead the evaluation of VIVO at each site, gathering information using data-
mining, surveys, observational analysis, and personal interviews. We will focus on usability and
outcome evaluations. The usability evaluation will be designed to document and analyze the
implementation of VIVO at the adoption sites assessing the implementation completion, consistency
among institutions, and identification of gaps between design and delivery. Outcome evaluations will
be designed to assess the impact, benefits, and changes at each institution. The evaluation will be
guided by the milestones outlined in Table 8 and Table 9 in section E.5.
As outlined by the National Institute of Standards and Technology, five key attributes will be assessed
through the usability evaluation: learnability, efficiency, memorability, errors, and user satisfaction75
using evaluation methods such as data-mining, surveys, task analyses, and focus groups. We will
employ data-mining metrics using WU-developed code or through a pre-packaged tool such as
Morae76 to conduct the usability evaluation. Through data-mining we will assess VIVO usage
monitoring, gathering data such as page views, number of visits and unique views to analyze the
usage of VIVO by volume of participants and quantity of information viewed. Additional measures may
include: referring and referral websites, and successful and failed search results, and path analysis.
While website monitoring will be continuous, data will be collected on a quarterly basis. User testing
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will be incorporated into the evaluation where trained evaluators and software developers will observe
and record end-users interacting with VIVO in both general and specific tasks. This will identify
specific uses and difficulties with VIVO for reporting and further action. To understand how end-users
utilize VIVO, we will conduct a task analysis and compare this with the goals of VIVO creators and
conduct focus groups to understand key information such as barriers to usage and suggestions for
improvements.
A set evaluation tool such as the MIT Usability Guideline77 will provide measurement consistency with
evaluators over the two-year project period. The guidelines include assessing navigation, functionality,
user control, language and content, online help and user guides, system and user feedback, web
accessibility, consistency, error prevention and correction, and architectural and visual clarity.
Adopting institutions will be given these guidelines at the beginning of the program, and two
assessments will take place for each institution with a report with recommendations returned to the
institutions within two months after evaluation completion.
Items to be assessed and analyzed for the outcomes evaluation include: inputs, activities conducted,
outputs, outcomes, and, outcome indicators. At the initiation of the program a survey will be designed
and administered to assess the expectations for VIVO program implementation and usage by
adopting institutions. Follow-up evaluations to the same persons will be conducted at the end of the
first and second year incorporating dissemination and adoption practices. All surveys will be
conducted on-line sending a link to potential respondent's e-mail. Personal interviews with
researchers, site representatives, IT implementers, and other key personnel will be conducted by Dr.
Leslie Mclntosh and a junior bioinformatics specialist. Additionally, we will conduct web searches for
VIVO references in presentations, papers, and other documentation sources. When necessary, both
quantitative and qualitative questions will be designed and delivered through structured and
unstructured interviews.
Through the methods described, we will answer the following questions:
1. How well does the software meet the needs of investigators for finding appropriate people for
collaboration and research?
2. How well does the software meet the needs of institutions for learning about their own
activities?
3. How much effort is involved in implementing, hosting and maintaining the system and the data
stored in the system?
4. How has the 2-year grant program addressed the issues of sustainability of development and
support for the software?
5. How accurate and timely are the data at each institution? Is the accuracy related to the
techniques used to implement and support the software? How? What recommendations can
be made for improvement?

We will apply for IRB exemption or submit the necessary paperwork to satisfy IRB requirements at
implementation sites for the evaluation. The evaluation team at Washington University will prepare
quarterly reports, which will be made available to the executive advisory board.
The project plan addresses governance, technical design, implementation, dissemination and
evaluation based on the development of community supported by the libraries, and focused technical
activity to extend VIVO's capabilities to for national networking of researchers.


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Table 5 Primary Objectives to be evaluated in VIVO assessment


Assessment

Identify individuals tasked with outreach
and support in the network
Evaluate communication/interaction among
persons


Evaluation method
Discussions with VIVO Wiki and
Advisory Board
On-line survey incorporating
social network analysis
Telephone interviews


Trained evaluators will employ
Visit VIVO websites at adopting institutions usability guidelines
VIVO implemented at
adopting institutions Web-based surveys to key personnel at Report the number of institutions
implementation sites using VIVO and descriptive
statistics of website use
VIVO support services and Evaluate success of training (both in-person Web-based surveys upon
training meets the needs of stuct ast ie completion of training modules
instruction as well as "just-in-time" web-
users at VIVO based tutorials) Follow-up survey within two
implementation sites months after training

Collect evidence demonstrating Web search of presentations
VIVO disseminated beyond presentations given to promote VIVO (e.g. use Google Scholar)
initial adopters national otrOn-line survey to key personnel
Educational outreach activitiesat implementation sites
at implementation sites
VIVO accessed and used t VO w s at adopg i ion Data-mine usage of VIVO sites
by diverse user community including incoming IP addresses


VIVO community support
developed beyond initial
implementers


Monitor on-line VIVO forums


Data-mine forum content,
robustness, and end-user usage


The project plan provides for governance, project organization, phased development and
implementation, and detailed evaluation with timely feedback to ensure a solution that
significantly enhances the ability to conduct research for all participants.

D. Role of the Participating Institutions and Staffing of the Project
D.1. Participating Institutions
Seven schools will serve as early adopters of the VIVO system (see Table 6). These schools
represent significant diversity in terms of size, geography, student population and NIH activity. All
seven schools have NCRR centers. Four of the schools have CTSA awards UF, Weill Cornell
Medical College, Scripps Research Institute and Washington University. Three schools UF, Cornell
University and Indiana University will participate in the technical activity required to develop
subsequent versions of VIVO. All seven schools will implement two versions of VIVO, the current
version and the version to be developed under this proposal (see Project Deliverables and Timeline).
As part of the implementation, all seven schools will participate in the evaluation of VIVO and its use
by researchers.


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Objective


Support network will be in
place


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Table 6 Participating Institutions
School Role
University of Florida NCRR, CTSA, Development, Implementation, Indexing,
Lead
Cornell University, Ithaca NCRR, Development, Implementation, Indexing
Indiana University NCRR, Development, Implementation
Washington University NCRR, CTSA, Implementation, Evaluation
Weill Cornell Medical College NCRR, CTSA, Implementation
Scripps Research Institute NCRR, CTSA, Implementation
Ponce Medical School, Puerto Rico NCRR, Implementation

The University of Florida (UF) will serve as the lead institution and developer of interfaces and
packaging for rapid deployment of VIVO at other institutions. UF is the fourth largest university in the
United States, with over 51,000 students on its Gainesville campus. As a land grant university, UF
operates in all 67 counties across the state of Florida. Research awards to UF faculty account for
$576M of external support annually. Through its Clinical and Translational Science Institute UF is
affiliated with the Moffitt Cancer Center78, Shands HealthCare79, the Malcom Randall Veterans
Association Medical Center of the North Florida/South Georgia Veterans Health System80, the largest
in the country, and the Burnham Research Institute81 in Orlando. UF is the lead institution for the
project. Efforts include overall project direction, facilitation of governance processes and structures,
local implementation and support, participation in evaluation, development of VIVOweb interfaces to
SOR and other platforms, packaging of VIVO software for rapid deployment, identity management
support, instructional media and design and coordination of site implementations.
Cornell University, Ithaca will serve as the lead institution for the extension of VIVO for national
networking. Founded in 1865 by Ezra Cornell and Andrew Dickson White, Cornell is the federal land-
grant institution of New York State, a private endowed university, a member of the Ivy League/Ancient
Eight, and a partner of the State University of New York. It consists of fourteen colleges and schools:
seven undergraduate units and four graduate and professional units in Ithaca, two medical graduate
and professional units in New York City, and one in Doha, Qatar. The Ithaca campus includes 1,627
faculty, 13,562 undergraduate students, and 6,077 graduate and professional students. Life Sciences
research at Cornell cuts across most of the colleges and schools with 44 graduate fields from animal
breeding to zoology. It is a particular focus of both Cornell's College of Agriculture and Life Sciences
and its College of Veterinary Medicine. The Cornell University Library is one of the twelve largest
academic research libraries in the United States, with a long history of research and development in
the area of digital information services. The Albert R. Mann Library, part of CUL and the home of
VIVO, offers one of the country's best library collections in agriculture, life sciences and human
ecology, as well as providing extensive computing facilities, a broad suite of digital media technology,
tools for GIS, hands-on workshops, customized reference consultations and a range of other services.
Mann Library is internationally known for its digital library efforts including VIVO, TEEAL (The
Essential Electronic Agricultural Library) and the USDA Economics, Statistics, and Market Information
System. Efforts at Cornell include leadership of the Technology Advisory Committee; technical
development of enhancements to VIVO including distributed, multi-institutional indexing, scalability,
and support for individual and team networking; and national coordination of the VIVOweb outreach
efforts.
Indiana University, Bloomington will lead development in social networking and ontologies. Indiana
University was founded in 1820 and is one of the state's leading research and educational institutions.
General information about Indiana University, including an overview of physical facilities, is available
online82. Indiana University includes two main research campuses and six regional (primarily
teaching) campuses. The Indiana University Bloomington campus includes 2,309 full- and part-time


