RELEASE DATE:  September 29, 2003
RFA Number:  RFA-RM-04-003 (formerly RFA-RR-04-001, see NOT-OD-04-008)

Department of Health and Human Services (DHHS)


National Institutes of Health (NIH) 

This RFA is developed as a roadmap initiative. All NIH Institutes and 
Centers participate in roadmap initiatives. 



o Purpose of this RFA
o Technical Assistance Workshop
o Research Objectives
o Organizational Structure of the National Centers
o Mechanism of Support 
o Funds Available
o Eligible Institutions
o Individuals Eligible to Become Principal Investigators
o Where to Send Inquiries
o Letter of Intent
o Submitting an Application
o Supplementary Instructions
o Peer Review Process
o Review Criteria
o Receipt and Review Schedule
o Award Criteria
o Required Federal Citations


The Institutes and Centers (ICs) of the National Institutes of Health 
invite applications for specialized centers in the area of biomedical 
computing. The U54 mechanism will be used to create NIH National 
Centers for Biomedical Computing (NIH NCBCs).  These centers, in 
conjunction with individual investigator awards, will create a 
networked national effort to build the computational infrastructure for 
biomedical computing in the nation, the National Program of Excellence 
in Biomedical Computing (NPEBC).  The establishment of the NIH NCBC was 
called for in the Biomedical Information Science and Technology 
Initiative report in 1999 
(, and their need has been 
reaffirmed by more recent workshops.  The NIH NCBC will be devoted to 
all facets of biomedical computing, from basic research in 
computational science to providing the tools and resources that 
biomedical and behavioral researchers need to do their work. In 
addition to carrying out fundamental research, it is expected that the 
NIH NCBC will play a major role in educating and training researchers 
to engage in biomedical computing.

To build the computational infrastructure for biomedical computing in 
the nation, the National Program will use a combination of NIH funding 
mechanisms that will be supported by multiple NIH Institutes and 
Centers.  The central constituent of the NPBEC, the NIH NCBC, is the 
focus of this RFA.  The NIH NCBC will provide tools and resources that 
biomedical and behavioral researchers can use at a variety of levels.  

The NIH NCBCs will be partnerships bringing together three types of 
scientists:  1) computational scientists, who invent and develop 
efficient and powerful languages, data structures, software 
architectures, hardware, and algorithms for solving biomedically 
significant computing problems; 2) biomedical computational scientists, 
who adapt and deploy resources from computational science to solve 
significant biomedical problems; and 3) experimental and clinical 
biomedical and behavioral researchers, who generate data that can be 
transformed into knowledge by computational simulation, analysis, 
modeling, data mining, and visualization.  These partnerships will be 
designed to produce, validate, and disseminate tools and computational 
environments that will be useful to a broad spectrum of biomedical 
researchers across the nation.  It is expected that the partnerships 
will be highly interactive.  Computational scientists should work with 
biomedical or behavioral researchers to develop the tools while the 
biologists validate these tools and provide feedback for the next 
generation of tools.  In some cases, the NIH NCBCs will enhance and 
extend existing tools; in other cases they will develop new tools and 
computational environments de novo.

Individual biomedical or behavioral investigators will make use of the 
NIH NCBCs in different ways.  Some investigators will simply use the 
on-line tools and services that the NIH NCBCs provide.  These 
investigators might never have direct contact with any researchers at 
the NIH NCBC, but they will download software or go to the NIH NCBC web 
site to make use of resources found there.

Biomedical and behavioral investigators for whom a greater level of 
interaction with the NIH NCBC is appropriate could follow two pathways.  

1) After the initial NIH NCBCs have been funded, NIH anticipates 
releasing a new program announcement that will support partnerships 
between individual investigators and the centers.  As an example, a 
biomedical research laboratory with software that is useful in modeling 
the function of the heart might seek to use the expertise of the NIH 
NCBC to modify the software to run on a computational grid.  
Alternatively, the biomedical researchers might seek support from the 
NIH NCBC to design and build hardware that would be well suited to 
solve their problems.  Individual investigators should monitor the 
BISTI web site ( for relevant program 
announcements. It is anticipated that the announcements for partnering 
projects will include both new RO1's and R21's and as well as 
competitively reviewed supplements to existing projects.

2) Individual investigators could be part of a Driving Biological 
Project (DBP) funded within the NIH NCBC.  These projects will be 
described in core 3 below.  An investigator who interacts with the 
center in this fashion will help the NIH NCBC focus its computational 
research on challenging biomedical problems selected for their broad 
biomedical significance and compatibility with the core computational 
expertise of the NIH NCBC.  Investigators involved in a DBP will have 
substantial interactions with researchers at the NIH NCBC.

NIH staff will conduct one technical assistance and information-sharing 
workshop in Bethesda, MD on November 3, 2003.  This workshop will allow 
applicants and NIH staff to discuss and clarify any issues or questions 
related to this RFA.  If you plan to attend the workshop, please 
contact Mr. Kevin Lauderdale (e-mail or phone 
301-451-6446) to reserve a space.  Detailed information about the time 
and location of the meeting will be available at the BISTI web site  To accommodate individuals who cannot attend 
the meeting, provisions will be made to distribute the information 
discussed.  These provisions will also be posted on the BISTI web site.

Increasingly, the most exciting science and the most fruitful 
scientific and technical approaches to biomedical and behavioral 
research require approaches that involve bioinformatics and 
computational biology as well as experimentation.  To meet the 
infrastructure needs of modern biomedical and behavioral research, the 
NIH is embarking on a long-term initiative aimed at deploying an 
integrated national biomedical computing environment.  This environment 
will enable the analysis, modeling, understanding, and prediction of 
dynamic and complex biomedical systems across time and distance scales 
and will allow the integration of biomedical and behavioral data and 
knowledge at all levels of organization.  All applications in response 
to this announcement will be evaluated primarily for the potential of 
the proposed activities to contribute to this long-term goal.

