Part I Overview Information


Department of Health and Human Services

Participating Organizations
National Institutes of Health (NIH) (http://www.nih.gov)

Components of Participating Organizations
National Institute of General Medical Sciences (NIGMS) (http://www.nigms.nih.gov)

Title: Escherichia Coli K-12 Model Organism Resource (U24)

Announcement Type
This is a reissue of RFA-GM-06-001.

Request For Applications (RFA) Number: RFA-GM-09-010

Catalog of Federal Domestic Assistance Number(s)
93.859

Key Dates
Release Date: October 9, 2008
Letters of Intent Receipt Date: November 4, 2008
Application Receipt Date: December 4, 2008
Peer Review Date: March-April 2009
Council Review Date: May 2009
Earliest Anticipated Start Date: July 1, 2009
Additional Information To Be Available Date (Url Activation Date): N/A
Expiration Date: December 5, 2008

Due Dates for E.O. 12372  

Not Applicable

Additional Overview Content

Executive Summary

Table of Contents


Part I Overview Information

Part II Full Text of Announcement

Section I. Funding Opportunity Description
1. Research Objectives

Section II. Award Information
1. Mechanism(s) of Support
2. Funds Available

Section III. Eligibility Information
1. Eligible Applicants
    A. Eligible Institutions
    B. Eligible Individuals
2.Cost Sharing or Matching
3. Other - Special Eligibility Criteria

Section IV. Application and Submission Information
1. Address to Request Application Information
2. Content and Form of Application Submission
3. Submission Dates and Times
    A. Receipt, Review and Anticipated Start Dates
         1. Letter of Intent
    B. Sending an Application to the NIH
    C. Application Processing
   D.  Application Assignment
4. Intergovernmental Review
5. Funding Restrictions
6. Other Submission Requirements and Information

Section V. Application Review Information
1. Criteria
2. Review and Selection Process
    A. Additional Review Criteria
    B. Additional Review Considerations
    C. Resource Sharing Plan(s)
3. Anticipated Announcement and Award Dates

Section VI. Award Administration Information
1. Award Notices
2. Administrative and National Policy Requirements
     A. Cooperative Agreement Terms and Conditions of Award
         1. Principal Investigator Rights and Responsibilities
         2. NIH Responsibilities
         3. Collaborative Responsibilities
         4. Arbitration Process
3. Reporting

Section VII. Agency Contact(s)
1. Scientific/Research Contact(s)
2. Peer Review Contact(s)
3. Financial/ Grants Management Contact(s)

Section VIII. Other Information - Required Federal Citations

Part II - Full Text of Announcement


Section I. Funding Opportunity Description


1. Research Objectives

The objective of this FOA is the development of a central knowledge and data resource (henceforth referred to as the “K-12 Resource”) for Escherichia coli strain K-12, related strains, their phage, and mobile genetic elements (henceforth referred to as the “K-12 Group”).  The K-12 Resource will provide a unified, high quality, single point of access to the data, information, and software tools that have been developed over the past six decades on the K-12 Group and thus leverage the considerable investment of public and private research funds in this suite of model organisms.  In particular, the K-12 Resource will complement Federal programs to provide integrated databases of information on other microbes, including agents of disease and bioterrorism that are closely related to E. coli K-12.  It is expected that all microbial database efforts will benefit by transparent links to the data and computational tools that exist or will be constructed for the K-12 Resource.

The proposed K-12 Resource will develop a central knowledge and data resource through the following functionalities:

The K-12 Resource will have a steering committee as the main policy-making body.  The steering committee will include scientist administrators from the NIH and possibly other federal agencies and outside experts from the appropriate user groups.

The informatics needs of the relevant research communities can be expected to evolve as the science progresses.  The K-12 Resource is expected to have the flexibility to adapt to changing needs.

A transition plan must be provided to ensure that when the award terminates the resource will continue to be available to the community.  This plan should take into account the following possible options at the end of the term: 1) continued, but possibly reduced federal grant support; 2) no further Federal grant support.  

Background

More is known about Escherichia coli strain K-12, its closely related strains, relatives, and their phage, than any other group of organisms.  This knowledge has provided biomedical science much of its information on fundamental molecular biology, metabolic pathways, gene and enzyme regulation, and detailed biochemical and biophysical mechanistic understanding of macromolecules.  More recently, these studies have expanded to include computational modeling of the large-scale organization and dynamics of its component systems.  This wealth of historical and current information continues to provide the larger biomedical research community with a context in which to understand, through comparative studies, the functioning of other organisms, and bacteria in particular.

The research community has identified a pressing need to bring together the multiple sources of existing knowledge and rapidly accumulating genome-wide data and to make this information optimally usable.  For many model organism research communities, this need is fulfilled by community genome databases such as Saccharomyces Genome Database, WormBase, and FlyBase for the yeast, worm, and fly communities, respectively.  In March 2003, NIGMS organized a meeting of researchers with expertise and interest in E. coli K-12, as well as other microorganisms, and database experts to discuss the informatics needs of the K-12 Group. A subcommittee of this meeting composed a White Paper on these needs, with recommendations (URL: http://www.nigms.nih.gov/news/reports/ecoli.html).  In brief, the consensus was that although there are a number of databases that currently focus on or include E. coli K-12 data and bioinformatics tools, there are significant gaps in what they cover, they are generally not well integrated with one other, they are of variable quality and utility, and there is no single point of entry for users.  This subcommittee recommended the establishment of a resource that organizes and updates available information and presents it in a manner comparable to that of other model organism databases.  Although no particular structure for such a resource was defined by this subcommittee, the goal of the K-12 Resource proposed herein is to address the broad and specific issues raised by the White Paper.