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faculty, 5,201 professional staff, 8,596 graduate and professional students and 30,394 undergraduate
students.
Washington University School of Medicine (WUSM) Adoption Team will perform evaluation of
implementation and integration of the VIVO application at all partner institutions and will serve as an
implementation site for VIVO. Washington University (WU) has a rich tradition of academic, research,
and clinical excellence. WU includes the School of Medicine located at the Medical Center Campus
and six other schools (Arts and Sciences, Business, Design and Visual Arts, Engineering and Applied
Science, Law, and Social Work) located at the Danforth Campus two miles away. The two campuses
are connected by a regular shuttle service and the public light rail service. WU has 105 academic
departments with 11,158 full time students. WU has a history of distinguished faculty: 30 are currently
members of the National Academy of Sciences, 26 are members of the Institute of Medicine, 19 hold
MERIT awards from NIH, and six are Howard Hughes Medical Institute investigators. Twenty-two
Nobel laureates have been associated with WU as faculty or students, 17 from the School of
Medicine. The WUSM is organized into 20 departments, four teaching and research divisions, and
seven graduate training divisions with a total of 1,727 faculty, 594 medical students, and 638 graduate
students. The Division of Biology and Biomedical Sciences oversees an array of graduate training
programs, including the largest Medical Scientist Training Program (MD/PhD) in the country. More
than 90% of the Medical Scientist Training Program graduates are actively involved in research. In
FY07, NIH grants awarded to WUSM faculty totaled $365,986 million ranking amongst the top NIH
funded medical schools in the country. WU also has outstanding patient care programs through its
affiliation with BJC Healthcare, a 13-hospital integrated health care delivery network in the Midwest,
which is anchored by two nationally ranked teaching hospitals, Barnes-Jewish Hospital and St. Louis
Children's Hospital. These resources make WU well-suited to act as a key participant in the VIVO
project as both an implementation site as well as the lead for evaluation efforts of the VIVO
consortium. WU has a keen understanding of institutional, collaborative, cultural, and regulatory
challenges that slow the process of transferring basic and clinical scientific discoveries into
improvements in human health and looks forward to participating in this important effort which will
facilitate academic collaborations, thus ultimately speeding the implementation of scientific
discoveries.
Weill Cornell Medical College joined with 6 partners, Cornell University, Ithaca, Cornell University
Cooperative Extension, New York City, Hospital for Special Surgery, Hunter Center for Study of Gene
Structure and Function, Hunter-Bellevue School of Nursing and Memorial Sloan-Kettering Cancer
Center to devise a strategy for creating a Clinical and Translational Science Center. The mission of
this Center is to nurture and promote a research environment that would accelerate the clinical
application of basic science discoveries. We are shaping programs to integrate clinical and
translational science across multiple departments, schools, clinical and research institutes and
hospitals. We developed mechanisms to foster the creation of multidisciplinary research teams,
incubators to develop innovative research tools and information technologies, which ultimately would
advance the application of new knowledge and techniques to good clinical practice in patient care.
Weill Cornell is already a participant in VIVO through Cornell Ithaca. We will extend our
implementation with the new features and semantics and extend the VIVO functionality to our partner
CTSC institutions.
The Scripps Research Institute (TSRI) will be an early adopter of VIVO. One of the world's largest
independent, non-profit biomedical research organizations, The Scripps Research Institute operates
two campuses with headquarters in LaJolla, California, and a new campus focused on basic
biomedical science, drug discovery, and technology development in Jupiter, Florida. TSRI is
internationally recognized for its discoveries in immunology, molecular and cellular biology, chemistry,
neuroscience, autoimmune, cardiovascular, and infectious diseases, and synthetic vaccine
development. Established in its current configuration in 1961, it employs approximately 3,000


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scientists, postdoctoral fellows, scientific and other technicians, doctoral degree graduate students,
and administrative and technical support personnel.
Ponce School of Medicine, Puerto Rico will be an early adopter of VIVO. Founded in 1977, Ponce
now holds nationally accredited graduate programs in the disciplines of Medicine, Clinical Psychology,
and Biomedical Sciences, and a Masters Degree in Public Health. The Ponce School of Medicine
Partnership with the Moffitt Cancer Center83 addresses the cancer problem in Puerto Rico focusing on
basic research, cancer education and training, outreach and tissue procurement. Ponce is a member
of the Alliance for Advancement in Biomedical Research in Puerto Rico84, an NCRR funded center.
D.2. Staffing of the Project
Dr. Michael Conlon will serve as principal investigator and project director. Dr. Conlon has extensive
experience in large-scale software development and deployment and in biomedical research. Dr.
Conlon led the development of the software used in the INVEST clinical trial85, collecting and
processing data from over 850 physicians offices in 14 countries. Dr. Conlon led the technical
implementation of the UF PeopleSoft System (myUFL86) and built and managed a team that
implemented infrastructure, system interfaces, data conversions and system configuration for 18
modules in 18 months. The $29M project was delivered on-time and on-budget. Dr. Conlon led the
design and implementation of the UF Directory87, an identity management system containing records
of over 1.7 million current and former faculty, staff and students of UF and supporting federated
identity through Shibboleth88 for 170,000 current credential holders. Dr. Conlon led the efforts to
create UF's Active Directory89 system supporting servers in 50 locations across the State of Florida, a
BizTalk90 system providing service oriented architecture services to enterprise applications, and UF
Exchange91 UF's implementation of Microsoft Exchange and Microsoft Office Communications
Server. Dr. Conlon is Associate CIO for IT Architecture at UF as well as Associate Director of the UF
Clinical and Translational Science Institute92 and Interim Director of Biomedical Informatics in the
College of Medicine. A former CIO of the UF Health Science Center and Research Associate
Professor of Biostatistics, Dr. Conlon is a frequent presenter on identity and access management and
serves on the InCommon93 Research Administration working group.
Valrie Davis will serve as site liaison, and coordinate implementation of VIVO at all seven institutions.
Davis has co-led the local VIVO implementation called GatorScholar at UF. She is a member of the
UF Libraries' Emerging Technologies Committee and leads local exploration of ontologies and
assists in the dissemination of technologies across the campus community. She coordinates library-
based services for off-campus users including more than 995 faculty and staff located at 13 Research
& Education Centers and 67 County Extension offices throughout the State of Florida. She also
supports a variety of on-campus agricultural and life science departments. As a library instructor, she
presents specialized face-to-face training sessions and develops specialized training tutorials using
software such as Camtasia. A member of the Born Digital Initiative Working Group, Policy
Development and Grant Writing Sub-Committee, she assisted in the identification of preservation and
access issues related to a national interface for born-digital and reborn digital agricultural resources.
She is an active member in many national organizations where she provides expertise in the
agricultural sciences, information sharing technologies, and electronic resource development. Ms.
Davis will serve as site liaison, coordinating implementation of VIVO at participating schools.
Dr. Sara Russell Gonzalez will lead the local UF implementation, expanding the current
implementation to all of UF. She co-led UF's initial test implementation of the VIVO database. She is
the Physical Sciences librarian at the Marston Science Library at UF, providing research assistance
and instruction in the subjects of Physics, Astronomy, and Geology. Through her liaison work to
these departments, Dr. Russell Gonzalez has developed an expertise in harvesting and retrieval of
scientific publications. Her research interests include applying bibliometrics to understanding the
publishing behavior of scientists. She was recently a consultant on a NASA grant with members of
the UF Astronomy department to acquire and setup an Astrowall for display of 3-D astronomical data
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for educational purposes. Prior to joining UF, Dr. Russell Gonzalez was a research seismologist with
Weston Geophysical Corporation investigating discrimination and location of nuclear explosions.
Dr. George Hack will serve as the lead in the development of instructional support and media for
VIVOweb. George Hack has been on faculty at the University of Florida since 1997 serving in the
Institute of Food and Agricultural Sciences as coordinator of extension education programs, teaching
graduate and undergraduate technology courses in the College of Education, and as Assistant
Director for Instruction and Information systems in the Health Science Center Libraries. Dr. Hack has
a doctorate in Educational Technology and has designed online and face-to-face instruction at the
University of Florida and other universities. Recently he has collaborated on the Compendium for
Children's Health with a team of international physicians, setting up an online environment for
Pediatricians to receive instruction in Community Pediatrics. His current research investigations
include human-computer interactions as they relate to information resources and information seeking
behaviors. He plans to use the findings from this research to better inform interface development,
bibliographic instruction, physical and technology spaces within the library, and web design.
Christopher Barnes manages software development for the Clinical and Translational Informatics
Program at UF. Mr. Barnes has led the development of hundreds of research systems including
those supporting the Florida Brain Tumor Registry, the Emerging Pathogens Institute, the Claude
Pepper Center for Aging, the Texas Medicare data repository, and the portal of the UF Clinical and
Translational Science Institute. He has significant experience with Drupal, Shibboleth, and research
software development. Mr. Barnes will lead the UF development teams responsible for VIVO
packaging, incorporation of federated identity management using Shibboleth, the construction of
interfaces for systems of record and interfaces for Sakai and Drupal.
Dr. Michele R. Tennant is the Bioinformatics Librarian at the UF Health Science Center Libraries and
U.F. Genetics Institute. Dr. Tennant has provided reference and liaison services at the library since
1995. Since 2001 she has served as embedded librarian in the UF Genetics Institute, providing
consultations and extensive instruction in the use of bioinformatics and more traditional library
resources. As liaison and embedded librarian, she has forged strong professional relationships with
UF biomedical researchers, particularly those whose work has genetic-, molecular- or bioinformatics-
related components. She currently serves as contact for implementation of GatorScholar at the UF
Health Sciences Center. Dr. Tennant was part of two teams of information professionals from
throughout the country that created online educational materials for National Center for Biotechnology
Resources, and taught courses onsite and on a regional basis for the NCBI. Dr. Tennant's research
interests include how scientists use bioinformatics-related databases, in particular those developed by
the NCBI, and attitudes of researchers and librarians to library-based bioinformatics support. She is
active at the national level in the Medical Library Association and the Special Libraries Association,
and is currently a member of the National Library of Medicine's Biomedical Library and Informatics
Review Committee. Dr. Tennant's work on the proposed grant is fourfold: 1. She will serve as
researcher support at the University of Florida; 2. She will coordinate the UF liaison librarians'
outreach efforts (marketing, instruction, and communication to the technical team of researchers'
needs related to VIVOweb) and will perform these same functions with her research clients; 3. She
will serve on the team coordinating national activities (efforts to recruit additional libraries, present and
exhibit at national and regional conferences, etc.); 4. She will assist UF's ontology team.
Dr. Dean Krafft is the Chief Technology Strategist at the Cornell University Library and a Senior
Research Associate in Information Science. Dr. Krafft will lead the Cornell effort, overseeing the
VIVOweb technical development at Cornell. He will also chair the project's Technical Advisory Board,
working with technical experts from across the country. As the former Director of IT for Computing and
Information Science at Cornell and the former Principal Investigator on the National Science Digital
Library (NSDL) project94, he has extensive experience in managing large software development
projects, in IT support and production, and in working in large, complex virtual organizations. While