This RFA provides for the establishment of NIH supported National 
Centers for Biomedical Computing in the service of this long-term 
initiative.  The National Centers will be charged with core 
responsibilities in implementing and coordinating a national project to 
make, improve, and integrate components of biomedical computing.  For 
example a particular NIH NCBC could focus on algorithms, software 
development and engineering, definition of hardware requirements, and 
user interface development to provide an excellent computational 
environment for one or more classes of biomedically important 
computing, such as:

o Comparative genomics
o Biomolecular modeling and simulation
o Analysis and modeling based on high throughput experimental 
o Image analysis and reconstruction
o Clinical trial management
o Epidemiological analysis and modeling
o Use of biomimetic principles in device design
o Multiscale simulation of biological processes
o Computational and information frameworks for integrating biological 
and behavioral data

Examples of computational environments that might ultimately be created 
could include:

o A graphical user interface (GUI)-enabled environment that would 
integrate homology and motif search tools, phylogenetic profiling, 
proteomics and microarray analysis, and intelligent text-mining to 
identify of gene function and networks of interacting gene products.

o An environment that would integrate molecular modeling and simulation 
tools including homology-based structural modeling, electronic 
structure calculations, classical molecular dynamics and Monte Carlo 
sampling, electrostatics, molecular docking, and stochastic dynamics, 
to provide the best possible inference of structure-function 
relationships in biomolecules.

o A GUI-enabled environment that would integrate sequence analysis, 
traditional and high-throughput cell and molecular biology data 
analysis, clinical and behavioral data analysis, and intelligent text 
data mining, to understand the significance of single-nucleotide 
polymorphisms in determining varied response of individual patient 
responses to clinical interventions.

o A software development and dissemination environment, or software 
framework, that would enable concurrent developer access to a moderated 
repository for the purpose of multi-scale organ modeling.  Such an 
environment would allow a geographically diverse team to work on a 
significant biomedical problem.

The above lists are intended to be exemplary rather than exhaustive or 

The environments should be constructed by considering the entire range 
of computational techniques that apply to a particular biomedical 
issue.  In these environments all the relevant computational techniques 
will be embodied in components that are robust, efficient, easy to use, 
widely disseminated, interoperable, versatile, in conformity with best 
practices in software engineering, and well tuned to the most 
appropriate and powerful free-standing hardware and grid computing 
environments.  Applicants for the NIH NCBCs are encouraged to consider 
similar far-reaching scenarios, as a guide to long-term goals for the 
NIH NCBC. Although these centers as a whole will be aimed at solving a 
large, long-term problem, each individual center will be focused on 
solving smaller problems in a 5 to 10 year time frame.


Each NIH NCBC will be required to perform or facilitate seven different 
core functions:  (1) conducting core research in relevant science, such 
as algorithm creation and optimization, creation of appropriate 
languages, or the creation of hardware architectures applicable to the 
solution of biomedical problems, (2) conducting core research and 
development in biomedical computational science by developing and 
deploying tools designed to solve particular biomedical problems, (3) 
establishing Driving Biological Projects (DBP) to allow experimental 
biomedical and behavioral researchers to interact with and drive 
computational research in the NIH NCBC, (4) providing infrastructure to 
serve the needs of the broad community of biomedical and behavioral 
researchers, (5) enhancing the training for a new generation of 
biomedical researchers in appropriate computational tools and 
techniques, (6) disseminating newly developed tools and techniques to 
the broader biomedical research community, and (7) providing an 
administrative core to ensure that these large centers achieve their 
goals within the 5 to 10 year funding lifetime of the center.

Cores 1 and 2 in an NIH NCBC should propose research that is important 
to biomedical or behavioral researchers and interesting to researchers 
in computational biology.  These cores will be the largest component of 
the NIH NCBC.  The chosen research problem should be significant, but 
it should also be possible to achieve substantial progress in a 5 to 10 
year timeframe.  It is expected that the personnel associated with core 
1 will have a computer science or other mostly computational 
background.  In contrast, it is likely that the personnel associated 
with core 2 will have some computational background, but they will also 
have a significant background in some area of biomedical or behavioral 
research.  Cores 1 and 2 do not have to be the same size, but both must 
exist.  While no distribution of expenditures is prescribed for the NIH 
NCBC, it is envisaged that cores 1 and 2 together will comprise 
approximately half of the overall budget. 

Close and effective collaboration between the leaders of Core 1 and 
Core 2 is key to the success of the NIH NCBCs.  The NIH NCBCs will need 
cutting edge computer science, as represented by Core 1, and strong 
leadership in translating that computer science into effective 
algorithms and environments for solving real biological problems.  
Reviewers will be instructed to evaluate applications for evidence of 
strong synergy between these two cores in conceptualizing, planning, 
and implementing the NIH NCBC.  While it is not required that the 
leaders of core 1 and core 2 be at the same institution, applicants 
will have to present a convincing plan for any proposed collaboration 
at a distance. 

In core 3, an investigator will propose 2-4 collaborations with NIH 
funded biomedical or behavioral researchers to address a 
biomedical/behavioral question using computational approaches.  It is 
not essential that the biomedical researchers have expertise in 
computational biology, but they should have a question that will drive 
the fundamental computational research in cores 1 and 2.  The purpose 
of this core is to ensure that the research carried out in cores 1 and 
2 has direct relevance to biomedical or behavioral research.  It may be 
useful for these Driving Biological Projects (DPB's) to have a focus on 
a particular disease or organ, but that sort of focus might not be 
appropriate for all NIH NCBCs.  It is expected that many of the 
biomedical researchers in core 3 will not be at the same institution as 
the parent NIH NCBC.  In such cases, convincing plans for collaboration 
at a distance must be presented in the proposal.  An individual DBP 
will last for at most three years.  If the problem addressed by the DBP 
is not going to be completely solved in a 3 year period, the principal 
investigator and collaborating researchers must present plans to 
compete for independent funding for continuation of the work.  Plans 
must also be presented to recruit and select additional DBPs after 
collaborations with the initial "founding" DBPs under the NIH NCBC have 
been completed.  While no distribution of expenditures is mandated, it 
is envisaged that approximately one quarter of the budget in the NIH 
NCBC will be used to support the participation of the DBPs in the NIH 

The new tools that are being developed are likely to require 
substantial infrastructure to allow the larger community of biomedical 
researchers to utilize these tools.  Core 4 will provide that 
infrastructure.  Examples of the infrastructure include user support 
personnel, servers from which users can download software or through 
which users can access the software on a national or regional facility, 
technical support to a national or regional facility on which users use 
the software, or related items to enable biomedical researchers to have 
ready access to the products of the particular NIH NCBC.  