In addition to serving the needs of the basic research communities, the K-12 Resource will provide, through its coordination with other microbial databases, important foundations of knowledge for pathogenic microbes, including those of concern for bioterrorism. Such coordination will insure that the Federal investment in microbial research is optimally leveraged to generate new knowledge and protect the public.

This FOA is a reissue of a similar initiative RFA-GM-06-001 http://grants.nih.gov/grants/guide/rfa-files/RFA-GM-06-001.html.  The outcome of that initiative was the awarding of a Cooperative Agreement research resource award U24 for the development of the EcoliHub project.  EcoliHub (http://www.ecolihub.org) uses Web services to make bidirectional connections to various existing K-12 resources.  In addition, EcoliHub provides several other services, including a K-12-focused web search of at least 19 K-12 databases, a workbench for analyzing K-12 information, software to analyze K-12 structural information (EcoliPredict), a community forum, and a wiki-based community information and annotation platform called EcoliWiki (http://www.ecoliwiki.net).  Applicants are strongly encouraged to become familiar with the various aspects of EcoliHub.  A competitive application will thoroughly describe how the applicant will either 1) build upon and expand the current EcoliHub system or 2) obtain current EcoliHub information and build a new system.  Both options must maximize the utility of K-12 information and describe plans for community participation.

Specific Research Objectives

There are four key areas that applications for the K-12 Resource must address:

Content

The K-12 Resource will include information specific to E. coli K-12 as well as relevant data from strains C and B, and information and data on the principal phage and plasmids that contribute to our basic knowledge of gene transactions, self-assembly processes, and bacterial functioning through the host-parasite relationship. The content must be current, documented, and reflect uncertainties. The application will provide a plan for:

Database and Web Interface Design

It is a goal of this solicitation that the Resource create a structure and management plan that will 1) integrate the most valuable sources; 2) provide complementary information and tools; 3) coordinate with related microbial database resources to maximize the utility of the information and services; and 4) provide for timely updates and quality assurance.  The final interface should present different forms and types of data in a convenient format for the user while preserving attribution of the data sources.  It is not the intention of this solicitation to prescribe any particular structure, but applications must reference the utility of the existing EcoliHub and its resident services.  Innovation in this difficult task is expected.

A key requirement for the K-12 Resource is that it serves a wide spectrum of users whose needs and expertise may be different.  This requirement must be satisfied with a website that emulates, or preferably improves upon, the best of existing model organism database interfaces.  Among the characteristics of such interfaces are: an intuitive, logical structure; simplicity in layout; clear paths to diverse datasets; and user-friendly analytic tools.  Where possible, the K-12 Resource should build upon tools developed by other related resources, e.g., the components developed for the Generic Model Organism Database Construction Set (http://www.gmod.org/).  In order to promote utility across other resources the database will coordinate with other related informatics resources to develop or adopt protocols for standardization of syntax, ontologies and vocabularies, and data representation.  It is essential that data can readily be shared.  Participation in the Gene Ontology (GO) consortium is required, and documented agreements for coordination with other U.S.-funded resources with which it overlaps or shares common spheres of data must be included.  In particular, there must be coordination with the National Institute of Allergy and Infectious Diseases (NIAID) ERIC program (http://www.niaid.nih.gov/dmid/genomes/brc/PDF/eric.pdf), which focuses on closely related organisms of pathological interest.

The application should explain how efficient and unencumbered access to the K-12 Resource will be maintained beyond the award term.  A method for freely downloading large datasets from the K-12 Resource, so that users can acquire and analyze all or large parts of the data, should be included. The capacity of the K-12 Resource to expand to accommodate an increase in database entries and information must be described. The K-12 Resource should be easily accessible with multiple methods of querying, including simple web interfaces for common standard queries and tools for more complex queries.

Management

The organization, updating, curation, and maintenance of the E. coli K-12 Resource will require a management structure that supports the goal of providing timely updating of the informatics resources and quality assurance.  To achieve this, the K-12 Resource must, to the degree possible, develop cooperative relationships with owners of existing sources of data and related information.  Examples are the NCBI, the Coli Genetics Stock Center, the NIAID ERIC resource, and other domestic and foreign individual and collective sources, as well as other model organism resources.  Applicants should explain how the projects to be supported by this award will coordinate with related projects supported by other funding.  Some examples are the organization of meetings for annotation and other specialized community purposes, meetings to coordinate database interoperability efforts, and plans to disseminate information on the K-12 Resource.  If awarded, the K-12 Resource, in concert with federal officials, will identify a steering committee that will provide overall policy guidance for the K-12 Resource; this committee should reflect the diversity of expected users of the K-12 Resource.

The application should discuss how the K-12 Resource will set priorities to accomplish the requirements above within the limitations of the proposed budget.  The application should provide specific plans for operating in a cost-effective manner. 

Given the complex and diverse nature of any proposed resource, a project manager may be required to oversee and coordinate the day-to-day operation and development of such a resource.

The Multiple Investigator option (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-07-017.html) is strongly encouraged but not required.  If used, a Leadership Plan is required that will detail the relationships and management structure of the project. 

Community Relationships

The E. coli K-12 Resource is expected to operate as a general forum for a multitude of investigators; some will be content experts in the K-12 Group, and their cooperation will be critical in keeping the K-12 Resource content current.  Although the Steering Committee will play a valuable role in providing scheduled, periodic input to the K-12 Resource, ongoing discussions, announcements and observations from the general community also should be accommodated within the K-12 Resource.  Budget resources should be requested and justified in order to build and maintain community participation.

