Department of Health and Human Services
Part 1. Overview Information
Participating Organization(s)

National Institutes of Health (NIH)

Components of Participating Organizations

This Funding Opportunity Announcement (FOA) is developed as a Common Fund initiative through the NIH Office of the NIH Director, Office of Strategic Coordination.  The FOA will be administered by the
National Cancer Institute (NCI) on behalf of the NIH.

Funding Opportunity Title

4D Nucleome Network Data Coordination and Integration Center (U01)

Activity Code

U01 Research Project – Cooperative Agreements

Announcement Type

New

Related Notices

None

Funding Opportunity Announcement (FOA) Number

RFA-RM-14-011

Companion Funding Opportunity

RFA-RM-14-006, U54 Specialized Center - Cooperative Agreements

RFA-RM-14-007, U01 Research Project - Cooperative Agreements

RFA-RM-14-008, U01 Research Project - Cooperative Agreements

RFA-RM-14-009, U01 Research Project - Cooperative Agreements

RFA-RM-14-010, U01 Research Project - Cooperative Agreements

Catalog of Federal Domestic Assistance (CFDA) Number(s)

93.310

Funding Opportunity Purpose

The purpose of this Funding Opportunity Announcement (FOA) is to identify and support a Four-Dimensional Nucleome (4DN) Network Data Coordination and Integration Center (DCIC). The overarching mission of 4DN-DCIC will be to collect, store, curate, and display all data, metadata, and analysis tools generated by the 4DN Network. The DCIC will also assist in the development and dissemination of metadata and standards to be adopted by the community at large, approaches for integrative analysis of a wide-range of data types, and visualization and analysis tools to facilitate access and understanding of complex datasets to non-expert users.

Key Dates
Posted Date

September 24, 2014

Open Date (Earliest Submission Date)

November 16, 2014

Letter of Intent Due Date(s)

November 16, 2014

Application Due Date(s)

December 16, 2014, by 5:00 PM local time of applicant organization. All types of non-AIDS applications allowed for this funding opportunity announcement are due on this date.

Applicants are encouraged to apply early to allow adequate time to make any corrections to errors found in the application during the submission process by the due date.

AIDS Application Due Date(s)

Not Applicable

Scientific Merit Review

February-March 2015

Advisory Council Review

May 2015

Earliest Start Date

July 2015

Expiration Date

December 17, 2014

Due Dates for E.O. 12372

Not Applicable

Required Application Instructions

It is critical that applicants follow the instructions in the SF424 (R&R) Application Guide, except where instructed to do otherwise (in this FOA or in a Notice from the NIH Guide for Grants and Contracts). Conformance to all requirements (both in the Application Guide and the FOA) is required and strictly enforced. Applicants must read and follow all application instructions in the Application Guide as well as any program-specific instructions noted in Section IV. When the program-specific instructions deviate from those in the Application Guide, follow the program-specific instructions. Applications that do not comply with these instructions may be delayed or not accepted for review.

Table of Contents

Part 1. Overview Information
Part 2. Full Text of the Announcement
Section I. Funding Opportunity Description
Section II. Award Information
Section III. Eligibility Information
Section IV. Application and Submission Information
Section V. Application Review Information
Section VI. Award Administration Information
Section VII. Agency Contacts
Section VIII. Other Information

Part 2. Full Text of Announcement
Section I. Funding Opportunity Description
Purpose

The purpose of this Funding Opportunity Announcement (FOA) is to identify and support a Four-Dimensional Nucleome (4DN) Network Data Coordination and Integration Center (DCIC). The overarching mission of 4DN-DCIC will be to collect, store, curate, and display all data, metadata, and analysis tools generated by the 4DN Network. The DCIC will also assist in the development and dissemination of metadata and standards to be adopted by the community at large, approaches for integrative analysis of a wide-range of data types, and visualization and analysis tools to facilitate access and understanding of complex datasets to non-expert users.

Background

It has been more than a decade since the human genome was completely sequenced.  Despite vastly improved technologies and many important foundational discoveries, our understanding of how genomic information specifies proper execution of spatial and temporal gene expression programs remains to be fully elucidated. This knowledge is essential for understanding how cells divide or respond to their environment, for identifying the regulatory mechanisms that control development and are dysregulated in disease, and for studying phenotypic variations among human populations. It is now clear that while mammalian genomes encode genetic information in their linear sequence, the appropriate cell type specific expression of their genes depends on higher order nuclear organization, from the folding of chromosomes into three-dimensional structures, to chromatin loops that connect genes and transcriptional regulatory complexes, to larger chromosomal domains and nuclear compartments.  Defining chromatin interactions and the ways in which nuclear architecture constrains/enables interactions, and describing the relationships of genomic regions to transcription, RNA processing and chromatin regulatory machineries, is likely to reveal how individual cells access, read and interpret genetic information.  Because this spatial organization of genomes is dynamic, we also need to understand how it changes in response to environmental challenges and cellular processes such as cell cycle, differentiation, or neoplastic transformation. A comprehensive understanding of the contribution of the structural and functional organization of the mammalian genome to development and disease in both space (3D Nucleome) and time (4D Nucleome) will require major efforts.

The Four-Dimensional Nucleome (4DN) was selected by the NIH Leadership as the focus for a Common Fund Program following a series of discussions with panels of scientific experts and stakeholders, and with input from the broad community solicited via a Request for Information early in 2014 (NOT-RM-14-010).  The impetus for its selection as a Common Fund program was the growing awareness that understanding the architecture of the cell nucleus may have widespread and profound implications for human health and disease, but our current ability to study nuclear organization is hindered by a number of outstanding technological and conceptual challenges.

Experts from the research community identified the following scientific priorities as areas that represent challenges and opportunities for investment by the NIH: 1) next-generation, high-resolution and high-throughput tools to explore the relationships between nuclear organization and the regulation of gene expression programs, including with single cell resolution; 2) computational tools to integrate existing data sets, and to manage, analyze, and visualize the datasets generated by a community effort;  3) predictive models of nuclear structure/function relationships in the context of various cellular states or transitions (differentiation, reprogramming, cell cycle, responses to external stimuli, disease development); 4) next-generation tools to explore nuclear dynamics through controlled disruption of nuclear conformation, and imaging in live cells and tissues; and 5)  “pilot” maps (using in-development technologies) and “reference” maps (using robust and validated technologies) of the 3D architecture of the interphase nucleus for a variety of eukaryote cells and tissues.

The Common Fund 4DN Program has been developed to address these critical issues. The overarching goals of the 4DN Program are to understand the principles that guide the spatial and temporal organization of the nucleus, the role of this organization in orchestrating the transcriptional complexity in individual cells and tissues, and the way in which changes in nuclear organization affect development and disease processes. The Program consists of 6 initiatives, of which this FOA is one. Specifically, the initiatives are:

RFA-RM-14-006 Nuclear Organization and Function Interdisciplinary Consortium (U54)

RFA-RM-14-007 Nucleomics Tools (U01)

RFA-RM-14-008 Study of Nuclear Bodies and Compartments (U01)

RFA-RM-14-009 4D Nucleome Imaging Tools (U01)

RFA-RM-14-010 4D Nucleome Network – Organizational Hub (U01)

RFA-RM-14-011 4D Nucleome Network – Data Coordination & Integration Center (U01)

Awards funded under these FOAs are anticipated to pursue research activities conducted by multidisciplinary teams of investigators. In addition, all awardees from all 6 initiatives will form the 4DN Network, with the overarching goal of determining the fundamental principles of nuclear organization. Validation and comparisons across studies will be essential to establish these cross-cutting principles so investigators must be willing to work collaboratively as part of the Network.