The long-term goals of the NIH in bioinformatics and computational 
biology include the development of a new generation of multi-
disciplinary biomedical computing scientists.  In core 5, each center 
should propose plans to ensure that graduate students and postdoctoral 
fellows receive broad relevant training beyond the specific 
contributions they make to the infrastructure and research projects of 
the center.  This training should occur in both directions.  Students 
and postdoctoral fellows with a background in computational science 
should receive training in biomedical and behavioral science and those 
with a background in biomedical and behavioral science should receive 
training in computational sciences.  In addition, plans should be 
presented for workshops or other activities to train the larger 
biomedical community about the new tools and techniques that the NIH 
NCBC is developing.  It may be most effective if some workshops occur 
in the context of important biomedical or behavioral science meetings, 
at universities or medical schools, or using resources such as the 
Access Grid rather than at the NIH NCBC itself.  The rationale for the 
structure and venue of the workshops should be carefully thought out 
and presented in the application.

The focus of core 6 is to disseminate new discoveries and resources to 
the biomedical community.  Publications and a good web site are 
excellent ways to broadcast some of the discoveries of the NIH NCBC, 
but those routes may not be sufficient to inform biomedical and 
behavioral investigators who require guidance in pursuing computational 
solutions to their questions.  Innovative plans to disseminate 
discoveries to this biomedical community should be presented in core 6.  
Applicants must discuss how software will be made available to the 
community in this core and to justify any restrictions they might place 
on software dissemination.  Finally, plans to make data sets and 
databases available after funding for the NIH NCBC has ceased should be 

It is essential to provide an appropriate administrative structure to 
manage the many facets of these large, complex centers.  The 
administrative plan should be presented as core 7.  Investigators are 
strongly encouraged to consider proposing a project manager for the NIH 
NCBC.  In addition to a project manager, it is expected that each NIH 
NCBC will have an external advisory committee.  This committee should 
meet at least on an annual basis to review progress and offer advice.  
Potential members of the external advisory committee should not be 
contacted until after an award has been made, and these members should 
not be listed in the application.  Core 7 should also address how the 
NIH NCBC will accommodate requests from individual investigators who 
want to make use of the centers via the anticipated individual 
investigator program announcements.

While no distribution of expenditures is mandated, it is anticipated 
that cores 4, 5, 6, and 7 will together account for approximately one 
quarter of the total budget of the NIH NCBC.

The NIH previously supported Planning Grants for Programs of Excellence 
in Biomedical Computing (pre-NPEBC) using the P20 mechanism under 
PAR-00-102.  Recipients of those awards are welcome to apply for the U54 
centers in this announcement.  Investigators who did not apply for or 
receive a pre-NPEBC award may also apply for the new U54 centers.  No 
programmatic preference will be given either to recipients or non-
recipients of pre-NPEBC awards.


This RFA will use NIH U54 award mechanism.  As an applicant you will be 
solely responsible for planning, directing, and executing the proposed 
project.  The anticipated award date is September 15, 2004. 

The ICs intend to reissue this RFA at least once to allow funded 
centers to have the chance for a competing continuation.  This future 
RFA is likely to allow applications from new centers.  The initial 
period of support for a U54 center will be five years.  No center will 
receive more than ten years total of NIH funding.  

This RFA uses just-in-time concepts.  It also uses the non-modular 
budgeting formats.  This program does not require cost sharing as 
defined in the current NIH Grants Policy Statement at  

The NIH U54 is a cooperative agreement award mechanism.  In the 
cooperative agreement mechanism, the Principal Investigator retains the 
primary responsibility and dominant role for planning, directing, and 
executing the proposed project, with NIH staff being substantially 
involved as a partner with the Principal Investigator, as described 
under the section "Cooperative Agreement Terms and Conditions of 

The participating ICs intend to commit $14 million to $17 million in FY 
2004 to fund 3 to 4 new centers in response to this RFA. An applicant 
should request a project period of 5 years.  The budget (direct costs) 
may not exceed $3 million per year.  The F&A costs (sometimes known as 
indirect costs) of subcontractors will not count against this $3 
million limit.  Because the nature and scope of the proposed research 
will vary from application to application, it is anticipated that the 
size of each award will also vary.  Although the financial plans of the 
ICs provide support for this program, awards pursuant to this RFA are 
contingent upon the availability of funds and the receipt of a 
sufficient number of meritorious applications.
You may submit (an) application(s) if your institution has any of the 
following characteristics:

o Public or private institutions, such as universities, colleges, 
hospitals, and laboratories 
o Units of State and local governments
o Eligible agencies of the federal government
o Foreign institutions are not eligible to apply for NIH NCBC centers, 
but foreign institutions can participate in the DPBs.

Any individual with the skills, knowledge, and resources necessary to 
carry out the proposed research is invited to work with their 
institution to develop an application for support.  Individuals from 
underrepresented racial and ethnic groups as well as individuals with 
disabilities are always encouraged to apply for NIH programs.   


As part of the U54 Specialized Center Grant process, the following 
Terms and Conditions of Award and details of the arbitration procedures 
pertaining to the scope and nature of the interaction between the NIH 
staff and the participating awardees will be incorporated into the 
Notice of Grant Award and provided to the Principal Investigator and 
the institutional official at the time of award.  These procedures will 
be in addition to the customary programmatic and financial negotiations 
that occur in the administration of grants.