See Section VIII, Other Information - Required Federal Citations, for policies related to this announcement.

Section II. Award Information


1. Mechanism of Support

This funding opportunity will use the Cooperative Agreement U24 award mechanism. 

This FOA uses “Just-in-Time” information concepts. It also uses non-modular budget formats described in the PHS 398 application instructions (see http://grants.nih.gov/grants/funding/phs398/phs398.html). 

This funding opportunity will use a cooperative agreement award mechanism. In the cooperative agreement mechanism, the Project Director/Principal Investigator (PD/PI) 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 VI. 2. Administrative Requirements, "Cooperative Agreement Terms and Conditions of Award.”  It is not known at this time if this funding opportunity will be re-issued. 

A transition plan must be provided to ensure that when the award terminates the resource will continue to be available to the community.  This plan should take into account the following possible options at the end of the term: 1) continued, possibly reduced federal grant support; 2) no further federal grant support.

2. Funds Available

The estimated amount of funds available for support of 1 project awarded as a result of this announcement is $1,000,000 total costs for fiscal year 2009Future year amounts will depend on annual appropriations.

Because the nature and scope of the proposed research will vary from application to application, it is anticipated that the size and duration of the award will also vary.  Although the financial plans of the NIGMS provide support for this program, awards pursuant to this funding opportunity are contingent upon the availability of funds and the receipt of a sufficient number of meritorious applications.

Facilities and administrative costs requested by consortium participants are not included in the direct cost limitation, see NOT-OD-05-004.

NIH grants policies as described in the http://era.nih.gov/ElectronicReceipt/preparing.htm for instructions).

The decision of whether to apply for a grant with a single PD/PI or multiple PDs/PIs is the responsibility of the investigators and applicant organizations, and should be determined by the scientific goals of the project. Applications for grants with multiple PDs/PIs will require additional information, as outlined in the instructions below. The NIH review criteria for approach, investigators, and environment have been modified to accommodate applications involving either a single PD/PI or multiple PDs/PIs. When considering multiple PDs/PIs, please be aware that the structure and governance of the PD/PI leadership team as well as the knowledge, skills and experience of the individual PDs/PIs will be factored into the assessment of the overall scientific merit of the application.  Multiple PDs/PIs on a project share the authority and responsibility for leading and directing the project, intellectually and logistically. Each PD/PI is responsible and accountable to the grantee organization, or, as appropriate, to a collaborating organization, for the proper conduct of the project or program, including the submission of required reports. For further information on multiple PDs/PIs, please see http://grants.nih.gov/grants/multi_pi.

2. Cost Sharing or Matching

This program does not require cost sharing as defined in the current NIH Grants Policy Statement.

3. Other-Special Eligibility Criteria

Applicants are not permitted to submit a resubmission application in response to this FOA.

Renewal applications will be permitted for this FOA.

Applicants may submit more than one application, provided each application is scientifically distinct.

Section IV. Application and Submission Information


1. Address to Request Application Information

The PHS 398 application instructions are available at http://grants.nih.gov/grants/funding/phs398/phs398.html in an interactive format. Applicants must use the currently approved version of the PHS 398. For further assistance contact GrantsInfo, Telephone (301) 435-0714, Email: GrantsInfo@nih.gov.

Telecommunications for the hearing impaired: TTY 301-451-5936.

2. Content and Form of Application Submission

Applications must be prepared using the most current PHS 398 research grant application instructions and forms. Applications must have a D&B Data Universal Numbering System (DUNS) number as the universal identifier when applying for Federal grants or cooperative agreements. The D&B number can be obtained by calling (866) 705-5711 or through the web site at http://www.dnb.com/us/. The D&B number should be entered on line 11 of the face page of the PHS 398 form.

The title and number of this funding opportunity must be typed in item (box) 2 only of the face page of the application form and the YES box must be checked.

SPECIAL INSTRUCTIONS

Applications with Multiple PDs/PIs 

When multiple PD/PIs are proposed, use the Face Page-Continued page to provide items 3a – 3h for all PD/PIs. NIH requires one PD/PI be designated as the “contact PD/PI” for all communications between the PD/PIs and the agency. The contact PD/PI must meet all eligibility requirements for PD/PI status in the same way as other PD/PIs, but has no special roles or responsibilities within the project team beyond those mentioned above. The contact PD/PI may be changed during the project period. The contact PD/PI should be listed in block 3 of Form Page 1 (the Face Page), with all additional PD/PIs listed on Form Page 1-Continued. When inserting the name of the PD/PI in the header of each application page, use the name of the “Contact PD/PI, et. al.” The contact PD/PI must be from the applicant organization if PD/PIs are from more than one institution.

All individuals designated as PD/PI must be registered in the eRA Commons and must be assigned the PD/PI role in that system (other roles such as SO or IAR will not give the PD/PI the appropriate access to the application records). Each PD/PI must include their respective eRA Commons ID in the eRA Commons User Name field.

All projects proposing Multiple PDs/PIs will be required to include a new section describing the leadership plan approach for the proposed project.

Multiple PD/PI Leadership Plan: For applications designating multiple PDs/PIs, a new section of the research plan, entitled “Multiple PD/PI Leadership Plan” must be included. A rationale for choosing a multiple PD/PI approach should be described. The governance and organizational structure of the leadership team and the research project should be described, and should include communication plans, process for making decisions on scientific direction, and procedures for resolving conflicts. The roles and administrative, technical, and scientific responsibilities for the project or program should be delineated for the PDs/PIs and other collaborators. 