This initiative is funded through the NIH Common Fund, which supports crosscutting programs that are expected to have exceptionally high impact. All Common Fund initiatives invite applicants to develop bold, innovative, and often-risky approaches to address problems that may seem intractable or to seize new opportunities that offer the potential for rapid progress.

Research Objectives

The purpose of this Funding Opportunity Announcement (FOA) is to identify and support a Four-Dimensional Nucleome (4DN) Network Data Coordination and Integration Center (DCIC). The overarching mission of 4DN-DCIC will be to collect, store, curate, and display all data, metadata, and analysis tools generated by the 4DN Network. The DCIC will also assist in the development and dissemination of metadata and standards to be adopted by the community at large, approaches for integrative analysis of a wide-range of data types, and visualization and analysis tools to facilitate access and understanding of complex datasets to non-expert users. The 4DN-DCIC, the 4DN Organizational Hub (4DN-OH), the Nuclear Organization and Function Interdisciplinary Consortium (NOFIC) Steering Committee (NOFIC-SC), the 4DN Network Steering Committee (4DN-SC), all 4DN Network investigators, and NIH staff will need to work closely together to accomplish the goals of the 4DN-DCIC in a manner that will best benefit all 4DN investigators as well as the broader scientific community.

Specific activities and roles of the 4DN-DCIC will include, but are not limited to:

  • Collaborating closely with 4DN-OH to develop a data portal for user-friendly submission of and access to 4DN data (both raw data and derived datasets), metadata, and analysis and visualization tools. The web-interface should provide controlled-access to both 4DN Network participants and the broader scientific community, and should be accessible through the main 4DN website to be developed by the 4DN-OH;
  • Establishing a back-end database with an application framework to facilitate complex data loading including detailed experimental descriptions and metadata, especially for experimental results generated using high throughput or data-intensive approaches. The database should be flexible and extensible to manage and integrate multiple types of data, including next-generation sequencing and complex image-based datasets that may be generated by 4DN Network investigators;
  • Working closely with 4DN Network investigators and NIH staff through the NOFIC-SC and the 4DN-SC and specialized 4DN Network working groups to establish metadata requirements, controlled vocabularies, standardized data formats, and quality control metrics for all 4DN data to ensure that the data are interoperable, transportable, and maximally useful to the public;
  • Working closely with 4DN Network investigators to analyze data and develop analysis strategies to integrate the diverse range of 4DN datasets in synergistic ways, and incorporate relevant datasets not supported by the 4DN Program;
  • Providing software, "apps", or other user-friendly computational analysis tools to enable both naïve and experienced investigators, within and outside of the 4DN Network, to query, integrate, analyze, visualize, and model the data, and to compare their own datasets to data generated by 4DN Network investigators;
  • Facilitating data use by the broader scientific community by depositing datasets generated by 4DN Network investigators in appropriate public or controlled-access databases and providing user-friendly access;
  • Collaborating with 4DN-OH to develop and make available tutorials, detailed walkthroughs, virtual machines, etc. that facilitate use of program-generated data by the broader scientific community;
  • Working with NOFIC-SC and 4DN-OH to develop training and outreach strategies to further develop a cadre of multidisciplinary 4DN researchers and to disseminate 4DN data, resources, and analytical tools to the broader scientific community;
  • Working collaboratively with 4DN-OH, NIH staff and relevant public data/resource repositories to ensure the long-term archiving and distribution of the most important datasets and resources developed by the 4DN Network beyond its funding period

Development of the 4DN-DCIC will require the DCIC team to work closely with all units of the 4DN Program, particularly the 4DN-OH, the NOFIC-SC, the 4DN-SC, and NIH staff, to establish data and metadata standards, develop data submission pipelines, establish data freezes and public release of data, and coordinate data integration and analysis. The DCIC will be required to abide by all data sharing and governance policies of the 4DN Program. We anticipate that the majority of datasets handled by the DCIC will be next-generation sequencing data and imaging data. However, it is difficult to predict the exact volume and types of data that will be submitted over the lifetime of the 4DN Program. Increasing efficiencies in generating data along with potential changes in technology platforms may dramatically alter the types and volume of data to be stored, curated, and analyzed by the 4DN-DCIC. Furthermore, the integration of datasets generated outside of the 4DN Network to 4DN databases is likely to add data volume and complexity. Additionally, 4DN-DCIC applicants need to keep in mind that 4DN data will likely be generated across many different model organisms and a variety of cell and tissue types, adding another layer of complexity to the curation and mining of the data. 4DN-DCIC applicants will have to demonstrate that their team and project will have the expertise and flexibility to accommodate increasing data volume and evolving data types.

The 4DN-DCIC is also expected to evolve, adapt and improve during the course of the project in response to the needs of the 4DN Network community. The DCIC team should solicit user feedback and otherwise evaluate all aspects of the usability of the DCIC to best serve the needs of the 4DN Research Network. As the data storage, analysis, and dissemination needs of the 4DN program evolve over time, the DCIC may be asked to implement modifications to its workflows as agreed upon by the 4DN-SC and NIH staff. The DCIC should be  flexible in their implementation of data coordination, analysis, and outreach workflows.

4DN Cooperative Agreement

This FOA uses the U01 Cooperative Agreement mechanism. Successful applicants will become members of the larger 4D Nucleome Network composed of investigators who have been funded in response to at least one of the six related 4DN Network FOAs. In addition to completing the research goals outlined in their applications, successful applicants will be expected to work collaboratively with all members of the 4D Nucleome Network, including the 4DN Network Organizational Hub (RFA-RM-14-010) and the 4DN Network Data Coordination & Integration Center (RFA-RM-14-011), to help develop common standards, metrics for data generation and storage, and data analysis and visualization tools that can be used by the broader scientific community. The 4DN Network will encourage the initiation of new collaborative research projects across the entire network. Some of these interactions could be facilitated by an Opportunity Pool of funds that will be managed by the 4DN Organizational Hub and NIH Program Staff.

A key aspect of this program is the formation of a consortium-type partnership amongst all 4DN Network awardees. Shared responsibilities derived from the use of the Cooperative agreement mechanism are described later in this FOA, and will be further articulated during the kickoff meeting of the 4DN Network that will take place a few months after awards are made. All 4DN Network investigators will be required to attend this initial 4DN Kickoff meeting, as well as annual 4DN investigator meetings and regular teleconferences with Network members and NIH Staff for the duration of the funding cycle. 

All applicants are strongly encouraged to contact NIH Staff to discuss the alignment of their proposed work with the goals of this FOA, and the 4DN Program. A Technical Assistance teleconference will be held for potential applicants.   NIH staff will be available to answer questions related to this FOA.  Time, date, and dial in information for the call will be announced in an NIH Guide Notice and will be posted on the 4DN website: http://commonfund.nih.gov/4Dnucleome/index.

Section II. Award Information
Funding Instrument

Cooperative Agreement: A support mechanism used when there will be substantial Federal scientific or programmatic involvement. Substantial involvement means that, after award, NIH scientific or program staff will assist, guide, coordinate, or participate in project activities.