Cooperative agreements are assistance mechanisms subject to the same 
administrative requirements as grants.  The special Terms and 
Conditions of Award are in addition to, and not in lieu of, otherwise 
applicable OMB administrative guidelines, HHS Grant Administration 
Regulations at 45 CFR Part 74 and 92, and other HHS, PHS, and NIH grant 
administration policies and procedures.  Cooperative Agreements are 
subject to the administrative requirements outlined in pertinent OMB, 
HHS, PHS, and NIH guidelines, with particular emphasis on HHS 
regulations at 42 CFR Part 52 and 45 CFR Part 74.  Facilities and 
Administrative Cost (indirect cost) award procedures will apply to 
cooperative agreement awards in the same manner as for grants.

The administrative and funding instrument used for this program is a 
Cooperative Agreement (U54), an "assistance" mechanism (rather than an 
"acquisition" mechanism) in which substantial NIH scientific and/or 
programmatic involvement with the awardee is anticipated during 
performance of the activity.  Under the cooperative agreement, the NIH 
purpose is to support and/or stimulate the recipient's activity by 
involvement in and otherwise working jointly with the award recipient 
in a partner role, but it is not to assume direction, prime 
responsibility, or a dominant role in the activity.  Consistent with 
this concept, the dominant role and prime responsibility for the 
activity resides with the awardee(s) for the project as a whole, 
although specific tasks and activities in carrying out the studies will 
be shared among the awardees and NIH Science Officers (defined below).

Failure of the awardees to meet the performance requirements, including 
these special terms and conditions of award, or significant changes in 
level of performance, may result in a reduction of budget, withholding 
of support, suspension and/or termination of the awards.

1.  Awardee Rights and Responsibilities

Awardees have primary authorities and responsibilities to define 
objectives and approaches, and to plan, conduct, analyze, and publish 
results, interpretations, and conclusions of their studies.  The 
primary responsibilities of the awardees are to:

o  Define the research objectives.

o  Conduct specific studies.

o  Analyze and interpret research data.

o  Establish an External Advisory Committee for the center. 

o  Provide information to the NIH Science Officer and NIH Program 
Officer concerning progress.

o  Maintain career development opportunities to encourage new 
investigators to work in computational biology.

Awardees will retain custody of and primary rights to their data and 
intellectual property developed under the award subject to current 
government policies regarding rights of access as consistent with 
current HHS, PHS, and NIH policies and subject to the terms and 
conditions of this RFA.

Principal investigators and key personnel as appropriate are expected 
to participate in an annual meeting of the NIH NCBCs in the Washington, 
DC area.  Funds for travel to the meeting should be requested in the 

2.  NIH Responsibilities

NIH Science Officers:

NIH Science Officers will be NIH staff who will have substantial 
scientific involvement during the conduct of this activity, through 
technical assistance, advice, and coordination above and beyond normal 
program stewardship for grants.  Each center will have one or more 
designated NIH Science Officer(s).  A given individual may be the NIH 
Science Officer for more than one center.  The NIH Science Officer(s) 
will be selected by the primary IC supporting the award.  The degree of 
involvement by the NIH Science Officer(s) will include the following:

o  Assist in avoiding unwarranted duplication of effort across centers; 
help coordinate collaborative research efforts that involve multiple 

o  Review and comment on critical stages in the research program before 
subsequent stages are implemented.

o  Assist in the interaction between the awardee and investigators at 
other institutions.

o  Retain the option of recommending termination of studies if 
technical performance falls below acceptable standards, or when 
specific lines of research cannot be effectively pursued in a timely 

o  Retain the option to recommend additional research endeavors within 
the constraints of the approved research and negotiated budget.

To help carry out these duties, Science Officers may consult with non-
NIH experts in the field.

NIH Program Officer:

NIH will appoint a Program Officer who will have program oversight 
responsibilities for each center.  This individual will not be a 
Science Officer.  The Program Officer will:

o  Have the option to recommend withholding support to a participating 
institution if technical performance requirements are not met.

o  Exercise the normal stewardship responsibilities of an NIH Program 

o  Carry out continuous review of all activities to ensure objectives 
are being met.

3.  Arbitration Process

When agreement between an awardee and NIH staff on 
scientific/programmatic issues that may arise after the award is made, 
an arbitration panel will be formed.  The arbitration panel will 
consist of one person selected by the Director of the Center, one 
person selected by the NIH, and a third person selected by both NIH 
staff and the Director.  The decision of the arbitration panel, by 
majority vote, will be binding.  The special arbitration procedure in 
no way affects the right of an awardee to appeal any adverse action in 
accordance with PHS Regulations at 42 CFR Part 50, Subpart D, and HHS 
Grant Administration Regulations at 45 CFR Part 74, section 304, and 
HHS Regulations at 45 Parts 16 and 75.

4.  Progress Reviews

The progress of the NIH NCBC will be reviewed annually by the NIH 
Program Officer to assure that satisfactory progress is being made in 
achieving the project objectives.  During the first year of funding, 
and during subsequent years if deemed necessary by the Program Officer, 
reviews may be more frequent.  Should problems arise in the conduct of 
the study, the NIH Program Officer may require that the awardee submit 
quarterly reports on progress and fiscal matters.  

The progress report will have two components.  The first will be the 
standard NIH progress report (Form 2590).  The second will be a more 
specialized report that will go to the NIH Science Officer(s) and the 
NIH Program Officer.  This specialized report should be included as an 
attachment to the standard progress report.  The report will contain a 
narrative section describing the progress in each of the seven cores 
over the past year.  The report will also contain at least two 
"highlights".  Each highlight will be based on a publication or other 
product of the NIH NCBC, less than a year old, which acknowledges 
support from the NIH NCBC.  The highlight will be written at a level 
that is understandable by a technically literate, but non-expert 
individual.  The report will also contain details of the federally 
funded investigators that used the resources in the NIH NCBC during the 
preceding fiscal year.  The report will also contain a list of papers 
that acknowledge support from the NIH NCBC as well as publications that 
used the center but did not acknowledge support.  These two lists of 
publications will be presented separately.