If budget allocation is planned, the distribution of resources to specific components of the project or the individual PDs/PIs should be delineated in the Leadership Plan. In the event of an award, the requested allocations may be reflected in a footnote on the Notice of Award.

Additional information is available in the PHS 398 grant application instructions.

3. Submission Dates and Times

Applications must be received on or before the receipt date described below (Section IV.3.A). Submission times N/A.

3.A. Receipt, Review and Anticipated Start Dates
Letters of Intent Receipt Date: November 4, 2008
Application
Receipt Date: December 4, 2008
Peer Review Date: March-April 2009
Council Review Date: May 2009
Earliest Anticipated Start Date: July 1, 2009

3.A.1. Letter of Intent

Prospective applicants are asked to submit a letter of intent that includes the following information:

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 IC staff to estimate the potential review workload and plan the review.

The letter of intent is to be sent by the date listed in Section IV.3.A.

The letter of intent should be sent to:

Matthew E. Portnoy, Ph.D.
Division of Genetics and Developmental Biology
National Institute of General Medical Sciences
Building 45, 2AS.25P
45 Center Drive
Bethesda, MD 20892-6200
Telephone:  (301) 594-0943
Fax: (301) 480-2228
Email: mportnoy@nigms.nih.gov

3.B. Sending an Application to the NIH

Applications must be prepared using the forms found in the PHS 398 instructions for preparing a research grant application. Submit a signed, typewritten original of the application, including the checklist, and three 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 (U.S. Postal Service Express or regular mail)
Bethesda, MD 20817 (for express/courier service; non-USPS service)

Personal deliveries of applications are no longer permitted (see http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-040.html).

At the time of submission, two additional copies of the application and all copies of the appendix material must be sent to:

Helen R. Sunshine, Ph.D.
Chief, Office of Scientific Review
National Institute of General Medical Sciences
45 Center Drive, Room 3AN.12F, MSC 6200
Bethesda, MD 20892-6200
Telephone: (301) 594-2881
FAX: (301) 480-8506
Email: sunshinh@nigms.nih.gov

3.C. Application Processing

Applications must be received on or before the application receipt date) described above (Section IV.3.A.). If an application is received after that date, the application may be delayed in the review process or not reviewed.  Upon receipt, applications will be evaluated for completeness by the CSR and for responsiveness by the reviewing Institute Incomplete and/or non-responsive applications will not be reviewed.

The NIH will not accept any application in response to this funding opportunity 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 a funding opportunity, it is to be prepared as a NEW application. That is, the application for the funding opportunity 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.

Information on the status of an application should be checked by the Principal Investigator in the eRA Commons at: https://commons.era.nih.gov/commons/.

4. Intergovernmental Review

This initiative is not subject to intergovernmental review.

5. Funding Restrictions

All NIH awards are subject to the terms and conditions, cost principles, and other considerations described in the NIH Grants Policy Statement. The Grants Policy Statement can be found at NIH Grants Policy Statement.

Pre-award costs are allowable. A grantee may, at its own risk and without NIH prior approval, incur obligations and expenditures to cover costs up to 90 days before the beginning date of the initial budget period of a new or renewal award if such costs: 1) are necessary to conduct the project, and 2) would be allowable under the grant, if awarded, without NIH prior approval. If specific expenditures would otherwise require prior approval, the grantee must obtain NIH approval before incurring the cost. NIH prior approval is required for any costs to be incurred more than 90 days before the beginning date of the initial budget period of a new or renewal award.

The incurrence of pre-award costs in anticipation of a competing or non-competing award imposes no obligation on NIH either to make the award or to increase the amount of the approved budget if an award is made for less than the amount anticipated and is inadequate to cover the pre-award costs incurred. NIH expects the grantee to be fully aware that pre-award costs result in borrowing against future support and that such borrowing must not impair the grantee's ability to accomplish the project objectives in the approved time frame or in any way adversely affect the conduct of the project (see NIH Grants Policy Statement http://grants.nih.gov/archive/grants/policy/nihgps_2003/index.htm.)

6. Other Submission Requirements and Information

General Issues

Implementation Plan. Applications must include a timeline and milestones for the development of the K-12 Resource; the execution may be complex due to the need to reach agreements with outside providers of information, to develop the public interface, to organize and develop procedures for input from the research communities, and to create de novo procedures and instruments for database construction.  Plans to build upon and expand EcoliHub or to interact with and obtain current EcoliHub information must be included.

Annual Meeting. Applications should include funds to organize an annual steering committee meeting for the Principal Investigator, appropriate K-12 Resource personnel, steering committee members, and NIH personnel to discuss progress and results.  Funds requested should include meeting space logistics, travel, lodging, and per diem for approximately 10 attendees, not including federal officials.

Video/teleconferences. It may be necessary to have frequent consultation between the Steering Committee or its subcommittees and the PI. The application budget should provide funds to set up video conferencing via phone or computer links for this purpose. The Steering Committee and Program Director will coordinate the scheduling of these conferences on a schedule that will meet the needs of the K-12 Resource.

Letters of Collaboration. Arrangements by the PI to integrate various data and knowledge sources should be documented with letters specifically stating the terms of access; these may be provided as appendices.

Data and Resource Sharing Plans. Data sets, models and tools, including source code, will be made publicly available through the K-12 Resource portal according to NIH policy as listed below in “Resource Sharing Plan” and Section V.2.C and V.2.D.