Application Types Allowed

New

The OER Glossary and the SF424 (R&R) Application Guide provide details on these application types.

Funds Available and Anticipated Number of Awards

NIH Common Fund will commit at least $2.5 million/year for 5 years to support one award intended to be funded in 2015.

Although the financial plans of the NIH provides 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. Future year amounts will depend on annual appropriations.

Award Budget

Application budgets are limited to $2.5 million total costs per year and must reflect actual needs of the proposed project.

Award Project Period

The total project period requested for this FOA may not exceed five years.

NIH grants policies as described in the NIH Grants Policy Statement will apply to the applications submitted and awards made in response to this FOA.

Section III. Eligibility Information
1. Eligible Applicants
Eligible Organizations

Higher Education Institutions

  • Public/State Controlled Institutions of Higher Education
  • Private Institutions of Higher Education

The following types of Higher Education Institutions are always encouraged to apply for NIH support as Public or Private Institutions of Higher Education:

  • Hispanic-serving Institutions
  • Historically Black Colleges and Universities (HBCUs)
  • Tribally Controlled Colleges and Universities (TCCUs)
  • Alaska Native and Native Hawaiian Serving Institutions
  • Asian American Native American Pacific Islander Serving Institutions (AANAPISIs)

Nonprofits Other Than Institutions of Higher Education

  • Nonprofits with 501(c)(3) IRS Status (Other than Institutions of Higher Education)
  • Nonprofits without 501(c)(3) IRS Status (Other than Institutions of Higher Education)

For-Profit Organizations

  • Small Businesses
  • For-Profit Organizations (Other than Small Businesses)

Governments

  • State Governments
  • County Governments
  • City or Township Governments
  • Special District Governments
  • Indian/Native American Tribal Governments (Federally Recognized)
  • Indian/Native American Tribal Governments (Other than Federally Recognized)
  • U.S. Territory or Possession

Other

  • Independent School Districts
  • Public Housing Authorities/Indian Housing Authorities
  • Native American Tribal Organizations (other than Federally recognized tribal governments)
  • Faith-based or Community-based Organizations
  • Regional Organizations
Foreign Institutions

Non-domestic (non-U.S.) Entities (Foreign Institutions) are not eligible to apply.
Non-domestic (non-U.S.) components of U.S. Organizations are not eligible to apply.

Foreign components, as defined in the NIH Grants Policy Statement, are not allowed.

Required Registrations

Applicant Organizations

Applicant organizations must complete and maintain the following registrations as described in the SF 424 (R&R) Application Guide to be eligible to apply for or receive an award. All registrations must be completed prior to the application being submitted. Registration can take 6 weeks or more, so applicants should begin the registration process as soon as possible. The NIH Policy on Late Submission of Grant Applications states that failure to complete registrations in advance of a due date is not a valid reason for a late submission.

  • Dun and Bradstreet Universal Numbering System (DUNS) - All registrations require that applicants be issued a DUNS number. After obtaining a DUNS number, applicants can begin both SAM and eRA Commons registrations. The same DUNS number must be used for all registrations, as well as on the grant application.
  • System for Award Management (SAM) (formerly CCR) – Applicants must complete and maintain an active registration, which requires renewal at least annually. The renewal process may require as much time as the initial registration. SAM registration includes the assignment of a Commercial and Government Entity (CAGE) Code for domestic organizations which have not already been assigned a CAGE Code.
  • eRA Commons - Applicants must have an active DUNS number and SAM registration in order to complete the eRA Commons registration. Organizations can register with the eRA Commons as they are working through their SAM or Grants.gov registration. eRA Commons requires organizations to identify at least one Signing Official (SO) and at least one Program Director/Principal Investigator (PD/PI) account in order to submit an application.
  • Grants.gov – Applicants must have an active DUNS number and SAM registration in order to complete the Grants.gov registration.

Program Directors/Principal Investigators (PD(s)/PI(s))

All PD(s)/PI(s) must have an eRA Commons account.  PD(s)/PI(s) should work with their organizational officials to either create a new account or to affiliate their existing account with the applicant organization in eRA Commons. If the PD/PI is also the organizational Signing Official, they must have two distinct eRA Commons accounts, one for each role. Obtaining an eRA Commons account can take up to 2 weeks.

Eligible Individuals (Program Director/Principal Investigator)

Any individual(s) with the skills, knowledge, and resources necessary to carry out the proposed research as the Program Director(s)/Principal Investigator(s) (PD(s)/PI(s)) is invited to work with his/her organization 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 support.

For institutions/organizations proposing multiple PDs/PIs, visit the Multiple Program Director/Principal Investigator Policy and submission details in the Senior/Key Person Profile (Expanded) Component of the SF424 (R&R) Application Guide.

2. Cost Sharing

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

3. Additional Information on Eligibility
Number of Applications

Applicant organizations may submit more than one application, provided that each application is scientifically distinct.

The NIH will not accept duplicate or highly overlapping applications under review at the same time.  This means that the NIH will not accept:

  • A new (A0) application that is submitted before issuance of the summary statement from the review of an overlapping new (A0) or resubmission (A1) application.
  • A resubmission (A1) application that is submitted before issuance of the summary statement from the review of the previous new (A0) application.
  • An application that has substantial overlap with another application pending appeal of initial peer review (see NOT-OD-11-101).

In addition, the NIH will not accept a resubmission (A1) application that is submitted later than 37 months after submission of the new (A0) application that it follows.  The NIH will accept submission:

  • To an RFA of an application that was submitted previously as an investigator-initiated application but not paid;
  • Of an investigator-initiated application that was originally submitted to an RFA but not paid; or
  • Of an application with a changed grant activity code.
Section IV. Application and Submission Information
1. Requesting an Application Package

Applicants must download the SF424 (R&R) application package associated with this funding opportunity using the “Apply for Grant Electronically” button in this FOA or following the directions provided at Grants.gov.

2. Content and Form of Application Submission

It is critical that applicants follow the instructions in the SF424 (R&R) Application Guide, including Supplemental Grant Application Instructions except where instructed in this funding opportunity announcement to do otherwise. Conformance to the requirements in the Application Guide is required and strictly enforced. Applications that are out of compliance with these instructions may be delayed or not accepted for review.

For information on Application Submission and Receipt, visit Frequently Asked Questions – Application Guide, Electronic Submission of Grant Applications.

Letter of Intent

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.

By the date listed in Part 1. Overview Information, prospective applicants are asked to submit a letter of intent that includes the following information:

  • Descriptive title of proposed activity
  • Name(s), address(es), and telephone number(s) of the PD(s)/PI(s)
  • Names of other key personnel
  • Participating institution(s)
  • Number and title of this funding opportunity

The letter of intent should be sent to:

Sean E. Hanlon, Ph.D. on behalf of the NIH Common Fund 4DN Working Group
National Cancer Institute (NCI)
Division of Cancer Biology (DCB)
Telephone: 240-276-5061
Email: sean.hanlon@nih.gov

Page Limitations

All page limitations described in the SF424 Application Guide and the Table of Page Limits must be followed, with the following exceptions or additional requirements:

  • For this specific FOA, the Research Strategy section is limited to 12 pages.
Instructions for Application Submission

The following section supplements the instructions found in the SF424 (R&R) Application Guide and should be used for preparing an application to this FOA.

SF424(R&R) Cover

All instructions in the SF424 (R&R) Application Guide must be followed.  