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with NSDL, he led the effort to create Ncore95, an open-source technical infrastructure for digital
libraries, to support the thirteen NSDL Pathways partners and the over 130 collections that comprised
NSDL.
Dr. Medha Devare will serve as national coordinator for VIVO. Dr. Devare is a bioinformaticist based
in Cornell's Albert R. Mann Library, and has coordinated the implementation and outreach efforts for
VIVO across Cornell University's 11 colleges and 3 U.S. campus locations. She has also developed
relationships with and built interest in the VIVO platform at a number of institutions through liaison and
outreach activities and conference presentations. Apart from coordinating the VIVO project at Cornell,
Dr. Devare has taught bioinformatics workshops at Cornell (Ithaca) and at Weill Cornell Medical
College, and organized and taught a genomics course and co-taught a cropping systems course at
Cornell. She is currently working with faculty to recreate the introductory biology laboratory at Cornell.
Dr. Devare remains involved with research on agricultural biotechnology, with several reports and
publications out and in review on this topic. As national coordinator for VIVO, she will promote the
project, the VIVOweb platform and the library-based support model, and coordinate outreach efforts
with information specialists and other personnel at all seven schools, and at the national scale.
Instructional media and promotional materials will be developed under Dr. Devare's coordination with
the team from UF.
Jonathan Corson-Rikert will lead development teams at Cornell University to extend VIVO's
capabilities as described in this proposal. Mr. Corson-Rikert has been a programmer and project
leader in Information Technology Services at Cornell's Albert R. Mann Library since 2001, working on
projects including the Cornell University Geospatial Information Repository96 and e-Clips97, Cornell's
collection of digital video clips on entrepreneurship. He initiated development of the VIVO virtual life
sciences library98 software at Cornell in 2003 and has continued to lead the VIVO technical team.
Prior to joining Mann Library, he worked as research administrator for the Program of Computer
Graphics at Cornell, programmed geographic software at the Harvard Lab for Computer Graphics and
Spatial Analysis, and developed early digital cartography applications at the Dane County Regional
Planning Commission in Wisconsin.
Dr. Katy B'rner will direct efforts related to social networking, metrics and presentation. Borner is the
Victor H. Yngve Associate Professor of Information Science at the School of Library and Information
Science, Adjunct Associate Professor in the School of Informatics, Core Faculty of Cognitive Science,
Research Affiliate of the Biocomplexity Institute, Fellow of the Center for Research on Learning and
Technology, Member of the Advanced Visualization Laboratory, and Founding Director of the
Cyberinfrastructure for Network Science Center99 at Indiana University. She is a curator of the Places
& Spaces: Mapping Science exhibit100. Her research focuses on the development of data analysis and
visualization techniques for information access, understanding, and management. She is particularly
interested in the study of the structure and evolution of scientific disciplines; the analysis and
visualization of online activity; and the development of cyberinfrastructures for large scale scientific
collaboration and computation. She is the co-editor of the Springer book on 'Visual Interfaces to
Digital Libraries' and of a special issue of PNAS on 'Mapping Knowledge Domains' (2004). Her new
book 'Atlas of Science' published by MIT Press will become available in 2010.
Dr. Ying Ding will lead efforts pertaining to the development and maintenance of ontologies used by
the Semantic Web to represent scientists and investigators. Dr. Ying Ding is an Assistant Professor in
School of Library and Information Science, Indiana University. She previously worked as an Assistant
Professor at the University of Innsbruck, Austria and as a researcher at the Division of Mathematics
and Computer Science at the Free University of Amsterdam, the Netherlands. She has more than
eight years of experience and a strong research track in the Semantic Web area. She was involved in
the early development of the DAML+OIL language which evolved into OWL, the current W3C
standard for ontology definition. She has been involved in various European-Union funded projects in
the Semantic Web area (KnowledgeWeb, Ontoweb EASAIER, OntoKnowledge, IBROW, SWWS,


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COG, Htechsight, Esperonto, SEKT, DIP, Triple Space Computing). She was one of the major
organizers and initiators for International Semantic Web Conference, European Semantic Web
Conference and Asian Semantic Web Conference She has published more than 70 papers in
journals, conferences and workshops and has served as a program committee member for more than
80 international conferences and workshops. She is co-author of the book, "Intelligent Information
Integration in B2B Electronic Commerce," published by Kluwer Academic Publishers. She is also co-
author of book chapters in "Spinning the Semantic Web," published by MIT Press, and "Towards the
Semantic Web: Ontology-driven Knowledge Management," published by Wiley. Her current interest
areas include Semantic Web, Webometrics, citation analysis, information retrieval, knowledge
management and application of Web Technology.
Robert McDonald will provide Project Oversight for the implementation of VIVO at Indiana University,
Bloomington, through the IU Digital Library Program infrastructure, including oversight of all grant
personnel, coordination with the IUB Vice-Provost for Academic Affairs, the IUB Libraries, IU School
of Library and Information Science and institutions, and coordination with technical implementation.
Previously, McDonald was Co-PI on the Institute for Museum and Library Services National
Leadership Grants for Libraries Cornerstone Project, a collaborative statewide initiative to make
historical treasures from Alabama's archives, libraries, museums, and other repositories electronically
accessible. He was also Co-PI for the Library of Congress National Digital Information Infrastructure
and Preservation Program (NDIIPP) project: MetaArchive of Southern Digital Culture Partnership.
This partnership developed a MetaArchive of Southern Cultural Heritage by creating a distributed
digital preservation network for critical and at-risk content relative to Southern culture and history.
McDonald also served as Senior Personnel and Project Manager on the Library of Congress NDIIPP
sponsored Chronopolis Demonstration Project: A Grid Based Digital Preservation Environment.
Jon Dunn will be responsible for oversight of this project within the Indiana University (IU) Digital
Library Program, for technical coordination among IU Digital Library Program technical personnel and
with Indiana University's IUScholarWorks institutional repository service. Mr. Dunn will assist Mr.
McDonald in overall management of the project. Dunn is Associate Director for Technology in the
Indiana University Digital Library Program, holding a joint appointment between the IU Libraries and
University Information Technology Services. In this position, he oversees the development and
support of technical infrastructure at IU for digital collections storage, preservation, and access,
including the support and ongoing development of IU's digital repository services based on the
DSpace and Fedora software platforms. Prior to joining the Digital Library Program in 1997, Dunn
worked in IU's Cook Music Library as Technical Director for the Variations digital music library project.
Dunn has directed and managed numerous grant projects funded by IMLS, NSF, and the Andrew W.
Mellon Foundation in support of both digital library software development and collection digitization.
Dunn holds a BA in computer science from Rice University.
Dr. Rakesh Nagarajan will lead the Washington University effort. Dr. Nagarajan is the Biomedical
Informatics Program director of the WU CTSA, termed the Institute of Clinical and Translational
Sciences (ICTS), which has one of its sub aims to implement research networking solutions. Through
the ICTS and other initiatives, he leads the biomedical informatics infrastructure development effort at
Washington University as director of the WU Center for Biomedical Informatics (CBMI). Dr. Nagarajan
and his team are implementing a common informatics infrastructure to support the diverse needs of
physician-scientists and bench researchers.
Dr. Kristi Holmes is a bioinformaticist based in Becker Medical Library and will lead the outreach
efforts at WU, including promotion and training of VIVO at WU and assistance with ontology
development. At WU, she is tasked with the development and presentation of bioinformatics resource
workshops for the university community, integration of molecular biology information resources into
medical school and graduate-level curricula, and application of bioinformatics resources to research
problems through individualized consultations and collaborative relationships. She has also served as