Awardees must agree to the "Cooperative Agreement Terms and Conditions of Award" in Section VI.2.A "Award Administration Information.”

Research Plan Page Limitations

25 pages

Appendix Materials

All paper PHS 398 applications submitted must provide appendix material on CDs only. Include five identical CDs in the same package with the application.  See http://grants.nih.gov/grants/guide/notice-files/NOT-OD-08-031.html.

Do not use the Appendix to circumvent the page limitations of the Research Plan component. An application that does not observe the required page limitations may be delayed in the review process.

Resource Sharing Plan(s)

NIH considers the sharing of unique research resources developed through NIH-sponsored research an important means to enhance the value of, and advance research. When resources have been developed with NIH funds and the associated research findings published or provided to NIH, it is important that they be made readily available for research purposes to qualified individuals within the scientific community. If the final data/resources are not amenable to sharing, this must be explained in Resource Sharing section of the application. See http://grants.nih.gov/grants/policy/data_sharing/data_sharing_faqs.htm.

(a) Data Sharing Plan: Regardless of the amount requested, investigators are expected to include a brief 1-paragraph description of how final research data will be shared, or explain why data-sharing is not possible. Applicants are encouraged to discuss data-sharing plans with their NIH program contact. See Data-Sharing Policy or http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-032.html.

(b) Sharing Model Organisms: Regardless of the amount requested, all applications where the development of model organisms is anticipated are expected to include a description of a specific plan for sharing and distributing unique model organisms and related resources, or state appropriate reasons why such sharing is restricted or not possible. See Sharing Model Organisms Policy, and NIH Guide NOT-OD-04-042.

(c) Genome-Wide Association Studies (GWAS): Regardless of the amount requested, applicants seeking funding for a genome-wide association study are expected to provide a plan for submission of GWAS data to the NIH-designated GWAS data repository, or provide an appropriate explanation why submission to the repository is not possible.  A genome-wide association study is defined as any study of genetic variation across the entire genome that is designed to identify genetic associations with observable traits (such as blood pressure or weight) or the presence or absence of a disease or condition.  For further information see Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies, NIH Guide NOT-OD-07-088, and http://grants.nih.gov/grants/gwas/.

The reasonableness of the data sharing plan or the rationale for not sharing research data will be assessed by the reviewers.  However, reviewers will not factor the proposed data-sharing plan into the determination of scientific merit or the priority score.

Because the purpose of the K-12 Resource is to provide a community resource of data and other information for the scientific community, the investigator should describe briefly the expected schedule for data sharing, the format of the final dataset, the documentation to be provided, whether or not any analytic tools also will be provided, whether or not a data-sharing agreement will be required and, if so, a brief description of such an agreement (including the criteria for deciding who can receive the data and whether or not any conditions will be placed on their use), and the mode of data sharing (e.g., by mailing a disk or posting data on the K-12 Resource website.), consistent with achieving the goals of the program. References to data sharing may also be appropriate in other sections of the application.

NIH policy expects that grant awardee recipients will make unique research resources readily available for research purposes to qualified individuals within the scientific community after publication (NIH Grants Policy Statement http://grants.nih.gov/archive/archive/grants/policy/nihgps_2003/index.htm and http://grants.nih.gov/archive/grants/policy/nihgps_2003/index.htm#_Toc54600131). Investigators responding to this funding opportunity should include a plan for sharing research resources addressing how unique research resources will be shared or explain why sharing is not possible.

A software dissemination plan, if applicable, is expected to be included in the application.  There is no prescribed single license for software produced in this project.  However, this initiative includes goals for software dissemination, and reviewers will be instructed to make comments on the dissemination plan relative to these goals:

1) The software generated by the K-12 Resource 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 K-12 Resource-generated 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 packages. 

3) The terms of the K-12 Resource-generated software availability should include the ability of researchers outside the K-12 Resource and its collaborating projects to modify the source code for their own purposes. The K-12 Resource should stipulate that these modifications may be shared with other colleagues who have obtained the source code from the K-12 Resource, and should also be shared with the K-12 Resource. The application must 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 application.  Typically, the relevant responsible official will be in the applicant institution's office of technology transfer or intellectual property, as opposed to an academic official such as a department head or dean.

The adequacy of the resource sharing plans and any related data-sharing plans will be considered by program staff of the funding organization when making recommendations about funding applications. 

Section V. Application Review Information


1. Criteria (Update: Enhanced review criteria have been issued for the evaluation of research applications received for potential FY2010 funding and thereafter - see NOT-OD-09-025).

Only the review criteria described below will be considered in the review process.

2. Review and Selection Process

Applications that are complete and responsive to the FOA will be evaluated for scientific and technical merit by an appropriate peer review group convened by NIGMS and in accordance with NIH peer review procedures (http://grants1.nih.gov/grants/peer/), using the review criteria stated below.

As part of the scientific peer review, all applications will:

The following will be considered in making funding decisions:

The goals of NIH supported research are to advance our understanding of biological systems, to improve the control of disease, and to enhance health. In their written critiques, reviewers will be asked to comment on each of the following criteria in order to judge the likelihood that the proposed research will have a substantial impact on the pursuit of these goals. Each of these criteria will be addressed and considered in assigning the overall score, and weighted as appropriate for each application. Note that an application does not need to be strong in all categories to be judged likely to have major scientific impact and thus deserve a meritorious 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 or clinical practice be advanced? What will be the effect of these studies on the concepts, methods, technologies, treatments, services, or preventative interventions that drive this field?  Will the proposed K-12 Resource address the needs of the diverse constituent research communities?