SF424(R&R) Project/Performance Site Locations

All instructions in the SF424 (R&R) Application Guide must be followed.  

SF424(R&R) Other Project Information

All instructions in the SF424 (R&R) Application Guide must be followed.  

SF424(R&R) Senior/Key Person Profile

All instructions in the SF424 (R&R) Application Guide must be followed.  In addition applicants should:

  • Demonstrate strong scientific expertise in the areas that are critical to the success of the proposal.
  • Describe any experience in successfully leading the coordination of data intensive activities and management and analysis of high-throughput datasets such as those to be generated by the 4DN Network.
  • Provide evidence of research productivity as a data coordinating center/data analysis center in previous or ongoing genomics research networks.
  • Demonstrate experience and capabilities in designing tools for analysis and visualization of complex scientific data.
Modular or R&R Budget

All instructions in the SF424 (R&R) Application Guide must be followed.

Based on the complexity of 4DN-DCIC and the 4DN Program, the 4DN-DCIC PD(s)/PI(s) are strongly encouraged to propose and budget for a DCIC Administrator to manage day-to-day operations and work with the DCIC Director(s), NIH staff, and 4DN Program investigators to manage and coordinate the DCIC activities.

Budget requests must include costs for the PD/PI to attend the initial in-person 4DN Network kickoff meeting, and for the PI and up to three other members of the project team to attend the annual 4DN Network Investigator's meetings.

Applicants need to demonstrate an understanding of the costs associated with building and operating a Data Coordination and Integration Center and how to track them, in particular the costs for computational infrastructure and for personnel responsible for working with the data producers on data submission (data wranglers) and on data integration, analysis, and visualization (data analyzers). The description of cost should propose a standardized cost structure, including useful units (e.g., per submitted experiment or per terabyte of data) on which to base costs for different aspects of the proposed projects.  Applicants should describe how these costs will change over the course of the project.  All cost analyses should include an explicit item for Direct Costs and then be presented in terms of Total Costs.

R&R Subaward Budget

All instructions in the SF424 (R&R) Application Guide must be followed.

PHS 398 Cover Page Supplement

All instructions in the SF424 (R&R) Application Guide must be followed.  

PHS 398 Research Plan

All instructions in the SF424 (R&R) Application Guide must be followed, with the following additional instructions:

Specific Aims: Applicants should describe the ultimate goals/deliverables that will be generated by the U01. Deliverables should be quantitative whenever possible and would include items such as: (1) establishing consortium-wide consensus for data types and formats and metadata requirements; (2) establishing consortium-wide consensus for a data release policy; (3) establishing a 4DN Data Portal accessible through the main 4DN website that will be established by the 4DN-OH; (4) establishing data import and export pipelines; (5) developing user manuals and walk-throughs for the 4DN Data Portal; (6) developing analysis, integration, and visualization pipelines. As mentioned above, it will be difficult to predict the exact volume and types of data that will be submitted over the lifetime of the 4DN Program. As the data production, storage, analysis, and dissemination needs of the 4DN Network change with time, the 4DN-DCIC may be asked to implement modifications to their workflow and deliverables as agreed upon by the 4DN-SC. 4DN-DCIC applicants should indicate their willingness and aptitude to be flexible in their implementation of 4DN Network coordination.

Research Strategy: The following items must be addressed satisfactorily:

Management and Communication Plan - Applicants should describe the plans for management and integration of the 4DN-DCIC activities. Applicants should describe how s/he will manage the proposed project, who will oversee the day-to-day activities (e.g., a DCIC Administrator if not the PD/PI) and how the management structure will support achievement of the proposed goals and milestones. Useful elements of this description include the organization of the proposed project; its management structure; key personnel and leadership structure; and oversight mechanisms for evaluating progress towards milestones. Applicants should describe plans for ongoing communication and sharing of data and resources within the 4DN-DCIC and plans for addressing some of the anticipated challenges of the 4DN-DCIC.The plan should also describe how the various elements of the proposed production effort will be integrated, and how collaborations or subcontracts, if proposed, will be managed.

Milestones and Progress - A timeline (Gantt chart) including milestones is required for all 4DN applications. Milestones are intermediate steps towards the completion of concrete goals. They must include clear and quantitative criteria for success. Yearly quantitative milestones are required in order to provide clear indicators of a project's continued success or emergent difficulties and will be used to evaluate the application not only in peer review but also in consideration of the awarded project for funding of non-competing award years. The application must include clearly-specified, well-defined milestones, quantitative go/no go decision points, and timelines for assessing progress. Examples include, but are not limited to, milestones that track time to develop data standards and formats, turn-around time to either release submitted data to the Data Portal or analyze particular datasets, or analysis and visualization software development activities.  Applicants should include plans for critically evaluating and revising these milestones on a regular basis.  The number and duration of milestones will depend on the project being proposed, so applicants should include these items for every year, as appropriate. Applicants should describe how they will prioritize their activities to ensure that the main goals of the DCIC will be achieved. Milestones may be revised at the time of the award. Applicants should also describe plans to solicit user feedback, monitor metrics of DCIC usage, and otherwise evaluate all aspects of the usability of the DCIC. This plan should describe the frequency of these evaluations and how this information will be used to improve the utility of the 4DN-DCIC.

Data Portal Development – Applicants should describe plans for developing a data portal that can be accessible through the main 4DN Network web portal (to be developed by the 4DN-OH). The 4DN Data Portal will provide user-friendly submission of and access to 4DN data (both raw data and derived datasets), metadata, and analysis and visualization tools. The web-interface should provide controlled-access to both 4DN Network members and the broader scientific community. Applicants should describe a submission pipeline for both raw and derived datasets generated by 4DN Network investigators.  The DCIC must provide mechanisms and staff to interact with the data production groups to facilitate the timely and efficient transfer of data and metadata to the DCIC.  Each submitted dataset must be assigned a unique identifier that enables subsequent tracking for submitted data of all types.  This pipeline must include quality assurance steps to monitor the quality of the submitted data and metadata, along with steps to release these data and metadata to the public data portal in a timely fashion. As the identity of the actual funded projects will not be known at the time that the applications in response to this FOA are due, applicants should provide a general submission plan. The plan should describe how the DCIC will handle a range of data types from a variety of organisms and how the DCIC will provide the flexibility to accommodate increasing data volume and evolving data types. The plan should describe the capacity to scale activities as data volumes or complexity change over the course of the project. At the end of the project, the DCIC must be able to transfer the 4DN Network data to any other informatics resource, as designated by the NIH.

Information Technology and Technology Development - Applicants should discuss all pertinent informatics issues involved in providing the basic IT infrastructure/system administration for the proposed project.  The plan should describe a framework to facilitate complex data loading including detailed experimental descriptions and metadata, especially for experimental results generated using high throughput or data-intensive approaches. The database infrastructure should be flexible and extensible to manage and integrate multiple types of data, including next-generation sequencing and complex image-based datasets that may be generated by 4DN Network investigators. Incremental technology improvements may play an important role in increasing the efficiency and decreasing costs for the DCIC.  Applicants are encouraged to include plans for such technology development activities in their applications, such as supporting new software tools to improve data management or analysis or making existing software more efficient.  The plans for technology improvement should be well described and the cost of the proposed technology development should be justified in terms of reducing the overall operating costs for the DCIC.  Any needed software development to implement these technology development activities should be described in detail.

