CONTINUED DEVELOPMENT AND MAINTENANCE OF BIOINFORMATICS AND COMPUTATIONAL 
BIOLOGY SOFTWARE 

RELEASE DATE:  July 26, 2002

PA NUMBER:  PA-02-141 
(This PA has been reissued, see PAR-05-057. Also see addendum NOT-RR-04-007, NOT-LM-04-009, and NOT-CA-03-020)

EXPIRATION DATE: February 25, 2005

National Center for Research Resources (NCRR)
 (http://www.ncrr.nih.gov)
National Institute on Drug Abuse (NIDA)
 (http://www.nida.nih.gov/)
National Institute of Neurological Disorders and Stroke (NINDS)
 (http://www.ninds.nih.gov/)
National Institute of Mental Health (NIMH)
 (http://www.nimh.nih.gov/)
National Human Genome Research Institute (NHGRI)
 (http://www.nhgri.nih.gov/) 
National Institute of General Medical Sciences (NIGMS)
 (http://www.nigms.nih.gov/)
National Eye Institute (NEI)
 (http://www.nei.nih.gov)
National Institute of Biomedical Imaging and Bioengineering (NIBIB)
 (http://www.nibib.nih.gov/)
National Library of Medicine (NLM)
  (http://www.nlm.nih.gov/)
National Institute on Alcohol Abuse and Alcoholism (NIAAA)
 (http://www.niaaa.nih.gov/)

THIS PA CONTAINS THE FOLLOWING INFORMATION

o Purpose of the PA
o Research Objectives
o Mechanism(s) of Support 
o Eligible Institutions
o Individuals Eligible to Become Principal Investigators
o Special Requirements
o Where to Send Inquiries
o Submitting an Application
o Peer Review Process
o Review Criteria
o Award Criteria
o Required Federal Citations

PURPOSE OF THIS PA 

Biomedical research laboratories occasionally undertake a software 
development project to solve a problem the laboratory faces. These software 
packages sometimes evolve into a well-designed system that can be easily 
extended and that is useful to a much broader community other than the 
members of the originating laboratory. The goal of this PA is to support the 
continued development, maintenance, testing and evaluation of existing 
software. The proposed work should apply best practices and proven methods 
for software design, construction and implementation to extend the 
applicability of existing bioinformatics/computational biology software to a 
broader biomedical research community.

RESEARCH OBJECTIVES

This initiative is inspired by the parallel achievements and increased 
interdependence of the biological and computing sciences. These circumstances 
offer an unprecedented opportunity for sophisticated approaches to computer-
enabled life sciences research. This initiative also recognizes the benefits 
to be realized from skillful and timely action to assure the availability and 
usefulness of existing bioinformatics/computational biology software, as well 
as the costs associated with inaction.

This initiative pertains to bioinformatics/computational biology software 
that is recognized to perform an important function in furthering biomedical 
research. The software should perform reliably and precisely according to the 
computing demands of end-users. The algorithms that are employed by the 
software should be well documented, as should be the underlying assumptions 
of these algorithms to prevent potential misuse.

There are several desirable aspects of development and maintenance of 
bioinformatics/computational biology software. Contemporary software must be 
fully documented and easy to modify and extend. Defects that arise in any 
software must be correctable with limited effort. As the needs of a community 
of users change, the software that supports their research efforts must be 
easily modified. "Reparability" and "evolvability" are particularly important 
because the scientific discovery process is open-ended and ever-changing. 
Interoperability and portability are also a major concern. Where appropriate, 
software applications should operate on a variety of platforms employing 
different operating systems. 

Awards made under this PA will support continued software development, 
evaluation, and testing of pre-existing bioinformatics/computational biology 
software for data management and analysis, computational biology, and 
modeling and simulation. Support will be provided for porting software to new 
platforms and operating systems as well as the costs associated with 
maintaining the software as existing operating systems change. The proposed 
software should not substantially duplicate another software package that is 
already in wide use.

MECHANISM(S) OF SUPPORT 

This PA will use the NIH R01 award mechanism as well as competitive 
supplements to existing R01, R33, P01, P41, P50 and P60 grants that have 
already been awarded by one of the participating Institutes or Centers. 
Applications for competitive supplements cannot extend beyond the parent 
project period of performance and the principal investigator must be the 
same. As an applicant, you will be solely responsible for planning, 
directing, and executing the proposed project. 