Approach: Are the conceptual or clinical framework, design, methods, and analyses adequately developed, well integrated, well reasoned, and appropriate to the aims of the project? Does the applicant acknowledge potential problem areas and consider alternative tactics? For applications designating multiple PDs/PIs, is the leadership approach, including the designated roles and responsibilities, governance, and organizational structure, consistent with and justified by the aims of the project and the expertise of each of the PDs/PIs? Are the plans for implementing the K-12 Resource optimally designed to solicit input from the research communities? Is there adequate documentation of efforts to integrate existing resources?

Innovation:  Is the project original and innovative? For example: Does the project challenge existing paradigms or clinical practice; address an innovative hypothesis or critical barrier to progress in the field? Does the project develop or employ novel concepts, approaches, methodologies, tools, or technologies for this area?   

Investigators: Are the PD/PI(s) and other key personnel 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? Do the PD/PI(s) and investigative team bring complementary and integrated expertise to the project? 

Environment:  Do(es) the scientific environment(s) in which the work will be done contribute to the probability of success? Do the proposed studies benefit from unique features of the scientific environment, or subject populations, or employ useful collaborative arrangements? Is there evidence of institutional support?  

2.A. Additional Review Criteria:

In addition to the above criteria, the following items will continue to be considered in the determination of scientific merit and the rating:

Protection of Human Subjects from Research Risk: The involvement of human subjects and protections from research risk relating to their participation in the proposed research will be assessed (see the Research Plan section on Human Subjects in the PHS 398 instructions).

Inclusion of Women, Minorities and Children in Research: The adequacy 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 will be assessed. Plans for the recruitment and retention of subjects will also be evaluated (see the Research Plan section on Human Subjects in the PHS 398 instructions).

Care and Use of Vertebrate Animals in Research: If vertebrate animals are to be used in the project, the five points described in the Vertebrate Animals section of the Research Plan will be assessed.

Biohazards: If materials or procedures are proposed that are potentially hazardous to research personnel and/or the environment, determine if the proposed protection is adequate.

2.B. Additional Review Considerations

Budget: The reasonableness of the proposed budget and the requested period of support in relation to the proposed research. The priority score should not be affected by the evaluation of the budget.

2.C. Resource Sharing Plan(s)   

When relevant, reviewers will be instructed to comment on the reasonableness of the following Resource Sharing Plans, or the rationale for not sharing the following types of resources. However, reviewers will not factor the proposed resource sharing plan(s) into the determination of scientific merit or priority score, unless noted otherwise in the FOA. Program staff within the IC will be responsible for monitoring the resource sharing.

The effectiveness of the resource sharing will be evaluated as part of the administrative review of each non-competing Grant Progress Report (PHS 2590, http://grants.nih.gov/grants/funding/2590/2590.htm). See Section VI.3. Reporting.

If funded, the terms and conditions of award will specify the need for a report from the Steering Committee following its annual meeting, and documentation of efforts to coordinate with other related Federally funded databases, e.g., ERIC and the Coli Genetics Stock Center, and summary data on the use of the K-12 Resource. See Section VI.2.A.3 Collaborative responsibilities.

3. Anticipated Announcement and Award Dates

Not Applicable

Section VI. Award Administration Information


1. Award Notices

After the peer review of the application is completed, the PD/PI will be able to access his or her Summary Statement (written critique) via the eRA Commons.

If the application is under consideration for funding, NIH will request "just-in-time" information from the applicant. For details, applicants may refer to the NIH Grants Policy Statement Part II: Terms and Conditions of NIH Grant Awards, Subpart A: General.

A formal notification in the form of a Notice of Award (NoA) will be provided to the applicant organization. The NoA signed by the grants management officer is the authorizing document. Once all administrative and programmatic issues have been resolved, the NoA will be generated via email notification from the awarding component to the grantee business official (designated in item 12 on the Application Face Page). If a grantee is not email enabled, a hard copy of the NoA will be mailed to the business official.

Selection of an application for award is not an authorization to begin performance. Any costs incurred before receipt of the NoA are at the recipient's risk. These costs may be reimbursed only to the extent considered allowable pre-award costs. See Also Section IV.5. Funding Restrictions.

2. Administrative and National Policy Requirements

All NIH grant and cooperative agreement awards include the NIH Grants Policy Statement as part of the NoA. For these terms of award, see the NIH Grants Policy Statement Part II: Terms and Conditions of NIH Grant Awards, Subpart A: General (http://grants.nih.gov/archive/grants/policy/nihgps_2003/index.htm) and Part II Terms and Conditions of NIH Grant Awards, Subpart B: Terms and Conditions for Specific Types of Grants, Grantees, and Activities (http://grants.nih.gov/archive/grants/policy/nihgps_2003/index.htm).

The following Terms and Conditions will be incorporated into the award statement and will be provided to the Principal Investigator as well as to the appropriate institutional official, at the time of award.

2.A. Cooperative Agreement Terms and Conditions of Award

The following special terms of award are in addition to, and not in lieu of, otherwise applicable OMB administrative guidelines, HHS grant administration regulations at 45 CFR Parts 74 and 92 (Part 92 is applicable when State and local Governments are eligible to apply), and other HHS, PHS, and NIH grant administration policies.