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a course developer and instructor for the NCBI Advanced Workshop for Bioinformatics Information
Specialists offered by the National Center for Biotechnology Information (NCBI). Dr. Holmes is well-
suited for leading outreach efforts at WU, given her active role in investigating collaboration and
faculty profiling applications, her involvement in assessing issues related to research impact, and her
efforts to provide instruction, training resources and support materials to researchers.
Dr. Leslie Mclntosh of Washington University will serve as implementation lead and will also
coordinate project evaluation activities for participating institutions. Dr. Mclntosh will be able to serve
in this position as she has an extensive background in database, web site, and on-line survey
development for both educational and private institutions. In addition, Dr. Mclntosh has experience
performing evaluations in other projects including designing, conducting, and analyzing quantitative
and qualitative evaluations of Evidence-Based Public Health training within the Missouri Public
Health departments, national public health department, and the World Health Organization;
conducting evaluations of table-top exercises to assess public health disaster preparedness; and,
evaluating youth attitudes, opinion, and beliefs from on-line forums using text analysis. She has also
been a consultant with the FBI to assist in survey techniques for collecting social network data.
Dr. Curtis Cole will lead the implementation of VIVOweb at the Weill Cornell Medical College. Dr.
Cole, board certified in internal medicine, is Chief Medical Information Officer of Weill and Acting co-
director of the Weill Clinical and Translational Science Center Biomedical Informatics Program.
Dr. Gerald Joyce of The Scripps Research Institute is dean of the faculty and Co-Program Director
and Director for Translational Science, Scripps Translational Science Institute, NIH Clinical and
Translational Science Award (CTSA) Consortium. Dr. Joyce will lead the implementation of VIVOweb
at the Scripps Research Institute.
Paula King of the Scripps Research Institute is the Director of the Kresge Library and will lead the
researcher support processes for TSRI.
Dr. Richard Noel is Associate Professor of Biochemistry at Ponce Medical School and internal
advisor for the Ponce Medical School Moffitt Cancer Center Partnership. Dr. Noel will serve as
institutional liaison for Ponce Medical School and will lead its implementation and support efforts.
A strong and diverse consortium of institutions has been assembled to develop and pilot
national networking. The collaborators have significant expertise in all areas of social
networking, system development, deployment and support.

E. Project Deliverables and Timeline
VIVO work will proceed along three major activities product development, community support
development and governance. Product development will be driven by three releases. Release 1 is
focused on institutional setting deployments. Release 2 implements national networking scientists.
Release 3 integrates resource discovery and features originating from community development.
Complimentary community support is developed along adoption, implementation and use processes.
The goal of the community support effort during the project is to create sustainability support activity
for VIVO after the end of the project. The governance processes provide a means for accepting
community input and determining the future direction of VIVO. An open, participatory governance
process will drive adoption of the national network and create value for all participating scientists and
institutions.
Table 7 VIVO Project Deliverables
Deliverable Description
VIVO Release 1 Scientist discovery in the institutional setting
VIVO Release 2 National Networking of Scientists
VIVO Release 3 National Networking of Scientists and Resource Discovery
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Community Support Process On-going support for adoption, implementation and use
Product Development Process On-going support for software development and maintenance
Governance Process On-going processes for community input and decision-making
Final Report Summary, Accomplishments, Challenges, Lessons Learned,
Results of Evaluation, Next Steps

E.1. VIVO Release 1
VIVO Release 1 is a refinement of the existing VIVO platform. It is focused on researcher discovery
within an institution. Data will be exposed via the Semantic Web and interoperable with Linked Data.
Release 1 will include additional features for interfacing to systems of record, as well as
improvements in packaging the scripts and procedures used to install the software, as well as
instructional materials for installation.
E.2. VIVO Release 2
Release 2 includes all social networking features as well as visualization. Release 2 includes support
for federated identity management as well as support for groups. Indexing features will be provided
for semantic query across institutions. Release 2 constitutes the full national networking capability
described in this proposal.
E.3. VIVO Release 3
Release 3 includes features identified by evaluation and vetted by governance processes throughout
the grant period. Release 3 includes integration with the resource discovery platform described in the
U24 Request for Application.
E.4. Community Support Process
A critical component of the project plan is the development of on-going, community-based support for
VIVO. As previously described, the libraries constitute a natural foundation for this support.
Throughout the project, the libraries will develop and provide support for adoption, implementation
and use of VIVO. They will lay the foundation for on-going sustainability. Technical, support and
governance of VIVO must be sustained.
Support sustainability is in the best interests of the institutions which have adopted VIVO. As the
VIVO community grows, the resources to support VIVO on-line grow. Each institution will need to
commit to some support of their faculty and scientists in the on-going use of VIVO. In this way, on-
going support activity is created during implementation and use of VIVO.
E.5. Product Development Process
During the grant period, the VIVOweb team will develop sustainable product development process,
ensuring the long-term viability of the VIVOweb technical platform. Based on existing open source
models, the VIVOweb development process will provide on-going enhancements and maintenance of
the VIVOweb software. Technical sustainability will be achieved by creating an open source
community around VIVO in much the same way as communities have developed in support of Sakai,
Drupal, and Kuali101 The support for technical sustainability will be generated during the project by the
libraries. All activities are oriented to the ultimate goal of a self-sustaining, community-based
technical activity. Participants share ideas and code for the purpose of supporting and improving
VIVO.
E.6. Governance Process
On-going governance of VIVO will be developed over the course of the project. The CTSAs and other
interested groups of schools, as well as the NIH, have a strong vested interest in the continuation of
VIVO governance.


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E.7. Final Report
The project will produce a final report summarizing the work of the two year period and laying out the
next steps for continued development and support of VIVO in the open source community. The final
report will include summary evaluation by Dr. Leslie Mclntosh as well as lessons learned, challenges
and how they were addressed and any remaining challenges with proposals for addressing them.
The final report will be prepared with input from all elements of the project the project teams, the
principal investigator, the advisory groups and the evaluation team.
E.8. Timeline
The project timelines for year 1 and year 2 are shown in Table 8 and Table 9. Major goals for the first
year include 1) establish all governance, support and development teams, structures and processes;
2) Finalize release 1, implement at participating institutions; 3) establish adoption, implementation,
use and sustain support activities.
Table 8 VIVO Project Timeline, Year 1


Tasks
Governance
Establish governance groups and support structures
Executive Advisory meetings
Scientific and Technical Advisory processes
Evaluation activities and reporting
Support
Staff support teams
Community outreach efforts for release 1
Development
Establish development coordination
Staff development teams
Complete release 1
Develop release 2
Adoption
Facilitate adoption of release 1 beyond initial participants
Implementation
Consortium schools implement release 1
Feedback from release 1
Use
Support release 1
Sustain
Establish web sites, download
APIs for module development
Support community development
Establish community input process


Qtr I Qtr 2 Qtr 3 Qtr 4


X
X
X X


X X X




X X X

X X


X X X


X X


By the completion of year 1, the participating schools will have completed their implementations in
stand-alone and institutional settings. A community of practice will be in place to drive the adoption of
VIVO at institutions beyond those participating in the project. A support network for the use of VIVO
will be in place. Development of release 2 will be more than 50% complete. The executive and
governance processes will be constituted and functioning. An open source community will be
established to support the continuing development and technical support of VIVO.


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Year 2 focuses on completion of release 2 with its deployment and support activities,
needed to create an on-going support system for VIVO.
Table 9 VIVO Project Timeline, Year 2


and the activities


Tasks
Governance
Technical and Scientific Advisory processes continue
Executive Advisory meetings
Evaluation activities and reporting
Final report
Support
Staff support teams
Community outreach efforts for release 1
Development
Staff development teams
Complete release 2
Develop release 3
Transition to community development
Adoption
Presentations at conferences
Adoption by professional societies
Implementation
Consortium schools implement release 2
Feedback from release 2
Use
Support release 1
Support release 2
Sustain
Develop community of adoption
Develop community of implementation support
Develop community of usage support
Maintain community develoDment


Qtr I Qtr 2 Qtr 3 Qtr 4


X X
X
X X


X X
X
X X
X X


X X X


X X X
X


The VIVO implementation plan focuses on the development of a strong product and the
development of a strong community. The product and community generate support for
adoption, implementation and use. Activities throughout the project are oriented to the
purpose of creating an on-going, sustainable community of technical and support resources
for the national networking of scientists supported by VIVO.

F. Data and Software Sharing Plan
All software from this project will be made available freely to researchers and their institutions for
educational, research and non-profit purposes.
Licensing. All software developed under this project will be freely available for educational, research
and non-profit purposes under the terms of the VIVO software license to be developed in conjunction
with the NIH. The VIVO software license will be an appropriately modified version of non-commercial
open source licenses that will permit the use of the software at participating institutions. No claims of
suitability will be made and no warranty of any kind will be made. VIVO software can be modified, but
under no conditions can anyone assert ownership over the code or its modifications.