We encourage inquiries concerning this RFA and welcome the opportunity 
to answer questions from potential applicants.  Inquiries may fall into 
three areas:  scientific/research, peer review, and financial or grants 
management issues:

o Direct your questions about scientific/research issues to:

Greg Farber, Ph.D.
Division of Biomedical Technology
National Center for Research Resources
6701 Democracy Boulevard, Room 960
Bethesda, MD  20892-4874
Telephone:  (301) 435-0778
FAX:  301-480-3659

Peter Good, Ph.D.
National Human Genome Research Institute
Building 31, Room b2b07
31 Center Drive, MSC 2152
Bethesda, MD 20892-2152
Telephone:  (301) 435-5796
FAX:  301-480-2770

Eric Jakobsson, Ph.D.
National Institute of General Medical Sciences
Building 45, Room 2AS55H
45 Center Drive MSC6200
Bethesda, MD   20892-6200
Telephone:  301-594-5236

Peter Lyster, Ph.D.
National Institute for Biomedical Imaging and Bioengineering
6707 Democracy Boulevard
Bethesda, MD 20892-5469
Telephone: 301-402-1337 

Milton Corn, M.D.
National Library of Medicine
6705 Rockledge Drive
Building 1  Suite 301
Bethesda, MD 20892
Telephone: 301-496-4621

o Direct your questions about peer review issues to:

Donald Schneider, Ph.D.
Center for Scientific Review
National Institutes of Health
6701 Rockledge Drive
Bethesda, MD  20892-7806
Telephone:  (301) 435-1727
FAX:  (301) 480-1988

o Direct your questions about financial or grants management matters 

Ms. Sheryl Lane
Office of Grants Management
National Center for Research Resources
6701 Democracy Boulevard, Room 1044
Bethesda, MD  20892-4874
Telephone:  (301) 435-0846
FAX:  301-480-3777

Ms. Linda Roberts
Grants Management
45 Center Drive, MSC 6200
Bethesda, MD  20892-6200 
Phone: (301) 594-5141
Fax: (301) 480-2554
Mr. Dwight Mowery 
National Library of Medicine
6705 Rockledge Drive
Building 1  Suite 301
Bethesda, MD 20892
Telephone: 301-496-4221

Prospective applicants should submit a letter of intent that includes 
the following information:

o Descriptive title of the proposed research
o Name, address, and telephone number of the Principal Investigator
o Names of other key personnel including those involved with the 
Driving Biological Projects
o Participating institutions
o Number and title of this RFA

The letter of intent (and the subsequent proposal itself) should NOT 
include names of potential members of the proposed center's External 
Advisory Committee.

Although a letter of intent is not required, is not binding, and does 
not enter into the review of a subsequent application, the information 
that it contains allows CSR staff to estimate the potential review 
workload and plan the review.

The letter of intent is to be sent by the date listed at the beginning 
of this document.  The letter of intent should be sent to:

Mr. Kevin Lauderdale
Center for Bioinformatics and Computational Biology
National Institute of General Medical Sciences
45 Center Drive
Building 45, Room 2AS55D, MSC 6200
Bethesda, MD  20892-6200
Telephone:  301-451-6446
FAX:  301-480-2802


Applications must be prepared using the PHS 398 research grant 
application instructions and forms (rev. 5/2001). Applications must 
have a DUN and Bradstreet (D&B) Data Universal Numbering System (DUNS) 
number as the Universal Identifier when applying for Federal grants or 
cooperative agreements. The DUNS number can be obtained by calling 
(866) 705-5711 or through the web site at The DUNS number should be entered on 
line 11 of the face page of the PHS 398 form. The PHS 398 document is 
available at in 
an interactive format.  For further assistance contact GrantsInfo, 
Telephone (301) 710-0267, Email:

The U54 center will be required to have seven cores:  (1) conducting 
core research in computational science, (2) conducting core research 
applying computing to biomedical and behavioral problems, (3) 
establishing Driving Biological Projects to allow biomedical and 
behavioral researchers to interact with and drive research in the NIH 
NCBC, (4) providing infrastructure (hardware, software, and personnel 
as appropriate) to serve the needs of the broad community of biomedical 
researchers, (5) enhancing the training for a new field of biomedical 
researchers in appropriate computational tools and techniques, (6) 
disseminating newly developed tools and techniques to the broader 
biomedical research community, and (7) providing an administrative core 
to ensure that these large centers achieve their goals within the 5 to 
10 year funding lifetime of the center.  

It is recognized that the proposals in response to this RFA will be 
longer and more complex than many other NIH proposals.  In order to 
ensure effective review, the Research plan should be divided into 
sections according to the above-defined cores, and separate page limits 
should be observed for each section.

For Core 1 and Core 2, the computer science and computational science 
underlying the work of the proposed NCBC, the combined total page limit 
is 140 pages. 

For Core 3, the descriptions of the Driving Biological Projects, the 
total page limit is 25 pages per DBP.  Since 2-4 DBPs are required, the 
page limits for this section are 50-100 pages.

For Core 4, establishing and maintaining an infrastructure for enabling 
the national community to access and utilize the tools created by the 
proposed NIH NCBC, the page limit is 20 pages.

For Core 5, the education and training plan of the proposed NIH NCBC, 
the page limit is 20 pages.

For Core 6, the plan to disseminate software, data, and new discoveries 
to the national community, the page limit is 20 pages.

For Core 7, the management plan for the proposed NIH NCBC, the page 
limit is 20 pages.

Both reviewers and program staff appreciate brevity and clarity in the 
application.  Required information, in addition to that requested in 
the Form PHS 398 instructions, is listed below, by section.  