The administrative and funding instrument used for this program will be the cooperative agreement an "assistance" mechanism (rather than an "acquisition" mechanism), in which substantial NIH programmatic involvement with the awardees is anticipated during the performance of the activities. Under the cooperative agreement, the NIH purpose is to support and stimulate the recipients' activities by involvement in and otherwise working jointly with the award recipients in a partnership role; it is not to assume direction, prime responsibility, or a dominant role in the activities. Consistent with this concept, the dominant role and prime responsibility resides with the awardees for the project as a whole, although specific tasks and activities may be shared among the awardees and the NIH as defined below.

2.A.1. Principal Investigator Rights and Responsibilities

The Principal Investigator will have the primary responsibility for:

Awardees will retain custody of and have primary rights to the data and software developed under these awards, subject to Government rights of access consistent with current HHS, PHS, and NIH policies.

2.A.2. NIH Responsibilities

An NIH project scientist will have substantial programmatic involvement that is above and beyond the normal stewardship role in awards, as described below.

NIH project scientists with expertise in relevant areas will serve on the Steering Committee as representatives of the NIH extramural staff and will help guide the development of the Resource by providing overall advice and coordination. They will have responsibility for:

NIH staff will facilitate, not direct, activities. Decisions will be reached through consensus with the Principal Investigator and other members of the Steering Committee.

Additionally, an agency program official or IC program director will be responsible for the normal scientific and programmatic stewardship of the award and will be named in the award notice.

2.A.3. Collaborative Responsibilities

The E. coli K-12 Resource Steering Committee will include representation from selected scientists from outside the Resource and possibly other Federal officials in order to gain a breadth of input into the informational needs of the experimental and bioinformatics research communities.  Federal scientists will not comprise more than 40% of the voting members on the Steering Committee.  The NIGMS Program Director is not a member of the Steering Committee, but will facilitate formation of the group, selecting the Chair of the Committee in consultation with the PI, and will attend all meetings.  A federal official may not serve as Chair.  The Chair is responsible for developing meeting agendas, chairing meetings, and preparing a report in consultation with NIH project scientists.  The Steering Committee decides on the schedule of meetings, at least once each year.  The Steering Committee may establish subcommittees as necessary.  The Steering Committee also may add members, with the approval of the NIGMS Program Director.

The Steering Committee will:

Each full member will have one vote. Awardee members of the Steering Committee will be required to accept and implement policies approved by the Steering Committee.

2.A.4. Arbitration Process

Any disagreements that may arise in scientific or programmatic matters (within the scope of the award) between award recipients and the NIH may be brought to arbitration. An Arbitration Panel composed of three members will be convened. It will have three members: a designee of the Steering Committee chosen without NIH staff voting, one NIH designee, and a third designee with expertise in the relevant area who is chosen by the other two; in the case of individual disagreement, the first member may be chosen by the individual awardee. This special arbitration procedure in no way affects the awardee's right to appeal an adverse action that is otherwise appealable in accordance with PHS regulations 42 CFR Part 50, Subpart D and HHS regulations 45 CFR Part 16.

3. Reporting

Awardees will be required to submit the Non-Competing Continuation Grant Progress Report (PHS 2590) annually and financial statements as required in the NIH Grants Policy Statement.

A final progress report, invention statement, and Financial Status Report are required when an award is relinquished when a recipient changes institutions or when an award is terminated.

Section VII. Agency Contacts


We encourage your inquiries concerning this funding opportunity 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:

1. Scientific/Research Contacts:

Matthew E. Portnoy, Ph.D.
Division of Genetics and Developmental Biology
National Institute of General Medical Sciences
Building 45, 2AS.25P
45 Center Drive
Bethesda, MD 20892-6200
Telephone:  (301) 594-0943
Fax: (301) 480-2228
Email: mportnoy@nigms.nih.gov

2. Peer Review Contacts:

Helen R. Sunshine, Ph.D.
Chief, Office of Scientific Review
National Institute of General Medical Sciences
45 Center Drive, Room 3AN.12F, MSC 6200
Bethesda, MD 20892-6200
Telephone: (301) 594-2881
FAX: (301) 480-8506
Email: sunshinh@nigms.nih.gov

3. Financial or Grants Management Contacts:

Marcia F. Cohn
Grants Administration Branch, Division of Extramural Activities
National Institute of General Medical Sciences
Building 45, Room 2AN.50E
45 Center Drive, MSC 6200
Bethesda , MD 20892-6200
Telephone: (301) 594-3918
FAX: (301) 480 2554
Email: cohnm@nigms.nih.gov

Section VIII. Other Information


Required Federal Citations

Use of Animals in Research:
Recipients of PHS support for activities involving live, vertebrate animals must comply with PHS Policy on Humane Care and Use of Laboratory Animals (http://grants.nih.gov/grants/olaw/references/PHSPolicyLabAnimals.pdf) as mandated by the Health Research Extension Act of 1985 (http://grants.nih.gov/grants/olaw/references/hrea1985.htm), and the USDA Animal Welfare Regulations (http://www.nal.usda.gov/awic/legislat/usdaleg1.htm) as applicable.

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 (http://www.hhs.gov/ohrp/humansubjects/guidance/45cfr46.htm).

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). Monitoring should be commensurate with risk. The establishment of data and safety monitoring boards (DSMBs) is required for multi-site clinical trials involving interventions that entail potential risks to the participants (NIH Policy for Data and Safety Monitoring, NIH Guide for Grants and Contracts, http://grants.nih.gov/grants/guide/notice-files/not98-084.html).