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Availability. The software will be freely available under the terms of the VIVO license to all
biomedical researchers, educators and institutions in the non-profit sector such as education,
research institutions and government laboratories. Software will be available for free unrestricted
download under the terms of the license, from sites at participating institutions, including UF and
Cornell University.
Open Source Community. While the source code for the VIVO software is already publicly
available, the VIVOweb project will cultivate an active open-source development community by
providing extensive developer documentation and a plug-in architecture enabling others to contribute
new functionality to VIVO. Because VIVO is built on the popular Jena Semantic Web library, RDF
tools developed in other contexts should in many cases be easy to integrate into the VIVO
environment with minimal modification.
Timeline. Three releases of the software will be made by the project. Release 1 will be completed
within three months of project start date. This release will include VIVO, and its required software
environment for deployment in a stand-alone setting. Release 2 will be completed eighteen months
from the project start date. This release will contain all features described in this proposal as well as
support for all use cases described in this proposal. All consortium members will upgrade to release 2
during the course of the project. All schools will provide evaluation and feedback regarding release 2.
Release 3 will be completed before the end of the project. It will include all features recommended
and approved by the governance process. (See Section E for details of project plan and timeline.)
Enhancements. A community of practice will develop around VIVO to support it after the proposal
period. Community activity includes the submission of enhancements for inclusion in future releases.
The R Project for Statistical Computing102 is an example of a vibrant open source community
supporting a complex software system for statistical and data analysis. The VIVO community will
operate in a similar fashion, establishing and archive and providing mirror sites for downloads, as well
as on-line technical support through a blog and wiki.
Commercialization. The VIVO software license permits, under appropriate terms, the use of the
software in commercial settings, as well as modification of the software by commercial entities and
inclusions of it and/or subsets of it in other software packages. Under no conditions will software
provided to the commercial entities under the terms of the VIVO license become the property of a
commercial entity.
Required Components. VIVO requires the use of other open source components. No commercial
software is required to run or host VIVO. Specifically, VIVO requires the use of Apache Tomcat03.
Shibboleth104 is required for support of federated identity use cases. VIVO and its required
components can be run on a wide variety of operating systems, both open source and commercial.
VIVO and its required components can be run on a wide-range of commercially available hardware. It
is strongly recommended that VIVO be deployed in accord with all institutional information security
and privacy requirements.
Data. All data residing in VIVO systems remains the property of the institutions hosting VIVO.
Institutions control the release of data residing in VIVO to the Semantic Web for the purpose of
enabling national networking of researchers. No other use of the data is implied. Data may reside in
indexing systems as part of the operation of the Semantic Web. Data in indexing systems remains
the property of the host institutions. Host institutions providing data to indexing systems can terminate
or alter their release policies at any time.
Data and software sharing for VIVO will support the goals of the NIH in enabling national
networking of scientists. The community approach supporting adoption, implementation, use
and sustainability through an open process facilitated by libraries coupled with the simplicity
and power of a completely semantic-based approach to data and social networking enable
simple and compelling discovery for scientists and institutions.
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102 R Software Project Home Page. http://www.r-proiect.orq. Accessed May 30, 2009.
103 Apache Tomcat Home Page. http://tomcat.apache.orq. Accessed May 30, 2009.
104 Shibboleth Home Page. http://shibboleth.internet2.edu. Accessed May 30, 2009.


Continuation Format Page


PH S 398/2590 (Rev. 11 /07)


Page 141









I. 1It' I I 'Il I ili.' r ,i ,l tIt Iq 'hwit it, td17 ,' -z,. -l, 14
FT Pm. I rvv u h.0 I %w #417 ? Id Nw
Cornell University iu...> iN ..,..
Office of Sponsored Programs




June ). 200')

)r Michael ( onlol
Director. BMI
I nrnrst\ olf Irwlda
II S PO Box 14t i
(,nics,.e llie. FI 12"604


Dlar D onionlo.

Conluicl ,nl\.~ ci- ir pleased io submit the enclosed doclumle'irs iI he ;i sihcoiiiractor to tie 1 universityt of
Florida umder a proposal heirng submilled In the Nnllniill nsilIsuIe of I Wnlthl. mnder ARRA-RF A-RR-09-
009). Th iitile lof ('nif' |i prerijlt is "V IV( Frnnhling Nationall Neiwlworkiuig o Scinlisis" nuiider tce
dircctioa otf Dcnn 11. Kralfl. Chid-t ecliTiolog Straiegy ani tie Cornel ll tiiversii Libnrua (Coriell',i
propose f period of perfonlance i's Ifromr Seplehmbr 1. 2009 ) r llouregh AuLguis 11. 2011 ft' a Iota;l prolecl
amount rleqiesMcld $1.(.60)60 0 wilh iI lirl yeiar Jiollurintil )llf .9 7.717 00)

(Commll appreciales .our connsiderntirn if dirs propusl. ShoiLld Ilis proposnu he sclclted Ior lilnding.
Cornell wvoiuld expect to nIeplinle ;a suhbclntracI illi Icnnrs and conditions llait are approprnie for ian
eduicalional insllitution and consistent wilh its policies. in particular those goveniiir intellcci.al properly)
con fidentiality and publication

It' .lcctied (1 falilndll1i pL'eas rC a llrril y ;iglytIicnl nJoi' nc Ils It1' iii> llclion It %II I ii Ve a 11.% CiClonL,
or need nddilionln iniormnlnlon. plc se cuall;act m al 607,25.12941 or Ihy lemil a i hlirim'or(onell.cdl.



Sinicichtl\.



Shomias 1I Frunk
Senior (ranl and Contra i Officci


P/rt'at" refer Io OSP ( S1 YS604-/ (frnri i v rrle nl3flhcmv


Consortium/Contractual Arrangements


PHS 398 (Rev. 11/07)


Page 142









qJ
INDIANA UNIVERSITY
SCHOOL OF LIBRARY AND INFORMATION SCIENCE



Michael Conlon, Ph.D
Associate Director, CTSI
University of Florida
105 NW 16 St. Room 330
Gainesville, FL 32603


June 24, 2009


Dear Dr. Conlon:

Indiana University is pleased to submit its proposal for "VIVO: Enabling National
Networking of Scientists" on behalf of Dr. Katy Borner. This proposal is for inclusion in your
grant application to the NIH-National Center for Research Resources agency and has been
administratively approved by the appropriate University officials. Support is requested for a 24
month period and is in the total amount of $1,895,292.

If this proposal is successful, the University will ensure compliance with all pertinent
federal regulations and policies. The subcontract agreement should be between your institution
and the Trustees of Indiana University. Administrative questions regarding this proposal should
be directed to:

Sponsored Research Services
Indiana University
P.O. Box 1847
Bloomington, IN 47402-1847

(812) 855-0516 phone
(812) 855-9943 fax
email: rugsaindiana.edu

Questions regarding the technical aspects of this proposal should be directed to Dr. Katy Bomer.


Sincerely,





Project Director Authorizing Official for the University
Katy Bomer Steven A. Martin
Assoc. Vice President for Research Administration


Herman B Wells Library 011 1320 E. 10th Street Bloomington, IN 47405-3907
Phone: (812) 855-2018 Fax: (812) 855-6166
http;//www.slis.indiana.edu


ConsortiumlContractual Arrangements


PHS 398 (Rev. 11/07)


Page 143









COOPERATING INSTITUTION CONSORTIUM STATEMENT


The (institution name) is proposing to participate in this application as described below:


PRIME GRANTEE/CONTRACTOR
Principal Investigator:
Sponsoring Agency:
Sponsor Number (if known):
Project Title:
Next Budget Period:
Total Project Period:


ORGANIZATION: University of Florida
Michael Conlon, PhD
NIH

VIVO: Enabling National Networking of Scientists
9/1/2009 8/31/2010
9/1/2009 8/31/2011


SUB-GRANTEE/CONTRACTOR: Ponce School of Medicine
Project Director: Richard J. Noel Jr.
Phone: 787-840-2575
Email: rnoel@psm.edu

Project/Subproject Title:


Human Subjects:
Animal Subjects:

First Year Budget
Period Costs

Total Project
Period Costs

F & A Cost Rate:


Yes X No
Yes _XNo

Direct: $56,695
F&A: $28,199

Direct: $156,705
F&A: $213,949


MTDC


TDC


_Other (Explain)


The appropriate programmatic and administrative personnel of Ponce School of Medicine
involved in this grant application are aware of the PHS consortium grant policy and will establish
the necessary inter-institutional agreements) consistent with that policy. Ponce School of
Medicine makes all applicable assurances/certifications, and has implemented a written policy
for Investigator Financial Disclosure and Conflict of Interest consistent with PHS requirements.




ignatue line
Jose A. Torres-Ruiz, Ph.D.
Associate Dean for Research and
Graduate Studies



6/1/2009
Date


Consortium/Contractual Arrangements


79%S/W


P HS 398 (Rev. 11 /07)


Page 144











I I


COOPERATING INSTITUTION CONSORTIUM STATEMENT

The Scripps Research Institution is proposing to participate in this application as descnbed
below


PRIME GRANTEE/CONTRACTOR
Principal Investigator:
Sponsoring Agency-
Sponsor Number (if known):
Project Title:
Next Budget Period:
Total Project Period:


ORGANIZATION University of Florida
Michael Conlon. PhD
NIH

VIVO: Enabling National Networking of Scientists
9/1/2009 8/31/2010
9/1/2009 8/31/2011


SUB-GRANTEE/CONTRACTOR The Scripps Research Institute
Project Director: Gerald F. Joyce
Phone 858-784-9844
Email: gjoyce@scripps.edu


Project/Subproject Title.