Form Pages 4-5: The budget should be completed as described in the 
instruction sheet for Application for a Public Health Service Grant 
(Form PHS 398).  Form Pages 4 (Detailed Budget) and 5 (Budget for 
Entire Proposed Project Period) should be provided for each of cores 1, 
2, 4, 5, 6, and 7.  Form Pages 4 and 5 should also be provided for each 
of the DBPs in core 3.  Each budget page should be clearly labeled.   

A combined total budget for the entire center should also be prepared 
using Form Pages 5.  This budget justification should include the 
justification for key personnel. As part of the justification, the 
percent effort that all staff spend on each core should be specified.  
For example, a particular postdoctoral fellow might spend 75% effort on 
core 1 and 25% effort on one DBP in core 3.  The PI for the project 
must devote at least 25% of his effort to the NIH NCBC.

A justification should be supplied for equipment over $25,000 requested 
for the NIH NCBC.  Details of the physical location for such equipment 
should be provided.  Similar existing equipment should also be 
described, and the need for the new equipment justified.

Form Pages 4 and 5 should be provided for any sub-contractual or 
consortium arrangements.  A detailed budget justification should also 
be provided for such arrangements.  Use continuation pages as needed. 

Section 9, Research Plan D:  Each of the seven cores should be 
described.  It will be best if the applicant uses separate headings for 
each of these cores.  Cores 1 (conducting core research in computing), 
2 (conducting core research applying computing to biomedical problems), 
and 3 (establishing Driving Biological Projects) should be broken into 
appropriate subheadings.

When developing the proposal, the applicant should be aware of the 
following points.

The annual progress report for the U54 award will use the standard 2590 
form as well as supplementary information that will be more extensive.  
Additional information in the progress report will include both the 
progress made in the center as well as the relationship between the 
center and collaborators.  Details of the U54 progress report are 
spelled out in the notice of grant award and in the Terms and 
Conditions section of this RFA.  Applications for U54 centers should 
contain appropriate personnel to collect the needed information and to 
prepare this progress report.

Because of the complexity of the NIH NCBC, program staff from NIH will 
likely visit periodically to conduct administrative site visits.  U54 
centers should be prepared for annual site visits and should budget 
appropriately (including travel for collaborators and other necessary 

Each center application is expected to include a well-developed 
management plan.  If appropriate, the management plan should include 
provisions for teleconferencing or videoconferencing.

The complexity of these centers suggests that it may be necessary to 
request a project manager.  U54 centers should budget appropriately for 
this manager.  One of the review criteria for these centers will be the 
qualifications of this project manager as well as whether the 
institution has an appropriate career pathway for this individual.  
Because of their important role, it is recommended that a project 
manager be listed as one of the key personnel.

Plans for the development of resources for use by the biomedical 
community should have appropriate timelines and mileposts.  Software 
development should include plans and timelines for alpha testing, beta 
testing, production release, interface development, bug reporting, 
integration with other codes, extension to multiple platforms, etc.  

A software dissemination plan must be included in the application.  
There is no prescribed single license for software produced in this 
project.  However NIH does have goals for software dissemination, and 
reviewers will be instructed to evaluate the dissemination plan 
relative to these goals:

1) The software should be freely available to biomedical researchers 
and educators in the non-profit sector, such as institutions of 
education, research institutes, and government laboratories.  

2) The terms of software availability should permit the 
commercialization of enhanced or customized versions of the software, 
or incorporation of the software or pieces of it into other software 

3) The terms of software availability should include the ability of 
researchers outside the center and its collaborating projects to modify 
the source code and to share modifications with other colleagues as 
well as with the center.  A center should take responsibility for 
creating the original and subsequent "official" versions of a piece of 
software, and should provide a plan to manage the dissemination or 
adoption of improvements or customizations of that software by others.  
This plan should include a method to distribute other user's 
contributions such as extensions, compatible modules, or plug-ins.  The 
application should include written statements from the officials of the 
applicant institutions responsible for intellectual property issues, to 
the effect that the institution supports and agrees to abide by the 
software dissemination plans put forth in the proposal. 

Data sharing will be as important as software sharing for many National 
Programs.  All awards made under this RFA are subject to the Final NIH 
Statement on Sharing Research Data 
USING THE RFA LABEL: The RFA label available in the PHS 398 (rev. 
5/2001) application form must be affixed to the bottom of the face page 
of the application.  Type the RFA number on the label.  Failure to use 
this label could result in delayed processing of the application such 
that it may not reach the review committee in time for review.  In 
addition, the RFA title and number must be typed on line 2 of the face 
page of the application form and the YES box must be marked. The RFA 
label is also available at:
SENDING AN APPLICATION TO THE NIH: Submit a signed, typewritten 
original of the application, including the Checklist, and five signed, 
photocopies and all appendix materials, in one package to:
Center For Scientific Review
National Institutes Of Health
6701 Rockledge Drive, Room 1040, MSC 7710
Bethesda, MD  20892-7710
Bethesda, MD  20817 (for express/courier service)
APPLICATION PROCESSING: Applications must be received on or before the 
application receipt date listed in the heading of this RFA.  If an 
application is received after that date, it will be returned to the 
applicant without review. 

Although there is no immediate acknowledgement of the receipt of an 
application, applicants are generally notified of the review and 
funding assignment within 8 weeks.
The Center for Scientific Review (CSR) will not accept any application 
in response to this RFA that is essentially the same as one currently 
pending initial review, unless the applicant withdraws the pending 
application.  However, when a previously unfunded application, 
originally submitted as an investigator-initiated application, is to be 
submitted in response to an RFA, it is to be prepared as a NEW 
application.  That is the application for the RFA must not include an 
Introduction describing the changes and improvements made, and the text 
must not be marked to indicate the changes from the previous unfunded 
version of the application.  

Upon receipt, applications will be reviewed for completeness by the CSR 
and responsiveness by program staff in the primary IC.  Incomplete or 
non-responsive applications will not be reviewed.  