Sharing Research Data:
Regardless of the amount requested, investigators are expected to include a brief 1-paragraph description of how final research data will be shared, or explain why data-sharing is not possible.  Applicants are encouraged to discuss data-sharing plans with their NIH program contact.  See Data-Sharing Policy or http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-032.html.

Investigators should seek guidance from their institutions, on issues related to institutional policies and local IRB rules, as well as local, State and Federal laws and regulations, including the Privacy Rule. Reviewers will consider the data sharing plan but will not factor the plan into the determination of the scientific merit or the priority score.

Policy for Genome-Wide Association Studies (GWAS):
NIH is interested in advancing genome-wide association studies (GWAS) to identify common genetic factors that influence health and disease through a centralized GWAS data repository. For the purposes of this policy, a genome-wide association study is defined as any study of genetic variation across the entire human genome that is designed to identify genetic associations with observable traits (such as blood pressure or weight), or the presence or absence of a disease or condition. All applications, regardless of the amount requested, proposing a genome-wide association study are expected to provide a plan for submission of GWAS data to the NIH-designated GWAS data repository, or provide an appropriate explanation why submission to the repository is not possible. Data repository management (submission and access) is governed by the Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies, NIH Guide NOT-OD-07-088. For additional information, see http://grants.nih.gov/grants/gwas/

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 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 funding opportunity 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.

Sharing of Model Organisms:
NIH is committed to support efforts that encourage sharing of important research resources including the sharing of model organisms for biomedical research (see http://grants.nih.gov/grants/policy/model_organism/index.htm). At the same time the NIH recognizes the rights of grantees and contractors to elect and retain title to subject inventions developed with Federal funding pursuant to the Bayh Dole Act (see the NIH Grants Policy Statement http://grants.nih.gov/archive/archive/grants/policy/nihgps_2003/index.htm). All investigators submitting an NIH application or contract proposal, beginning with the October 1, 2004 receipt date, are expected to include in the application/proposal a description of a specific plan for sharing and distributing unique model organism research resources generated using NIH funding or state why such sharing is restricted or not possible. This will permit other researchers to benefit from the resources developed with public funding. The inclusion of a model organism sharing plan is not subject to a cost threshold in any year and is expected to be included in all applications where the development of model organisms is anticipated.

Inclusion of Women And Minorities in Clinical Research:
It is the 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 103-43). All investigators proposing clinical research should read the "NIH Guidelines for Inclusion of Women and Minorities as Subjects in Clinical Research (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-02-001.html); a complete copy of the updated Guidelines is available at http://grants.nih.gov/grants/funding/women_min/guidelines_amended_10_2001.htm. 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 proposals 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 differences.

Inclusion of Children as Participants in Clinical Research:
The NIH maintains a policy that children (i.e., individuals under the age of 21) must be included in all clinical research, conducted or supported by the NIH, unless there are scientific and ethical reasons not to include them.

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 (http://grants.nih.gov/grants/funding/children/children.htm).

Required Education on the Protection of Human Subject Participants:
NIH policy requires education on the protection of human subject participants for all investigators submitting NIH applications for research involving human subjects and individuals designated as key personnel. The policy is available at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-00-039.html.

Human Embryonic Stem Cells (hESC):
Criteria for federal funding of research on hESCs can be found at http://stemcells.nih.gov/index.asp and at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-02-005.html. Only research using hESC lines that are registered in the NIH Human Embryonic Stem Cell Registry will be eligible for Federal funding (http://escr.nih.gov). 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.

NIH Public Access Policy Requirement:
In accordance with the NIH Public Access Policy (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-08-033.html) investigators must submit or have submitted for them their final, peer-reviewed manuscripts that arise from NIH funds and are accepted for publication as of April 7, 2008 to PubMed Central (http://www.pubmedcentral.nih.gov/), to be made publicly available no later than 12 months after publication. As of May 27, 2008, investigators must include the PubMed Central reference number when citing an article in NIH applications, proposals, and progress reports that fall under the policy, and was authored or co-authored by the investigator or arose from the investigator’s NIH award.  For more information, see the Public Access webpage at http://publicaccess.nih.gov/.

Standards for Privacy of Individually Identifiable Health Information:
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).

Decisions about applicability and implementation of the Privacy Rule reside with the researcher and his/her institution. The OCR website (http://www.hhs.gov/ocr/) 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 http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-025.html.

URLs in NIH Grant Applications or Appendices:
All applications and proposals for NIH funding must be self-contained within specified page limitations. For publications listed in the appendix and/or Progress report, internet addresses (URLs) must be used for publicly accessible on-line journal articles.  Unless otherwise specified in this solicitation, Internet addresses (URLs) should not be used to provide any other information necessary for 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 FOA 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 at http://www.cfda.gov/ and is not subject to the intergovernmental review requirements of Executive Order 12372. 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 http://grants.nih.gov/grants/policy/policy.htm.

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.

Loan Repayment Programs:
NIH encourages applications for educational loan repayment from qualified health professionals who have made a commitment to pursue a research career involving clinical, pediatric, contraception, infertility, and health disparities related areas. The LRP is an important component of NIH's efforts to recruit and retain the next generation of researchers by providing the means for developing a research career unfettered by the burden of student loan debt. Note that an NIH grant is not required for eligibility and concurrent career award and LRP applications are encouraged. The periods of career award and LRP award may overlap providing the LRP recipient with the required commitment of time and effort, as LRP awardees must commit at least 50% of their time (at least 20 hours per week based on a 40 hour week) for two years to the research. For further information, please see: http://www.lrp.nih.gov.


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