This PA uses just-in-time concepts. It also uses the modular and non-modular  
budgeting format for R01s. (see 
http://grants.nih.gov/grants/funding/modular/modular.htm). Specifically, if 
you are submitting an application with direct costs in each year of $250,000 
or less, use the modular format.  Otherwise, use the standard PHS 398 
instructions for detailed budgets.

ELIGIBLE INSTITUTIONS 

You may submit (an) application(s) if your institution has any of the 
following characteristics:
	
o For-profit or non-profit organizations 
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 Domestic or foreign

INDIVIDUALS ELIGIBLE TO BECOME PRINCIPAL INVESTIGATORS

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.  

SPECIAL REQUIREMENTS

Open-source or conditional open-source software is strongly encouraged. The 
software must be in a form such that if the original developer or team loses 
interest in the software another individual or team can make use of previous 
work to continue development and maintenance. 

WHERE TO SEND INQUIRIES

We encourage your inquiries concerning this PA 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:

Dr. Bret Peterson
National Center for Research Resources
One Rockledge Centre, Room 6152
6705 Rockledge Drive MSC 7965
Bethesda, MD 20892-7965
TEL: (301) 435-0758
FAX: (301) 480-3659
EMAIL: [email protected] 

Dr. Yuan Liu
National Institute of Neurological Disorders and Stroke (NINDS)
Neuroscience Building, Room 2110
6001 Executive Boulevard, MSC 9523
Bethesda, MD 20892-9523
TEL: (301) 496-1917 
FAX: (301) 480-2424
EMAIL: [email protected]

Dr. Karen Skinner 
Deputy Director for Science and Technology Development 
Division of Neuroscience and Behavior Research 
National Institute on Drug Abuse/NIH 
Room 4255 
6001 Executive Boulevard 
Bethesda, Maryland 20892-9651 
TEL: (301)435-0886
FAX: (301) 594-6043
EMAIL: [email protected]

Dr. Michael Huerta
Division of Neuroscience and Basic Behavioral Science
National Institute of Mental Health
6001 Executive Blvd. Room 7202, MSC 9645
Bethesda, MD  20892-9645
Rockville, MD  20852 for express or courier service
TEL:  (301) 443-3563  
FAX:  (301) 443-1731
EMAIL: [email protected]

Dr. James C. Cassatt
Division of Cell Biology and Biophysics
National Institute of General Medical Sciences
45 Center Drive, MSC 6200
Bethesda, MD  20892-6200
TEL:  (301) 594-0828
FAX:  (301) 480-2004
EMAIL: [email protected]

Dr. Richard E. Swaja
National Institute for Biomedical Imaging and Bioengineering
6707 Democracy Boulevard - Suite 900
Bethesda, MD  20892-5469
TEL:  301-451-4779
FAX:  301-480-4973
EMAIL: [email protected]

Dr. Charles Freidman
Extramural Programs
National Library of Medicine
Rockledge 1, Suite 301, 6705 Rockledge Drive
Bethesda, MD  20892
TEL:  (301) 594-4882
FAX:  (301) 402-2952
EMAIL: [email protected]

Dr. Peter Good
National Human Genome Research Institute 
Building 31, Room B2B07
Bethesda, MD 20892-2033
TEL: (301) 435-5796
FAX: (301) 480-2770
EMAIL: [email protected]


Dr. Ellen Liberman
National Eye Institute
Executive Plaza South, Suite 350
6120 Executive Blvd., MSC 7164
Bethesda, MD 20892-7164
TEL: (301) 451-2020
FAX:  (301) 502-0528
EMAIL: [email protected]

Dr. Antonio Norhona
National Institue on Alcohol Abuse and Alcoholism
6000 Executive Blvd
Bethesda, MD  20892-7003
TEL: (301) 443-7722
FAX: (301) 594-0673
EMAIL: [email protected]
 
o Direct your questions about peer review issues to:

Donald Schneider, Ph.D.
Division of Molecular and Cellular Mechanisms
Center for Scientific Review
Rockledge 2/RM 4172, MSC 7806            
Bethesda, MD  20892-7806
TEL:  (301) 435-1727
FAX:  (301) 480-2327 
EMAIL:  [email protected]

o Direct your questions about financial or grants management matters to:

Mary Niemiec
Office of Grants Management
National Center for Research Resources
One Rockledge Centre, Room 6086
6705 Rockledge Drive MSC 7965
Bethesda, MD 20892-7965
TEL: (301) 435-0842
FAX: (301) 480-3777
EMAIL: [email protected]