Human Subjects:
Animal Subjecls

First Year Budget
Period Costs

Total Project
Period Costs

F & A Cost Rate:


Yes _XNo
Yes _XNo

Direct: S 72,736
F&A $138.126

Direct: $147.653
F&A $280.393


X MTDC


TDC


Other (Explain)


The appropriate programmatic and administrative personnel of The Scripps Research Institute
involved in this grant application are aware of the PHS consortium grant policy and will establish
the necessary inler-institutional agreements) consistent with that policy (The Scripps
Research Institute) makes all applicable assurances/certifications, and has implemented a
written policy for Investigator Financial Disclosure and Conflict of Interest consistent with PHS
requirements.




E Fred Heaton, Manager
Pre-Award Administration




Dafe


Consortium/Contractual Arrangements


I


Page 145


PHS 398 (Rev. 11/07)













School of Medicine

STATEMENT OF INTENT TO ESTABLISH A CONSORTIUM AGREEMENT

Date: 6/3/2009

Washington University PI: Rakesh Nagarajan, MD, PhD

University of Florida PI: Michael Conlon, PhD

Application Title: VIVO: Enabling National Networking of Scientists

Proposed Project Period: 9/11/09-8/31/11

Washington University requested dollars:


First Year All Years
Direct Costs $ 265,056 Direct Costs $ 494,67!
F&A Costs $ 92,770 F&A Costs $ 173,131
Total Costs $ 357.826 Total Costs $ 667,81;

Are Animals Applicable to this Proposed Project? [ Yes [ No

Are Humans Applicable to this Proposed Project? Q Yes M No

The appropriate programmatic and administrative personnel of each institution involved in this
grant application are aware of the pertinent Federal regulations and policies and are prepared to
establish written inter-organizational agreements that will ensure compliance with all such policies.


Washington University,

Acting for John Michnowicz
John Michnowicz
Director, Grants & Contracts

Legal Entity Name: Washington University

Contact for negotiation and execution of consortium agreement:
Kaaren Downey
Asst. Director, Research Office
Washington University
One Brookings Drive- Box 1054
276 North Skinker Bldg., Ste. 220 (Needed for courier delivery)
St. Louis, MO 63130-4899
Phone: 314-935-8324
Fax: 314-935-5862
wucontracts@msnotes.wustl.edu


Consortium/Contractual Arrangements


9
8
7


Page 146


PHS 398 (Rev. 11107)












*Weill Cornell Medical College


Joan and Sanford I. Weill
Medical College


Date:


Statement of Intent to Establish a Consortium Agreement
(Sub-Grant/Sub-Contract)


June 4, 2009


Grant Number:



Application Title:


RFA-RR-09-009


Enabling National Networking of Scientists and Resource Discover
(324)


Proposed Project Period;


Sep 1. 2009


to Aug31.2011


The appropriate programmatic and administrative personnel of each institution
involved in this application are aware of the pertinent Federal regulations and
policies, and will establish the necessary inter-institutional agreements) consistent
with that policy.


University of Florida
Grantee Institution




Signature Date
Principal Investigator


Signature


Date


Official Authorized to Sign for
institution


- -o4-aneort 'L T. e't ,era Io

Consortium Institution


Curtis Cole -


Signature
Pri ipal investigator




Signat
Offici Au prized to Sign for
Institution


an 4. 20O

Date





ate


RASP 123-4- -03


ConsortlumlContractual Arrangements


PHS 398 (Rev. 11/07)


OftfN COl'nt &COnltalti Tefuli m Ib46) 96 Rl f
I0 W YOtr Avenu'. Boi a4 ban I 6461$) 0o2
New York, NY r 1065 Ermll r'a rwnd coenrr l nil,


Page 147














SCornell University



June 8. 2009

Center for Scienlific Review
National Institutes of Health
6701 Rockledge Drive. Room 1040, MSC 7710
Belhesda. MD 20817

To Whom II May Concern.

Please accept this letter of support for the application of the University of Florida. by Dr Michael
Conlon. Principle Investigator, titled "VIVO- Enabling National Networking of Scientists" in
response to RFA-RR-09-009. Recovery Act 2009 Limited Competition: Enabling National
Networking of Scientists and Resource Discovery (U24).

In the case of an award, we agree to perform the following work as described in the proposal:

Implement VIVO release 1 dunng the first year of the project period
Implement VIVO release 2 during the second year of the project penod
Collaborate with Indiana University and the University of Florida to extend VIVO software
for the purpose of simplifying the ingest of information inlo its semantic structures and
provision of information to external sources.
Collaborate with UF to develop and support a community of practice around the
adoption, implementation. use and sustainability of the VIVO software in the research
community.

The following people will participate in this work: Dean Krafft (Chief Technology Strategist.
Cornell University Library); Medha Devare (Bioinformatics and Life Sciences Librarian, Mann
Library); Jon Corson-Rikert (Head, Information and Technology Services, Mann Library), Brian
Lowe (Programmer. Mann Library), and Brian Caruso (Programmer, Mann Library)

We look forward to working with Dr. Conlon on this important work.

Regards,





Dean B. Krafft 06/05/2009 Fa
Chief Technology Strategist GranThomas Fr r
Comell University Library office oa
Sponsored Programs


Letters of Support


PHS 398 (Rev. 11/07)


Page 148











INDIANA UNIVERSITY
SCUUOL oF LIBRARY AND INFORMATION SCIENCE


June 24, 2009


Center for Scientific Review
National Institutes of Health
6701 Rockledge Drive, Room 1040, MSC 7710
Bethesda, MD 20817
To Whom It May Concern:

Please accept this letter of support for the application of the University of Florida, by Dr. Michael
Conlon, Principle Investigator, titled "VIVO: Enabling National Networking of Scientists" in
response to RFA-RR-09-009, Recovery Act 2009 Limited Competition: Enabling National
Networking of Scientists and Resource Discovery (U24).

In the case of an award, we agree to perform the following work as described in the proposal:
All: Implement VIVO release 1 during the first year of the project period
All: Implement VIVO release 2 during the second year of the project period
Indiana: Collaborate with Cornell University and the University of Florida to extend VIVO
software, leading the efforts to develop appropriate ontologies for the national network as
well as efforts to provide social networking capabilities for VIVO.
* Cornell: Collaborate with Indiana University and the University of Florida to extend VIVO
software for the purpose of simplifying the ingest of information into its semantic structures
and provision of information to external sources.
* Cornell: Collaborate with UF to develop and support a community of practice around the
adoption, implementation, use and sustainability of the VIVO software in the research
community.

The following people will participate in this work: Katy Borner and Ying Ding, both at SLIS,
IUB.

We look forward to working with Dr. Conlon on this important work.



Regards,



Dr. Katy B6rner
Victor I-. Yngve Associate Professor
School of Library and Information Science, Indiana University
Adjunct Associate Professor. School of Informatics, Indiana University
Founding Director, Cyberinfrastructure for Network Science Center, Indiana University
Phone: (812) 855-3256
Email: katyvtvindiana.edu WWW: http://clla.slis.indiana.edu/~katv/



Herman B Wells Library 011 1320 E. 10th Street Bloomington, IN 47405-3907
Phone: (812) 855-2018 Fax: (812) 855-6166
http://www.slis.indiana.edu


PHS 398 (Rev. 11/07)


Page 149


Letters of Support











INDIANA UNIVERSITY
SCHOOL OF LIBRARY AND INFORMATION SCIENCE







Ying Ding
Assistant Professor
School of Library & Information Science, Indiana University
1320 East 10th Street, Herman B Wells Library, LI029
Bloomington, IN 47405, USA
Phone: (812) 855 5388, Fax: (812) 855 6166
WWW: http://inft.slis.indiana.cdu/-dinLmint/


.1


Robert H. McDonald
Associate Dean for Library Technologies
Associate Director, Data to Insight Center-Pervasive Technology Institute
Indiana University, Herman B Wells Library 234
1320 East 10th Street, Bloomington, IN 47405
Phone: 812-856-4834
Email: rubertfaindiana.cdu


Herman B Wells Library 011 1320 E. 10th Street Bloomington, IN 47405-3907
Phone: (812) 855-2018 Fax: (812) 855-6166
http://www.slis.indiana.cdu


Letters of Support


PHS 398 (Rev. 11/07)


Page 150







4QOL Ponce School of Medicine

PO Box 7004, Ponce, Puerto Rico 00731
Telephone: 787-840-2575

Ext. 2158

TO Ext. 2159
Fax 787-841-1040

June 4, 2009

Center for Scientific Review
National Institutes of Health
6701 Rockledge Drive, Room 1040, MSC 7710
Bethesda, MD 20817

To Whom It May Concern:

Please accept this letter of support for the application of the University of Florida, by Dr. Michael Conlon,
Principle Investigator, titled "VIVO: Enabling National Networking of Scientists" in response to RFA-RR-09-
009, Recovery Act 2009 Limited Competition: Enabling National Networking of Scientists and Resource
Discovery (U24).