Interactions with 4DN Data Producers – Development of the 4DN-DCIC will require the DCIC team to work closely with 4DN Program Investigators and NIH staff. Applicants should describe plans and strategies for facilitating interactions that allow the efficient development of the DCIC. DCIC tasks that will require significant interaction with members of the 4DN Program include, but are not limited to:

  • Working with 4DN Program Investigators and NIH staff to establish standardized data types and machine readable data formats that will be transferred to the DCIC and develop data verification, validation, and quality metrics pipelines.
  • Working with 4DN Program Investigators and NIH staff to define standard experimental metadata required to be submitted with each dataset, including common data elements using well-defined formats and associated controlled vocabularies. 
  • Working with 4DN Program Investigators and NIH staff to establish regular data freezes to quantify productivity and facilitate analysis activities. 
  • Working with 4DN Program Investigators and NIH staff to establish a public data release policy.  The DCIC will need to be flexible and responsive in following the evolving NIH policies on data sharing.
  • Working with 4DN Program Investigators and NIH staff to establish a process for accepting or incorporating data produced outside the 4DN Network to help maximize the value of the 4DN datasets.

Data, Integration, Analysis, and Visualization - As the identity of the actual funded projects will not be known at the time that the applications in response to this FOA are due, applicants should provide general plans integrating, analyzing, and visualizing a range of 4DN datasets including next-generation sequencing data and imaging data. Plans should include approaches for integrating data across length-scales (e.g., sequencing and imaging data). Applicants should also describe analysis strategies to integrate the 4DN datasets in synergistic ways with other relevant datasets. Plans should include a description of all necessary expertise and approaches to support meaningful data integration, analysis, and visualization. Applicants should also describe plans for facilitating analysis interactions amongst 4DN Program investigators and between 4DN Program Investigators and the broader scientific community. These plans may include, but are not limited to, implementing regular Data Analysis Working Group conference calls and organizing data analysis and visualization workshops.

Integration, Analysis, and Visualization Tools - Applicants should describe plans for developing user-friendly analysis and visualization tools, software, and “apps” for both typical biomedical researchers and bioinformatics experts. Any tools and software proposed to be developed should be modular, open-source, and include appropriate documentation, so that it can work as a stand-alone package.  Software should not duplicate existing software with similar features and should leverage existing open-source tools projects as much as possible. Software should use standard formats for data input and output, to facilitate its use and interoperability with other software.

Data Export and Dissemination - Applicants should describe plans for developing an export process and pipeline to permit timely transfer of 4DN data from consortium data freezes or publications to appropriate public repositories and community databases.  These repositories may include, but are not limited to, the Gene Expression Omnibus (GEO) or dbGAP (in the case of control access datasets) at the National Center for Biotechnology Information (NCBI), ArrayExpress at the European Bioinformatics Institute (EBI), the UCSC Genome Browser at the University of California at Santa Cruz, Ensembl at the EBI and the Wellcome Trust Sanger Institute, and OMERO at the University of Dundee and Open Microscope Environment.  Regardless of where datasets are deposited, the 4DN-DCIC will provide access to the 4DN-generated data and metadata for the duration of the Program.  Data and metadata must be available in standard formats to facilitate additional analysis by members of 4DN Network and the broader scientific community. 

Outreach and Training - Applicants should describe a plan and allocate sufficient resources to provide outreach to the user communities to educate the community about the 4DN Network and its data and analytical tools, along with guides for how to access and use the 4DN data. This plan should include training both specialists and non-specialists to make the best use of the 4DN Network data and tools.  Examples include presentations, short courses, and/or symposia offered independently or in conjunction with scientific meetings attended by the user community; web-based tutorials; detailed walkthroughs; and user manuals and training guides that describe the features of the 4DN Data Portal.

Resource Sharing Plan: Individuals are required to comply with the instructions for the Resource Sharing Plans (Data Sharing Plan, Sharing Model Organisms, and Genome Wide Association Studies (GWAS)) as provided in the SF424 (R&R) Application Guide, with the following modifications:

  • Data Release Principles and Standards: All applications, regardless of the amount of direct costs requested for any one year, should include a Data Sharing Plan. Data from this FOA are expected to be shared in an easily accessible, machine readable format in order to increase the value of the significant public investment. Consistent with achieving the goals of this program, the NIH expects that information such as data syntheses, study protocols, bioinformatics tools, and any other metadata collected will be widely shared with the scientific community for research and made publicly available through the 4DN data portal and other data repositories. Applicants should indicate their willingness to cooperate with the 4DN Program, 4DN Network Steering Committee (4DN-SC), NIH staff, and other stakeholders in the development and implementation of research and standardization methods, data standards and formats, metadata requirements, and quality control metrics for this resource. Applicants should also describe prior experience in working as part of a research consortium, developing consensus approaches for data sharing and other research-related topics, or other collaborative activities to meet individual study and collaborative goals.
  • Data sharing: All controlled access data generated through this FOA are expected to be deposited into dbGaP (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap) or other NIH Trusted Partners databases. All data without privacy concerns are expected to be deposited in appropriate public databases and also made available via the 4DN Network Virtual Resource Repository (4DN-VRR) that will be built by the 4DN Network Organizational Hub (4DN-OH) to collect, curate and disseminate information regarding data, critical tools and reagents being developed by the  4DN Network. The 4DN-VRR will be accessible through the 4DN Network Portal. Applicants should indicate their willingness to abide by all data deposition and release policies defined by 4DN-SC and approved by NIH staff. In general, rapid deposition of data into repositories will be expected to maximize utility to the scientific community.  The applicant's milestones should reflect the expected broad and rapid data sharing as outlined in the new NIH data sharing policy (see https://grants.nih.gov/grants/guide/notice-files/NOT-OD-14-124.html ). Additionally, applicants are expected to adhere to future changes to NIH-wide data sharing policies.  Applicants should provide a specific proposal for release of data, and are encouraged to address the issue of frequency of the release, based on practical considerations or previous experience and the recommendations above. Applicants should address whether they anticipate any of their data requiring controlled access. The reasonableness of the proposed data sharing plan will be assessed by the reviewers.
  • Protocol, tool and reagent sharing: The applicant should discuss plans for sharing and distribution of non-data resources that will be generated by the proposed project, including models, protocols, computational tools, biomaterials, and reagents. As one of the essential goals of this program, NIH intends that tools and reagents generated by the 4DN Network be broadly available and distributed at minimal cost, and without undue intellectual property constraints, so that they can be as widely used as possible, thus enabling downstream applications for the reagents by the larger scientific community. The 4DN-OH will work with all 4DN Network investigators to collect, curate and disseminate information regarding critical tools and reagents being developed by the 4DN Network through the 4DN-VRR. 4DN Network investigators and the 4DN-OH will develop solutions to facilitate the request and distribution of 4DN Network-generated tools and reagents within and outside of the 4DN Network community. Whether tools and reagents are distributed by individual investigators or through public repositories, the 4DN-VRR is expected to serve as a "one-stop shop" for all 4DN Network-generated tools and reagents. Applicants should also be familiar with the NIH statements regarding intellectual property of resources developed with Federal funds (NIH Research Tools Policy (https://grants.nih.gov/grants/intell-property_64FR72090.pdf) and other related NIH sharing policies at http://sharing.nih.gov)

Appendix:  Do not use the Appendix to circumvent page limits. Follow all instructions for the Appendix as described in the SF424 (R&R) Application Guide.