Christina Zimmerman
National Institute of Neurological Disorders and Stroke (NINDS)
Neuroscience Building, Room 3273
6001 Executive Boulevard, MSC 9523
Bethesda, MD 20892-9523
TEL: (301) 496-3107
FAX: (301) 402-0219 (Fax)
EMAIL: [email protected]

Gary Fleming, J.D., M.A.
Grants Management Branch
National Institute on Drug Abuse
6001 Executive Boulevard
Bethesda, MD  20892-9541
TEL:  (301) 443-6710
EMAIL:  [email protected]

Joseph Ellis 
Grants Administration Branch 
National Institute of General Medical Sciences, NIH 
Bldg. 45, Room 2AN-32C
Bethesda, MD 20892-6200 
TEL: (301) 594-5135
FAX: (301) 480-1969
EMAIL: [email protected]

Carol J. Robinson
Grants Management Branch
National Institute of Mental Health
6001 Executive Boulevard, Room 6118 MSC 9605
Bethesda, MD 20892-9605
TEL:  (301) 443-3858
FAX:  (301) 443-6885
EMAIL:  Diana [email protected]

Annette Hanopole
Grants Management Officer
National Institute for Biomedical Imaging and Bioengineering
6706 Democracy Boulevard - Suite 900
Bethesda, MD  20892-5469
TEL:  301-451-4789
FAX:  301-480-4974
EMAIL:  [email protected]

Dwight Mowery
Extramural Programs
National Library of Medicine
Rockledge 1, Suite 301, 6705 Rockledge Drive
Bethesda, MD  20892
TEL: (301) 496-4221
FAX: (301) 402-0421
EMAIL: [email protected]

Ms. Jean Cahill 
Grants Administration Branch 
National Human Genome Research Institute 
Building 31, Room B2B34
Bethesda, MD 20892-2031
TEL: (301) 402-0733 
FAX: (301) 402-1951 
EMAIL: [email protected]

William Darby.
National Eye Institute
Executive Plaza South, Suite 350
6120 Executive Blvd., MSC 7164
Bethesda, MD 20892-7164
TEL: (301) 451-2020
FAX: (301) 502-0528
EMAIL: [email protected]

Judy Simons
Grants Management Officer
National Institute on Alcohol Abuse and Alcoholism
6000 Executive Blvd., Suite 504
Bethesda, MD 20892-7003
TEL: (301) 443-4704
FAX: (301) 443-3891
EMAIL: [email protected]

SUBMITTING AN APPLICATION

Applications must be prepared using the PHS 398 research grant application 
instructions and forms (rev. 5/2001). The PHS 398 is available at 
http://grants.nih.gov/grants/funding/phs398/phs398.html in an interactive 
format. For further assistance contact GrantsInfo, Telephone (301) 710-0267, 
Email: [email protected].

APPLICATION RECEIPT DATES: Applications submitted in response to this program 
announcement will be accepted at the standard application deadlines, which 
are available at http://grants.nih.gov/grants/dates.htm. Application 
deadlines are also indicated in the PHS 398 application kit.

SPECIFIC INSTRUCTIONS FOR MODULAR GRANT APPLICATIONS: Applications requesting 
up to $250,000 per year in direct costs must be submitted in a modular grant 
format. The modular grant format simplifies the preparation of the budget in 
these applications by limiting the level of budgetary detail. Applicants 
request direct costs in $25,000 modules. Section C of the research grant 
application instructions for the PHS 398 (rev. 5/2001) at 
http://grants.nih.gov/grants/funding/phs398/phs398.html includes step-by-step 
guidance for preparing modular grants. Additional information on modular 
grants is available at 
http://grants.nih.gov/grants/funding/modular/modular.htm. Modular budgets are 
not permitted for supplemental applications that increase the total annual 
direct cost of R01 or R33 grants to more than $250,000 or for all supplements 
to P01, P41, P50 and P60 grants.

SPECIFIC INSTRUCTIONS FOR APPLICATIONS REQUESTING $500,000 OR MORE PER YEAR: 
Applications requesting $500,000 or more in direct costs for any year must 
include a cover letter identifying the NIH staff member within one of NIH 
institutes or centers who has agreed to accept assignment of the application.  

Applicants requesting more than $500,000 must carry out the following steps:
	
1) Contact the IC program staff at least 6 weeks before submitting the 
application, i.e., as you are developing plans for the study; 

2) Obtain agreement from the IC staff that the IC will accept your 
application for consideration for award; and,
 
3) Identify, in a cover letter sent with the application, the staff member 
and IC who agreed to accept assignment of the application. 