In the case of an award, we agree to perform the following work as described in the proposal:

Implement VIVO release 1 during the first year of the project period
Implement VIVO release 2 during the second year of the project period

The following people will participate in this work:
Richard J. Noel Jr., PhD, Project Director
Damaris Torres Cruz, Implementation Leader
Ricardo Espada Colon, Developer

We look forward to working with Dr. Conlon on this important work.

Regards,








Richard J. Noel, Jr. Ph.D. Jose A. Torres-Ruiz, Ph.D.
Principal Investigator Associate Dean for Research and Graduate
Associate Professor Studies
Biochemistry Department

Date: 6/4/2009 Date: 6/4/2009


PHS 398 (Rev. 11/07)


Page 151


Letters of Support

















June 4, 2009



Center for Scientific Review
National Institutes of Health
6701 Rockledge Drive. Room 1040. MSC 7710
Bethesda, MD 20817

To Whom It May Concern.


Please accept this letter of support for the application of the University of Florida, by Dr Michael
Conlon, Principle Investigator, titled "VIVO Enabling National Networking of Scientists" in
response to RFA-RR-09-009, Recovery Act 2009 Limited Competition Enabling National
Networking of Scientists and Resource Discovery (U24),

In the case of an award, we agree to perform the following work as described in the proposal:


Implement VIVO release 1 during the first year of the project period
Implement VIVO release 2 during the second year of the project period


The following key people will participate in this work Gerald F Joyce M D. Ph.D.. Dean of the
Faculty and Paula King. Director of Libraries

We look forward to working with Dr Conlon on this important work


With Regards.



Gerald F Joyce. M D Ph.D Date
Dean of the Faculty
Principal Investigator


Kaye I ynne Date
V P Office of Sponsored Research


PHS 398 (Rev. 11107)


Page 152


Letters of Support









WVWshingr4nUniversity in StLouis

Department of Pathology & Immunology Rakesh Nagarajan. M.I..Ph.D.
Division of Lahoratory and Genomic Medicine Telephonc: .14-362-8X59
Center for Biomedical Informatics- Fax: 314-747-799Y
http://chmi.wustl.edu i-nmail: rakesharwustl.cdlu


June 2. 2009

Michael Conlon, Ph.D.
Associate Director, CTSI
University of Florida Health Science Center, Box 100152
Gainesville, FL 32610-0152

Dear Dr. Conlon:

I am thrilled to offer my enthusiastic support of your proposal titled, VIVO: Enabling National
Networking of Scientists, which will foster collaboration among scientists and the community. As
research becomes more inter-disciplinary, it becomes absolutely critical to highlight individual
and institutional strengths to promote potential collaborations. This proposed work offers an
exciting approach to many of the issues related to collaboration, information dissemination, and
data exchange as knowledge is transferred from the research laboratory to clinical applications
and care and treatment of medical patients.

With my expertise in biomedical informatics, I believe we will be able to be a strong collaborative
partner on this project. We are well suited to implement, test, and provide useful feedback
regarding VIVO. This effort will serve to strengthen the overall application, including its
application and usability in the clinical and translational research environment and beyond.
Furthermore, we will serve as the overall program evaluator to answer questions such as how
effective VIVO is in identifying potential collaborators, how cost effective and how maintainable
is the solution, and how accurate and timely is the data at each institution.

As you know, I lead the biomedical informatics infrastructure development effort at Washington
University as co-director of the Alvin J. Siteman Cancer Center (SCC) Bioinformatics Core,
Neuroscience Blueprint Biomedical Informatics Core, co-director of the Center for Kidney
Disease Research (CKDR) Translational Research Core, and director of Washington
University's CTSA Biomedical Informatics Program (BIP). These separate informatics groups,
as well as others, have been brought together through the establishment of the WU Center for
Biomedical Informatics (CBMI). My team is implementing a common informatics infrastructure
to support the diverse needs of physician-scientists and bench researchers. This includes a
comprehensive database to mine electronic health records for research purposes, an institution-
wide clinical studies and biospecimen data management system, and databases to store and
integrate genome-wide and proteomic profiling data sets. A crucial missing piece of this CTSA
infrastructure is tooling to promote collaborative projects through the facilitation of expertise and
resource discovery. Namely, in large, complex, research organizations such as ours, it is
incredibly difficult to identify potential collaborators and necessary core resources to execute
comprehensive projects studying multi-factorial diseases. VIVO fills this vital need, and I am
tremendously excited by the possibility of implementing and utilizing it across our academic and
health care organizations. Therefore. I am delighted to support your application without
reservation.


WaMhinglon Uni;,cfsily Sthouill oi McdtJinc a Washington University Medical Centcr.
( ..an pu' IBor 11 R8, i s. i.ucdid Avenue. 51. .ouis. Miouri 63110-1093


PHS 398 (Rev. 11/07)


Page 153


Letters of Support









SWashinton University in StIouis


Department of Pathology & Immunology
Division of Laboratory and Genomic Medicine
Center for Biomedical Informatics-
http://chmi.wustl.edu


Rakesh Nagarajan, NM.D..h.D.
Tclecphone: 314-362-XK.88
Iax. 314-747-7999
t--mail: rakcshawustl.cdu


Thank you again for including our team in the early adoption, testing, and evaluation of VIVO. If
you have any questions, please feel free to contact me.


Sincerely,



Rakesh Nagarajan, MD PhD
Assistant Professor, Department of Pathology & Immunology
Director, Center for Biomedical Informatics





































Washington Univcrrity Slthoiol of MIcdinc at Washington University Medikal Center.
(mpus1 Box 1 18. h0o 5. Euclid Avrnuc. St. Louis. Misouri 63110-1093


PHS 398 (Rev. 11/07)


Page 154


Letters of Support










Clinical & Translational Science Center
A Mulf-lnt liutlnal Conortium
Cornell University. Ithaca
Comell University Cooperative Extension, New York City
Hospital for Special Surgery
Hunter Center for Study of Gene Structure and Function
Hunter-Bellevue School of Nursing
Weill Cornell Medical College Memorial Sloan-Kettering Cancer Center
1300 York Ave, Box 149. New York, NY 10065 Tel 212746-4745 Fax 212-746-8922 www.med cornel.edu/clsc


June 5. 2009

Center for Scientific Review
National Institutes of Health
6701 Rockledge Drive, Room 1040, MSC7710
Bethesda, MD 20817

To Whom II May Concern


Please accept this letter of support for the application of the University of Florida, by Dr. Michael Conlon,
Principal Investigator, in response to RFA-RR-09-009, Recovery Act 2009 Limited Competition: Enabling National
Networking of Scientists and Resource Discovery (U24). We agree to perform the following work as described in
the proposal

WCMC resources for this proposal include: Cerebro a central data Integration hub which aggregates and shares
authoritative source data from multiple systems across the institution and its partners.

erechro takes authoritative data from one source and returns ditlerent ailhornlative data Io downsireaim recipients.
For example, a faculty tille comes from our Faculty Affairs database and is tlren forwarded to all other systems
that need Ihat title. Cerchro integrates in holh a passive and active mode depending on the sophistication of the
receiving or sending system. Passive integration allows simple file transfers but requires Cerebrm to dc-duplicate
and manage change logs. Some of our core clinical information systems can have their provider master files
entirely managed by Cerebro in this manner. Active integration allows for two way data exchange so thai data can
he updated either in Cerebro (or another Ccrebro source system) or the inlcgrated system

Other resources include: A Content Management System (CMS), which allows data updates across the web sites
automatically whenever a data object is updated in any one place; and our Researcher Profile System (RPS).
which provides investigator profiles on the web site and allows key data In the profile to be edited. RPS recently
underwent an upgrade and an active Integration with Cerebro is underway.

We currently send data to VIVO from various sources, and are thus aware that Investigators will resist entering
data in multiple locations. Consequently, the key content that VIVO needs for maximum utility should be as
simple as possible Given our experience federating data within our organization and local partners, we are well
positioned to develop simplified mechanisms for similar Institutional context VtVO users. WCMC will assist the
consortium in developing implementation documentation and best practices for future VIVO users.