Planned Enrollment Report

When conducting clinical research, follow all instructions for completing Planned Enrollment Reports as described in the SF424 (R&R) Application Guide. 

PHS 398 Cumulative Inclusion Enrollment Report

When conducting clinical research, follow all instructions for completing Cumulative Inclusion Enrollment Report as described in the SF424 (R&R) Application Guide. 

3. Submission Dates and Times

Part I. Overview Information contains information about Key Dates. Applicants are encouraged to submit applications before the due date to ensure they have time to make any application corrections that might be necessary for successful submission.

Organizations must submit applications to Grants.gov (the online portal to find and apply for grants across all Federal agencies). Applicants must then complete the submission process by tracking the status of the application in the eRA Commons, NIH’s electronic system for grants administration. NIH and Grants.gov systems check the application against many of the application instructions upon submission. Errors must be corrected and a changed/corrected application must be submitted to Grants.gov on or before the application due date.  If a Changed/Corrected application is submitted after the deadline, the application will be considered late.

Applicants are responsible for viewing their application before the due date in the eRA Commons to ensure accurate and successful submission.

Information on the submission process and a definition of on-time submission are provided in the SF424 (R&R) Application Guide.

4. Intergovernmental Review (E.O. 12372)

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.

Pre-award costs are allowable only as described in the NIH Grants Policy Statement.

6. Other Submission Requirements and Information

Applications must be submitted electronically following the instructions described in the SF424 (R&R) Application Guide.  Paper applications will not be accepted.

Applicants must complete all required registrations before the application due date. Section III. Eligibility Information contains information about registration.

For assistance with your electronic application or for more information on the electronic submission process, visit Applying Electronically.

Important reminders:
All PD(s)/PI(s) must include their eRA Commons ID in the Credential field of the Senior/Key Person Profile Component of the SF424(R&R) Application Package. Failure to register in the Commons and to include a valid PD/PI Commons ID in the credential field will prevent the successful submission of an electronic application to NIH. See Section III of this FOA for information on registration requirements.

The applicant organization must ensure that the DUNS number it provides on the application is the same number used in the organization’s profile in the eRA Commons and for the System for Award Management. Additional information may be found in the SF424 (R&R) Application Guide.

See more tips for avoiding common errors.

Upon receipt, applications will be evaluated for completeness by the Center for Scientific Review and responsiveness by components of participating organizations, NIH. Applications that are incomplete and/or nonresponsive will not be reviewed.  

Post Submission Materials

Applicants are required to follow the instructions for post-submission materials, as described in NOT-OD-13-030.

Section V. Application Review Information
1. Criteria

Only the review criteria described below will be considered in the review process. As part of the NIH mission, all applications submitted to the NIH in support of biomedical and behavioral research are evaluated for scientific and technical merit through the NIH peer review system.

Overall Impact

Reviewers will provide an overall impact score to reflect their assessment of the likelihood for the project to exert a sustained, powerful influence on the research field(s) involved, in consideration of the following review criteria and additional review criteria (as applicable for the project proposed).

Scored Review Criteria

Reviewers will consider each of the review criteria below in the determination of scientific merit, and give a separate score for each. An application does not need to be strong in all categories to be judged likely to have major scientific impact. For example, a project that by its nature is not innovative may be essential to advance a field.

Significance

Does the project address an important problem or a critical barrier to progress in the field? If the aims of the project are achieved, how will scientific knowledge, technical capability, and/or clinical practice be improved? How will successful completion of the aims change the concepts, methods, technologies, treatments, services, or preventative interventions that drive this field?

Specific to this FOA: How well do the proposed plans address the data coordination, integration, analysis, and visualization needs of the 4DN Network? How well will the proposed plans facilitate the research and analysis across the components of the 4DN Network? How well will the proposed plans address major challenges in data coordination, integration, analysis, and visualization? How well will the proposed 4DN-DCIC coordinate, integrate, analyze, and visualize data across length-scales (e.g., sequencing data and imaging data)?

Investigator(s)

Are the PD(s)/PI(s), collaborators, and other researchers well suited to the project? If Early Stage Investigators or New Investigators, or in the early stages of independent careers, do they have appropriate experience and training? If established, have they demonstrated an ongoing record of accomplishments that have advanced their field(s)? If the project is collaborative or multi-PD/PI, do the investigators have complementary and integrated expertise; are their leadership approach, governance and organizational structure appropriate for the project?

Specific to this FOA: Do the PD(s)/PI(s) have demonstrated experience with the development and management of computational infrastructures and tools to help coordinate, integrate, analyze, and visualize complex and high-throughput biomedical research datasets (e.g., next-generation sequencing data, complex imaging data)? Do the PD(s)/PI(s) provide evidence of experience working productively in collaborative environments and in large, distributed scientific projects? How well do the PD(s)/PI(s) and/or key personnel demonstrate scientific expertise and knowledge in the areas relevant to the 4DN Network? Will the PD(s)/PI(s) and additional key personnel provide the appropriate level of effort to effectively lead the project, coordinate with members of the 4DN Network, and meet milestones? Are the management plans, experience, and levels of effort appropriate for managing a project of this magnitude?

Innovation

Does the application challenge and seek to shift current research or clinical practice paradigms by utilizing novel theoretical concepts, approaches or methodologies, instrumentation, or interventions? Are the concepts, approaches or methodologies, instrumentation, or interventions novel to one field of research or novel in a broad sense? Is a refinement, improvement, or new application of theoretical concepts, approaches or methodologies, instrumentation, or interventions proposed?

Specific to this FOA: How well will the proposed analysis, integration, and visualization approaches address current scientific or technical challenges in creative ways? How well does the applicant propose innovative plans (e.g., outreach and communication strategies, data coordination solutions, data analysis approaches) for addressing the goals and challenges of the proposed 4DN-DCIC?

Approach

Are the overall strategy, methodology, and analyses well-reasoned and appropriate to accomplish the specific aims of the project? Are potential problems, alternative strategies, and benchmarks for success presented? If the project is in the early stages of development, will the strategy establish feasibility and will particularly risky aspects be managed? 

If the project involves human subjects and/or NIH-defined clinical research, are the plans to address 1) the protection of human subjects from research risks, and 2) inclusion (or exclusion) of individuals on the basis of sex/gender, race, and ethnicity, as well as the inclusion or exclusion of children, justified in terms of the scientific goals and research strategy proposed?

Specific to this FOA: How reasonable and appropriate are the plans to work with other 4DN Network members to develop data standards and formats, metadata requirements, and data release policies?  How reasonable and appropriate are the milestones, timelines, and goals proposed for the 4DN-DCIC? How reasonable and appropriate are the plans to import, store, and disseminate the relevant 4DN datasets? How reasonable and appropriate are the plans to develop the basic IT infrastructure/system administration for the 4DN-DCIC? How reasonable and appropriate are the plans for the release of 4DN data, metadata, software, or technologies? How reasonable and appropriate are the plans to integrate or link to data from other sources? How reasonable and appropriate are the plans to adapt to changing data types and volumes and feedback from the 4DN Network members? How reasonable and appropriate are the plans for training and providing support to users of the 4DN-DCIC with different levels of bioinformatics skills? What is the likelihood that the proposed project can effectively facilitate the integrative analysis of 4DN data? Are the plans to identify and recruit groups with needed expertise for the analyses reasonable and appropriate? How well does the DMRR overall plan allow for data transportability and data interoperability in the future?