This policy applies to all investigator-initiated new (type 1), competing 
continuation (type 2), competing supplement, or any amended or revised 
version of these grant application types. Additional information on this 
policy is available in the NIH Guide for Grants and Contracts, October 19, 
2001 at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-02-004.html. 

SENDING AN APPLICATION TO THE NIH: Submit a signed, typewritten original of 
the application, including the checklist, and five signed photocopies 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 by or mailed on or 
before the receipt dates described at 
http://grants.nih.gov/grants/funding/submissionschedule.htm. The CSR will not 
accept any application in response to this PA that is essentially the same as 
one currently pending initial review unless the applicant withdraws the 
pending application. The CSR will not accept any application that is 
essentially the same as one already reviewed. This does not preclude the 
submission of a substantial revision of an application already reviewed, but 
such application must include an Introduction addressing the previous 
critique.

PEER REVIEW PROCESS

Applications submitted for this PA will be assigned on the basis of 
established PHS referral guidelines. An appropriate scientific review group 
convened by the Center for Scientific Review in accordance with the standard 
NIH peer review procedures (http://www.csr.nih.gov/refrev.htm) will evaluate 
applications for scientific and technical merit. 

As part of the initial merit review, all applications will:

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

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 discuss the following 
aspects of your application in order to judge the likelihood that the 
proposed research will have a substantial impact on the pursuit of these 
goals: 

o Significance 
o Approach 
o Investigator
o Environment
 
The scientific review group will address and consider each of these criteria 
in assigning your application's overall score, weighting them as appropriate 
for each application. Your 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, you may propose to carry out 
important work that by its nature is not innovative but is essential to move 
a field forward.

SIGNIFICANCE: Does the study address an important problem?  If the aims of 
the project are achieved, how will they advance the field?  How will the 
scientific community benefit from successful completion of the proposed 
project?  How broad will its impact be?  Will it be more effective/useful 
than competing approaches?
APPROACH:  Are the conceptual framework, design, methods, and analyses 
adequately developed, well integrated and appropriate to the aims of the 
project?  Are potential problems considered and alternatives discussed?  Is 
the approach to software design appropriate? Is the proposed software 
development process appropriate and likely to succeed?  Are plans to document 
the software appropriate?  Are the plans to maintain the software 
appropriate?  Have scalability, extensibility, interoperability, testing and 
evaluation been appropriately addressed?  Are plans to make the software 
available to the scientific community appropriate?  Are plans proposed for 
incremental improvement of the software based on experience with its use?
INVESTIGATOR:  Do the principal investigator and the assembled team have the 
training and experience needed to carry out the proposed project?
ENVIRONMENT: Does the scientific environment contribute to the probability of 
success? Does the proposed work take advantage of the strengths of the local 
environment?

AWARD CRITERIA

Applications submitted in response to a PA will compete for available funds 
with all other recommended applications. The following will be considered in 
making funding decisions: 

o Scientific merit of the proposed project as determined by peer review
o Availability of funds 
o Relevance to program priorities

REQUIRED FEDERAL CITATIONS 

PUBLIC ACCESS TO RESEARCH DATA THROUGH THE FREEDOM OF INFORMATION ACT: 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 
http://grants.nih.gov/grants/policy/a110/a110_guidance_dec1999.htm.

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.

URLs IN NIH GRANT APPLICATIONS OR APPENDICES: All applications and proposals 
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 site.

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 PA 
is related to one or more of the priority areas. Potential applicants may 
obtain a copy of "Healthy People 2010" at http://www.health.gov/healthypeople.

AUTHORITY AND REGULATIONS: This program is described in the Catalog of 
Federal Domestic Assistance in the following citations and is not subject to 
the intergovernmental review requirements of Executive Order 12372 or Health 
Systems Agency review: Nos. 93.172, 93.242, 93.273, 93.279, 93.286, 93.371, 
93.821, 93.853, 93.855, 93.856, 93.859, 93.862, 93.867, and 93.879.  Awards 
are made under authorization of Sections 301 and 405 of the Public Health 
Service Act as amended (42 USC 241 and 284)and administered under NIH grants 
policies described at http://grants.nih.gov/grants/policy/policy.htm and 
under Federal Regulations 42 CFR 52 and 45 CFR Parts 74 and 92. 

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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