Weill Cornell Medical College and the Bioinformatics Core of the CTSC have extensive experience in managing
faculty identities in a complex organization. Its substantial resources, which together with those of its partners in
this grant will provide enhanced capability and functionality for connecting scientists and community engaged
in interdisciplinary collaboration and scientific exchange


PHS 398 (Rev. 11/07)


Page 155


Letters of Support













We will interface with a development version of VIVO locally as the functionality expands and continue to
integrate with the Cornell Ithaca production version during the first year of the project period. Initially this will
be passive integration moving toward active as the VIVO integration services are developed dunng the second
year of the project penod

The Clinical and Translational Science Center (CTSC) at Weill Cornell will Implement the VIVO system as an early
adopter for WCMC faculty, extending access to its partners: Hunter College Gene Center and School of Nursing.
Hospital for Special Surgery, Memorial Sloan Kettering Cancer Center. Cornell Cooperative Extension. New York
City, New York Presbyterian Hospital and affiliated community hospitals

We look forward to working with Dr Conlon on this important work.


tal>~u^^^ _______
(lianne Imperato M~ nley, MD 6/5/2009 Curtis Cole, MD 6/5/2009
Associate Dean. Translational Research and [ducatio Chief Medical Informalion Officer
Program Director, Clinical and Translational Associate Professor of Clinical Medicine
Science Center and Clinical Public Health
Abby Rockefeller Maure Distinguished Professor
of Endocrinology in Medicine


Bsr aPifel, JD, MBA, 6/5/2R /
Associate Dean. Sponsoed Programs'


Letters of Support


PHS 398 (Rev. 11/07)


Page 156














UNIVERSITY of

UFFLORIDA
SIII' I ,.irP ltif l lt r f l' I t; ll l \lttali)
Hiomedical Intnirmalic'
I 1 it \lk' 1illkd r


I'h \ \ I4' ir.r.

i..illi lllr I, I 12( '
\i kT'', I f, ',I


unre X, 21H1)

( kinl f lior l ir' 1.illi .10 R''.int
Nalonai.il In.sIiult'. I01 Ifi'lllil
0701t ROLkltkdge Drive, Rt mwi II-l, MS(' 77-1)
1thll'iida.. MI) 20817

I I Whoml It Ma.\ ( nttrn,


'Pl.'i a. tvI 'p Illfb IL.l-'r LIt sLpportl Itr Ihlr iqpplia .i 'nIt Ihe' Un.lv ers.ivI It lorida, by I) r.. M.iha.m l C. union.
I'nncipal invmtligat.lor, in response' in RI RA-RR-I1h-IN. RIuioverv A.d 21t)( l.mifl.'e ( nmi'ligin liFrhliing
Na'i t,'nal Ntlworkii rllg ,I S1 intliStN .1ild Rs Onirct I )D.-i%'tu'1v (JU21)

InT lhl' t ats, i .tn .ivar..l. w we ,igro.' ite rm p' rlIhrf i fi Iol nwing vtrk .is d 1. riln'd in ltu- prn4Fpo.al

S' rvv t ihlt 1'l1l institllmln L(ir .1 iol'lortium sit e 'vtnl insll 1tll -il I Uli llcs ll U-III'vtrsII ol f F-lndi,
(.ornmll Iflhica. Indiana I nive\rsliv, W Vill ( rn.ll Medc.al (C llt.'ge'. WI'ash gl tin Lnive.rsilv. Scripps
Kts-,arrh Inslulta and.inil 'ti MdtNl-.i S -hlitol. I'uierto Ri 1.
I'rovide' seven derlbtr.iables Wt1 Ihe Nil I as d Is'lriThfbJ n there proptl1al VIV( ) rti'as, I, 2 and 1. .
;sustl.iiii.na developlmetnl pIrT(.ce%, lor VIV(). 1a sllstlinalnl' gitoertman. prto 's- lor VIVt) and .1
.u.istainlh' suipptirt prii -.-. llr VIV( I
Impl'mt ntl VIV( I rela.114' I .il Ilhr Univ'r-sitv tp I lurilai luring f llit lirstl %'ar i1 thit' project ptrit il ..s
tilocribmi't in Il1'. prupisal
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tdelinrdi'l in rhe pnripStil

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Letters of Support


Page 157


PHS 398 (Rev. 11/07)


I )all













XAVIER UNIVERSITY OF LOUISIANA


DEPARTMENT OF CHEMISTRY




June 2, 2009


Michael Conlon, Ph.D.
Associate CIO, IT Architecture
University of Florida


Dear Mike,

I am delighted to support your submission to the NIH's Enabling National Networking of Scientists and
Resource Discovery Program. The platform articulated in your team's vision for facilitating research
collaborations and connections could be of great value in bridging geographic barriers. In addition, the
capability to search for these connections based on semantics as opposed to simple keywords adds a
dimension not currently available through any tools.

With this letter, I commit to serve as an advisor to your Steering Committee. I currently represent
Xavier University of Louisiana in Louisiana's NSF EPSCoR project: Cyber Tools and Science Drivers, which
connects STEM researchers and computational infrastructure and tools throughout the state. I also
serve as moderator for a network of academicians within the National Organization of Black Chemists
and Chemical Engineers (NOBCChE) and powered by Google Groups, and am also exploring ways to track
former NSF REU participants through Facebook. I hope these related experiences will be of use as your
network is developed. I also hope that we will be able to add Xavier University of Louisiana to the
network at some future date.

In closing, please accept my commitment and support of the Steering Committee with this letter. If
there is anything I can do to further assist you, do not hesitate to call.

With warm regards.

t'/t

Gloria Thomas MaGee, PhD
Assistant Professor of Chemistry








Gloria Thomas MaGee, Ph.D. 1 Drexel Drive Box 114 New Orleans, LA 70125
gmageel@xula.edu 504-520-7380voice 504-520-7942fax


PHS 398 (Rev. 11/07)


Letters of Support


Page 158






Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Data and Resource Sharing Plan
All software from this project will be made available freely to researchers and their institutions
for educational, research and non-profit purposes.
Licensing. All software developed under this project will be freely available for educational,
research and non-profit purposes under the terms of the VIVO software license to be developed
in conjunction with the NIH. The VIVO software license will be an appropriately modified
version of non-commercial open source licenses that will permit the use of the software at
participating institutions. No claims of suitability will be made and no warranty of any kind will
be made. VIVO software can be modified, but under no conditions can anyone assert
ownership over the code or its modifications.
Availability. The software will be freely available under the terms of the VIVO license to all
biomedical researchers, educators and institutions in the non-profit sector such as education,
research institutions and government laboratories. Software will be available for free
unrestricted download under the terms of the license, from sites at participating institutions,
including UF and Cornell University.
Open Source Community. While the source code for the VIVO software is already publicly
available, the VIVOweb project will cultivate an active open-source development community by
providing extensive developer documentation and a plug-in architecture enabling others to
contribute new functionality to VIVO. Because VIVO is built on the popular Jena Semantic Web
library, RDF tools developed in other contexts should in many cases be easy to integrate into
the VIVO environment with minimal modification.
Timeline. Three releases of the software will be made by the project. Release 1 will be
completed within three months of project start date. This release will include VIVO, and its
required software environment for deployment in a stand-alone setting. Release 2 will be
completed eighteen months from the project start date. This release will contain all features
described in this proposal as well as support for all use cases described in this proposal. All
consortium members will upgrade to release 2 during the course of the project. All schools will
provide evaluation and feedback regarding release 2. Release 3 will be completed before the
end of the project. It will include all features recommended and approved by the governance
process. (See Section Error! Reference source not found. for details of project plan and
timeline.)
Enhancements. A community of practice will develop around VIVO to support it after the
proposal period. Community activity includes the submission of enhancements for inclusion in
future releases. The R Project for Statistical Computing1 is an example of a vibrant open source
community supporting a complex software system for statistical and data analysis. The VIVO
community will operate in a similar fashion, establishing and archive and providing mirror sites
for downloads, as well as on-line technical support through a blog and wiki.
Commercialization. The VIVO software license permits, under appropriate terms, the use of
the software in commercial settings, as well as modification of the software by commercial
entities and inclusions of it and/or subsets of it in other software packages. Under no conditions
will software provided to the commercial entities under the terms of the VIVO license become
the property of a commercial entity.
Required Components. VIVO requires the use of other open source components. No
commercial software is required to run or host VIVO. Specifically, VIVO requires the use of


1 R Software Project Home Page. http://www.r-proiect.orq. Accessed May 30, 2009.


Resource Sharing Plan


PHS 398 (Rev. 11/07)


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


Apache Tomcat2. Shibboleth3 is required for support of federated identity use cases. VIVO and
its required components can be run on a wide variety of operating systems, both open source
and commercial. VIVO and its required components can be run on a wide-range of
commercially available hardware. It is strongly recommended that VIVO be deployed in accord
with all institutional information security and privacy requirements.
Data. All data residing in VIVO systems remains the property of the institutions hosting VIVO.
Institutions control the release of data residing in VIVO to the Semantic Web for the purpose of
enabling national networking of researchers. No other use of the data is implied. Data may
reside in indexing systems as part of the operation of the Semantic Web. Data in indexing
systems remains the property of the host institutions. Host institutions providing data to
indexing systems can terminate or alter their release policies at any time.
Data and software sharing for VIVO will support all the goals of the NIH in enabling
national networking of scientists. The community approach supporting adoption,
implementation, use and sustainability through an open process facilitated by libraries coupled
with the simplicity and power of a completely semantic-based approach to data and social
networking enable simple and compelling discovery for scientists and institutions.



































2 Apache Tomcat Home Page. http://tomcat.apache.orq. Accessed May 30, 2009.
3 Shibboleth Home Page. http://shibboleth.internet2.edu. Accessed May 30, 2009.


Resource Sharing Plan


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Program Director/Principal Investigator (Last, First, Middle): Conlon, Michael


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