Applications that are complete and responsive to the RFA will be 
evaluated for scientific and technical merit by an appropriate peer 
review group convened by CSR in accordance with the review criteria 
stated below.  As part of the initial merit review, all applications 

o Undergo a process in which only those applications deemed to have the 
highest scientific merit, generally the top half of the applications 
under review, will be discussed and assigned a priority score
o Receive a written critique 
o Receive a second level review by an appropriate national advisory 
council or board.

The goals of NIH-supported research are to advance our understanding of 
biological systems, improve the control of disease, and enhance health.  
In the written comments, reviewers will be asked to evaluate the 
application in order to judge the likelihood that the proposed research 
will have a substantial impact on the pursuit of these goals.  The 
scientific review group will address and consider each of the following 
criteria in assigning the application's overall score, weighting them 
as appropriate for each application. 

o Significance 
o Approach 
o Innovation
o Investigator
o Environment
The application does not need to be strong in all categories to be 
judged likely to have major scientific impact and thus deserve a high 
priority score.  For example, an investigator may propose to carry out 
important work that by its nature is not innovative but is essential to 
move a field forward.

SIGNIFICANCE: Does this study address an important problem? If the aims 
of the application are achieved, how will scientific knowledge be 
advanced? What will be the effect of these studies on the concepts or 
methods that drive this field?

APPROACH: Are the conceptual framework, design, methods, and analyses 
adequately developed, well-integrated, and appropriate to the aims of 
the project? Does the applicant acknowledge potential problem areas and 
consider alternative tactics?

INNOVATION: Does the project employ novel concepts, approaches or 
methods? Are the aims original and innovative? Does the project 
challenge existing paradigms or develop new methodologies or 

INVESTIGATOR: Is the investigator appropriately trained and well suited 
to carry out this work? Is the work proposed appropriate to the 
experience level of the principal investigator and other researchers 
(if any)?

ENVIRONMENT: Does the scientific environment in which the work will be 
done contribute to the probability of success? Do the proposed 
experiments take advantage of unique features of the scientific 
environment or employ useful collaborative arrangements? Is there 
evidence of institutional support?  

ADDITIONAL REVIEW CRITERIA: In addition to the above criteria, the 
following items will be considered in the determination of scientific 
merit and the priority score:
CORES 1-3: Will the work proposed in these cores help establish an 
integrated national biomedical computing environment?  Is the proposed 
work essential to establishing this environment?

CORE 3:  Do the investigators have appropriate plans to obtain support 
for the DBPs after their support from the NIH NCBC has terminated? 

CORE 4:  Are the infrastructure requests adequate to meet the demands 
that are likely to come from biomedical or behavioral researchers?

CORES 5 and 6:  Will the proposed training and dissemination tools help 
create a new group of multi-disciplinary or interdisciplinary 

CORE 7:  The reviewers will be asked to address the proposed management 
of the project.  Will the proposed management structure allow the NIH 
NCBC to achieve its goals?  Does the institution have an appropriate 
career path for the project manager?  Is the mechanism to terminate old 
DBPs and choose new ones adequate?  Will the plans to incorporate 
individual investigator awards work?

Reviewers should consider all seven components of the project as 
important, even if a particular component represents only a relatively 
small part of the budget.  For example outreach and training, while not 
as costly as the core development of the computational environment, is 
considered to be critically important for the NIH NCBC to have the 
appropriate impact on biomedical research.    

SOFTWARE AVAILABILITY:  Does the plan for distributing the software 
reasonable allow wide and easy access?  Are any fee structures 

DATA SHARING:  The adequacy of the proposed plan to share data 
including the use of appropriate data standards.
human subjects and protections from research risk relating to their 
participation in the proposed research will be assessed. (See criteria 
included in the section on Federal Citations, below).
of plans to include subjects from both genders, all racial and ethnic 
groups (and subgroups), and children as appropriate for the scientific 
goals of the research.  Plans for the recruitment and retention of 
subjects will also be evaluated. (See Inclusion Criteria in the 
sections on Federal Citations, below).

are to be used in the project, the five items described under Section f 
of the PHS 398 research grant application instructions (rev. 5/2001) 
will be assessed.  


BUDGET:  The reasonableness of the proposed budget and the requested 
period of support in relation to the proposed research.


Letter of Intent Receipt Date:  December 29, 2003
Application Receipt Date:  January 23, 2004
Peer Review Date:  June 2004
Council Review:  September 2004
Earliest Anticipated Start Date:  September 15, 2004


Award criteria that will be used to make award decisions include:

o Scientific merit (as determined by peer review)
o Availability of funds
o Programmatic priorities

HUMAN SUBJECTS PROTECTION: Federal regulations (45CFR46) require that 
applications and proposals involving human subjects must be evaluated 
with reference to the risks to the subjects, the adequacy of protection 
against these risks, the potential benefits of the research to the 
subjects and others, and the importance of the knowledge gained or to 
be gained.

DATA AND SAFETY MONITORING PLAN: Data and safety monitoring is required 
for all types of clinical trials, including physiologic, toxicity, and 
dose-finding studies (phase I); efficacy studies (phase II); efficacy, 
effectiveness and comparative trials (phase III).  The establishment of 
data and safety monitoring boards (DSMBs) is required for multi-site 
clinical trials involving interventions that entail potential risk to 
the participants. (NIH Policy for Data and Safety Monitoring, NIH Guide 
for Grants and Contracts, June 12, 1998:

SHARING RESEARCH DATA: Starting with the October 1, 2003 receipt date, 
investigators submitting an NIH application seeking more than $500,000 
or more in direct costs in any single year are expected to include a 
plan for data sharing or state why this is not possible.  Investigators should 
seek guidance from their institutions, on issues related to 
institutional policies, local IRB rules, as well as local, state and 
Federal laws and regulations, including the Privacy Rule.

policy of the NIH that women and members of minority groups and their 
sub-populations must be included in all NIH-supported clinical research 
projects unless a clear and compelling justification is provided 
indicating that inclusion is inappropriate with respect to the health 
of the subjects or the purpose of the research. This policy results 
from the NIH Revitalization Act of 1993 (Section 492B of Public Law 

All investigators proposing clinical research should read the "NIH 
Guidelines for Inclusion of Women and Minorities as Subjects in 
Clinical Research - Amended, October, 2001," published in the NIH Guide 
for Grants and Contracts on October 9, 2001 
a complete copy of the updated Guidelines are available at
The amended policy incorporates: the use of an NIH definition 
of clinical research; updated racial and ethnic categories in 
compliance with the new OMB standards; clarification of language 
governing NIH-defined Phase III clinical trials consistent with the new 
PHS Form 398; and updated roles and responsibilities of NIH staff and 
the extramural community.  The policy continues to require for all NIH-
defined Phase III clinical trials that: a) all applications or 
applications and/or protocols must provide a description of plans to 
conduct analyses, as appropriate, to address differences by sex/gender 
and/or racial/ethnic groups, including subgroups if applicable; and b) 
investigators must report annual accrual and progress in conducting 
analyses, as appropriate, by sex/gender and/or racial/ethnic group 

SUBJECTS: The NIH maintains a policy that children (i.e., individuals 
under the age of 21) must be included in all human subjects research, 
conducted or supported by the NIH, unless there are scientific and 
ethical reasons not to include them. This policy applies to all initial 
(Type 1) applications submitted for receipt dates after October 1, 

All investigators proposing research involving human subjects should 
read the "NIH Policy and Guidelines" on the inclusion of children as 
participants in research involving human subjects that is available at

policy requires education on the protection of human subject 
participants for all investigators submitting NIH applications for 
research involving human subjects.  You will find this policy 
announcement in the NIH Guide for Grants and Contracts Announcement, 
dated June 5, 2000, at

HUMAN EMBRYONIC STEM CELLS (hESC): Criteria for federal funding of 
research on hESCs can be found at 
and at  
Only research using hESC lines that are registered in the 
NIH Human Embryonic Stem Cell Registry will be eligible for Federal 
funding (see   It is the responsibility of the 
applicant to provide, in the project description and elsewhere in the 
application as appropriate, the official NIH identifier(s)for the hESC 
line(s)to be used in the proposed research.  Applications that do not 
provide this information will be returned without review. 

The Office of Management and Budget (OMB) Circular A-110 has been 
revised to provide public access to research data through the Freedom 
of Information Act (FOIA) under some circumstances.  Data that are (1) 
first produced in a project that is supported in whole or in part with 
Federal funds and (2) cited publicly and officially by a Federal agency 
in support of an action that has the force and effect of law (i.e., a 
regulation) may be accessed through FOIA.  It is important for 
applicants to understand the basic scope of this amendment.  NIH has 
provided guidance at

Applicants may wish to place data collected under this PA in a public 
archive, which can provide protections for the data and manage the 
distribution for an indefinite period of time.  If so, the application 
should include a description of the archiving plan in the study design 
and include information about this in the budget justification section 
of the application. In addition, applicants should think about how to 
structure informed consent statements and other human subjects 
procedures given the potential for wider use of data collected under 
this award.

The Department of Health and Human Services (DHHS) issued final 
modification to the "Standards for Privacy of Individually Identifiable 
Health Information", the "Privacy Rule," on August 14, 2002.  The 
Privacy Rule is a federal regulation under the Health Insurance 
Portability and Accountability Act (HIPAA) of 1996 that governs the 
protection of individually identifiable health information, and is 
administered and enforced by the DHHS Office for Civil Rights (OCR). 
Those who must comply with the Privacy Rule (classified under the Rule 
as "covered entities") must do so by April 14, 2003  (with the 
exception of small health plans which have an extra year to comply).  

Decisions about applicability and implementation of the Privacy Rule 
reside with the researcher and his/her institution. The OCR website 
( provides information on the Privacy Rule, 
including a complete Regulation Text and a set of decision tools on "Am 
I a covered entity?"  Information on the impact of the HIPAA Privacy 
Rule on NIH processes involving the review, funding, and progress 
monitoring of grants, cooperative agreements, and research contracts 
can be found at

applications for NIH funding must be self-contained within specified 
page limitations. Unless otherwise specified in an NIH solicitation, 
Internet addresses (URLs) should not be used to provide information 
necessary to the review because reviewers are under no obligation to 
view the Internet sites.   Furthermore, we caution reviewers that their 
anonymity may be compromised when they directly access an Internet 

HEALTHY PEOPLE 2010: The Public Health Service (PHS) is committed to 
achieving the health promotion and disease prevention objectives of 
"Healthy People 2010," a PHS-led national activity for setting priority 
areas. This RFA is related to one or more of the priority areas. 
Potential applicants may obtain a copy of "Healthy People 2010" at

AUTHORITY AND REGULATIONS: This program is described in the Catalog of 
Federal Domestic Assistance at and is not subject 
to the intergovernmental review requirements of Executive Order 12372 
or Health Systems Agency review.  Awards are made under the 
authorization of Sections 301 and 405 of the Public Health Service Act 
as amended (42 USC 241 and 284) and under Federal Regulations 42 CFR 52 
and 45 CFR Parts 74 and 92. All awards are subject to the terms and 
conditions, cost principles, and other considerations described in the 
NIH Grants Policy Statement.  The NIH Grants Policy Statement can be 
found at

The PHS strongly encourages all grant recipients to provide a smoke-
free workplace and discourage the use of all tobacco products.  In 
addition, Public Law 103-227, the Pro-Children Act of 1994, prohibits 
smoking in certain facilities (or in some cases, any portion of a 
facility) in which regular or routine education, library, day care, 
health care, or early childhood development services are provided to 
children.  This is consistent with the PHS mission to protect and 
advance the physical and mental health of the American people.

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