Environment

Will the scientific environment in which the work will be done contribute to the probability of success? Are the institutional support, equipment and other physical resources available to the investigators adequate for the project proposed? Will the project benefit from unique features of the scientific environment, subject populations, or collaborative arrangements?

Specific to this FOA: Is the computational infrastructure adequate to meet the needs of the project? How well does the environment promote collaborations and transdisciplinary approaches to solving the technical and scientific problems of the proposed 4DN-DCIC?

Additional Review Criteria

As applicable for the project proposed, reviewers will evaluate the following additional items while determining scientific and technical merit, and in providing an overall impact score, but will not give separate scores for these items.

Protections for Human Subjects

For research that involves human subjects but does not involve one of the six categories of research that are exempt under 45 CFR Part 46, the committee will evaluate the justification for involvement of human subjects and the proposed protections from research risk relating to their participation according to the following five review criteria: 1) risk to subjects, 2) adequacy of protection against risks, 3) potential benefits to the subjects and others, 4) importance of the knowledge to be gained, and 5) data and safety monitoring for clinical trials.

For research that involves human subjects and meets the criteria for one or more of the six categories of research that are exempt under 45 CFR Part 46, the committee will evaluate: 1) the justification for the exemption, 2) human subjects involvement and characteristics, and 3) sources of materials. For additional information on review of the Human Subjects section, please refer to the Guidelines for the Review of Human Subjects.

Inclusion of Women, Minorities, and Children 

When the proposed project involves human subjects and/or NIH-defined clinical research, the committee will evaluate the proposed plans for the inclusion (or exclusion) of individuals on the basis of sex/gender, race, and ethnicity, as well as the inclusion (or exclusion) of children to determine if it is justified in terms of the scientific goals and research strategy proposed. For additional information on review of the Inclusion section, please refer to the Guidelines for the Review of Inclusion in Clinical Research.

Vertebrate Animals

The committee will evaluate the involvement of live vertebrate animals as part of the scientific assessment according to the following five points: 1) proposed use of the animals, and species, strains, ages, sex, and numbers to be used; 2) justifications for the use of animals and for the appropriateness of the species and numbers proposed; 3) adequacy of veterinary care; 4) procedures for limiting discomfort, distress, pain and injury to that which is unavoidable in the conduct of scientifically sound research including the use of analgesic, anesthetic, and tranquilizing drugs and/or comfortable restraining devices; and 5) methods of euthanasia and reason for selection if not consistent with the AVMA Guidelines on Euthanasia. For additional information on review of the Vertebrate Animals section, please refer to the Worksheet for Review of the Vertebrate Animal Section.

Biohazards

Reviewers will assess whether materials or procedures proposed are potentially hazardous to research personnel and/or the environment, and if needed, determine whether adequate protection is proposed.

Resubmissions

Not Applicable

Renewals

Not Applicable

Revisions

Not Applicable

Additional Review Considerations

As applicable for the project proposed, reviewers will consider each of the following items, but will not give scores for these items, and should not consider them in providing an overall impact score.

Applications from Foreign Organizations

Not Applicable

Select Agent Research

Reviewers will assess the information provided in this section of the application, including 1) the Select Agent(s) to be used in the proposed research, 2) the registration status of all entities where Select Agent(s) will be used, 3) the procedures that will be used to monitor possession use and transfer of Select Agent(s), and 4) plans for appropriate biosafety, biocontainment, and security of the Select Agent(s).

Resource Sharing Plans

Reviewers will comment on whether the following Resource Sharing Plans, or the rationale for not sharing the following types of resources, are reasonable: 1) Data Sharing Plan; 2) Sharing Model Organisms; and 3) Genome Wide Association Studies (GWAS).

Budget and Period of Support

Reviewers will consider whether the budget and the requested period of support are fully justified and reasonable in relation to the proposed research.

2. Review and Selection Process

Applications will be evaluated for scientific and technical merit by (an) appropriate Scientific Review Group(s) convened by the Center for Scientific Review in accordance with NIH peer review policy and procedures, using the stated review criteria. Assignment to a Scientific Review Group will be shown in the eRA Commons.

As part of the scientific peer review, all applications:

  • May undergo a selection process in which only those applications deemed to have the highest scientific and technical merit (generally the top half of applications under review) will be discussed and assigned an overall impact score.
  • Will receive a written critique.

Appeals of initial peer review will not be accepted for applications submitted in response to this FOA.

Applications will be assigned on the basis of established PHS referral guidelines to the appropriate NIH Institute or Center. Applications will compete for available funds with all other recommended applications submitted in response to this FOA. Following initial peer review, recommended applications will receive a second level of review by the appropriate national Advisory Council or Board. The following will be considered in making funding decisions:

  • Scientific and technical merit of the proposed project as determined by scientific peer review.
  • Availability of funds.
  • Relevance of the proposed project to program priorities.
  • Compliance with data and resource sharing plan as appropriate
  • Adequacy of the milestone plan
3. Anticipated Announcement and Award Dates

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

Information regarding the disposition of applications is available in the NIH Grants Policy Statement.

Section VI. Award Administration Information
1. Award Notices

If the application is under consideration for funding, NIH will request "just-in-time" information from the applicant as described in the NIH Grants Policy Statement.

A formal notification in the form of a Notice of Award (NoA) will be provided to the applicant organization for successful applications. The NoA signed by the grants management officer is the authorizing document and will be sent via email to the grantee’s business official.

Awardees must comply with any funding restrictions described in Section IV.5. Funding Restrictions. 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.      

Any application awarded in response to this FOA will be subject to terms and conditions found on the Award Conditions and Information for NIH Grants website.  This includes any recent legislation and policy applicable to awards that is highlighted on this website.

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  and Part II: Terms and Conditions of NIH Grant Awards, Subpart B: Terms and Conditions for Specific Types of Grants, Grantees, and Activities. More information is provided at Award Conditions and Information for NIH Grants.

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 U01, 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.

The PI(s) will have the primary responsibility for:

  • The 4DN-DCIC PD/PIwill be primarily responsible for the planning and conduct of the operations defined by the terms and conditions of the cooperative agreement award.
  • The 4DN-DCIC PD/PI will assume responsibility and accountability to the applicant organization officials and to the NIH for the performance and proper conduct of the research and administrative functions supported under this FOA in accordance with the terms and conditions of award, as well as all pertinent laws, regulations, and policies.
  • The 4DN-DCIC PD/PI and all of her/his staff will be required to participate in a cooperative, interactive, and collaborative manner with NIH staff, 4DN Network investigators, and one another.
  • The 4DN-DCIC PD/PI and all of her/his staff will maintain the confidentiality of the information developed or handled by the 4DN-DCIC, including, without limitation, unpublished data, informatics tools, protocols, data analysis, confidential exchanges between members of the 4DN Network, etc. per policies approved by the 4DN Network Steering Committee, as well as any confidential information received by third party collaborators.
  • The 4DN-DCIC PD/PI agrees to serve on the 4DN Network Steering Committee (4DN-SC) and work with the 4DN-SC to establish agreements that address the following issues: (1) procedures for data sharing among consortium members, data sharing with the scientific community outside of the 4DN Network, and data sharing with industry partners; (2) procedures for safeguarding confidential information, including without limitation, any data generated by the consortium as well as information and/or data received from external collaborators; (3) procedures for addressing ownership of intellectual property that result from aggregate multi-party data; (4) procedures for sharing tools and reagents under an overarching MTA amongst consortium members that operationalizes material transfer in an efficient and expeditious manner; (5) publication policy for the entire 4DN Network, determining timing, authorship and content of co-publications, in order to facilitate collaborations and co-publications by consortium members while protecting each 4DN Network investigator’s primary ownership and authorship of their data and discoveries. 
  • The 4DN-DCIC PD/PI will appoint a 4DN-DCIC representative to the NOFIC-SC, and will be allowed to change this appointment at any time following consultation with the NOFIC-SC and NIH staff.
  • The 4DN-DCIC PD/PI, in collaboration with the 4DN-OH PI, are expected to facilitate the public release and dissemination of results, data, reagents, technologies and other products generated by 4DN Network investigators in a timely manner, consistent with achieving the goals of this program. The release and dissemination will be consistent with sharing policies and recommendations developed and approved by the 4DN-SC, NIH sharing policies, and the goals of the FOA.
  •  The 4DN-DCIC PD/PI agrees that industry collaborations should be governed by a research collaboration agreement (e.g. CTA, RCA, etc) with terms that ensure the collaboration is conducted in accordance with the Cooperative Agreement, applicable NIH policies and procedures and any policies and procedures developed by the 4DN-DCIC or the 4DN-SC.
  • The 4DN-DCIC PD/PI must operate in accordance with processes and goals as delineated in the Funding Opportunity Announcement.
  • The 4DN-DCIC PD/PI must operate in accordance with processes, goals, and policies established by the 4DN-SC.
  • The 4DN-DCIC PD/PI in collaboration with the 4DN-OH PI must ensure that data, metadata, models, software, and other tools developed as part of 4DN Program are deposited in the 4DN Data Portal in a timely manner that is consistent with 4DN Network policies.
  • Upon completion or termination of the 4DN-DCIC project, the Awardee is responsible for making all study materials, tools, databases and procedures developed by the 4DN Network broadly available (e.g., putting into the public domain) or making them accessible to the research community according to the NIH-approved plan submitted for each project, for making data and materials available to the scientific community and the NIH. The data sharing plan should include a plan to accomplish this at the end of the study.

Adherence to a 4DN Communication Plan:

A consensus 4DN Communication Plan will be drafted by the 4DN-SC during the kickoff meeting of the 4DN Network. This plan will clearly spell out interactive requirements that all 4DN investigators are expected to follow, including:

  • Participate on regular conference calls with fellow 4DN colleagues through contribution to various sub-committees and working groups;
  • Coordinate efforts with other awardees, in particular through interactions with the Organizational Hub and the Data Coordination & Integration Center;
  • Participate and present findings at annual workshops convened by Organizational Hub;
  • Jointly publish findings in a timely manner; a consensus guidance document articulating the clearance mechanism for joint publications will need to be developed by the 4DN-SC.

NIH staff have substantial programmatic involvement that is above and beyond the normal stewardship role in awards, as described below:

  • The NIH will designate program staff, including a Program Officer and a Grants Management Specialist to provide stewardship and administrative oversight of the cooperative agreement.  The Program Officer and Grants Management Specialist will be named in the Notice of Grant Award.
  • An NIH Project Scientist will be substantially involved in this project above and beyond the normal stewardship of an NIH Program Official as follows:
  • The NIH Project Scientist will coordinate and facilitate the activities of the 4DN-DCIC, attend and participate in administrative meetings involving the 4DN-DCIC as appropriate, and act as a liaison between the Awardee and the External Experts.
  • The NIH Project Scientist and Program Officer will review the progress and administrative accomplishments of the 4DN-DCIC, and review the project for compliance with operating policies developed by the 4DN Network Steering Committees and the NIH.  Based on this review, the Project Scientist in conjunction with the Program Officer may recommend to the NIH to continue funding, or to withhold or restrict support for lack of progress or failure to adhere to 4DN Network or NIH policies. Review of progress may include regular communications between the 4DN-DCIC PD/PI and NIH staff, periodic site visits for discussions with the 4DN-DCIC team, fiscal review, and other relevant matters. The NIH retains the option of organizing periodic external review of progress.
  • The NIH reserves the right to terminate the 4DN-DCIC award in the event of (1) A substantial shortfall in accomplishing the management goals and responsibilities as stated in the reviewed application, (2) A failure to meet the 4DN Network policies and procedures, (3) Substantive changes in the management of 4DN-DCIC that are not in keeping with the objectives of the FOA, and/or (4) failure to make substantial progress towards milestones keeping in mind the agreed upon go/no-go decisions.
  • The NIH Project Scientist will have substantial programmatic involvement in the coordination of the administrative management of the 4DN-DCIC and in monitoring the performance of the 4DN-DCIC. The dominant role and primary responsibility for the 4DN-DCIC organization and activities resides with the awardee, however, specific tasks and activities in carrying out the 4DN-DCIC functions will be shared among the awardee and the NIH Project Scientist. Functions of the NIH Project Scientist may include, but are not limited to:
  • Serving as a resource with respect to other ongoing NIH activities that may be relevant to 4DN-DCIC operations to facilitate compatibility and avoid unnecessary duplication of effort;
  • Developing and reviewing procedures for assessment and monitoring the performance of the 4DN-DCIC;
  • Enlisting additional scientific or administrative consultants as necessary from within the NIH to assist the Project Scientist in carrying out the goals or improving the performance of the 4DN-DCIC.
  • Participating in the preparation of pertinent manuscripts.
  • The NIH Project Scientist may be a co-author on study publications if s/he has contributed significantly and creatively to the activity of the 4DN-DCIC.

Areas of Joint Responsibility include

The 4DN-DCIC PD/PI in collaboration with the 4DN-OH PD/PI, 4DN Network Steering Committee, and NIH staff, will determine criteria and processes for quality control of information and data to be posted for the research community, consistent with NIH policies and achieving the goals of the program as described in the Funding Opportunity Announcement. There will be an initial face-to-face meeting of 4DN Network PIs soon after all 4DN Network awards have been made, followed by at least one 4DN Network investigator meeting annually. The 4DN-DCIC PD/PI, the 4DN-DCIC Project Scientist, the 4DN-DCIC Program Official are expected to attend these meetings.

  • 4DN Network Steering Committee (4DN-SC)

The awardee agrees to the role and authority of a 4DN Network Steering Committee (4DN-SC) that is responsible for joint governance of 4DN Network activities. The main characteristics and functions of the 4DN-SC are as follows:

  • The 4DN-SC will be composed at a minimum of its nine voting members: the 4DN-OH PD/PI, the 4DN-DCIC PD/PI, three elected members of the NOFIC Steering Committee (NOFIC-SC), three peer-elected PDs/PIs representing each one of the three technology-development FOAs (RFA-RM-14-007, RFA-RM-14-008 and RFA-RM-14-009) and one NIH Project Scientist involved in the management of the 4DN Network. The 4DN-OH PD/PI and 4DN-DCIC PD/PI will be permanent members of the 4DN-SC. All other members of the 4DN-SC will be selected by their peers to serve 2-year term on the 4DN-SC. Renewal or continuation of 4DN-SC membership will be decided during the in-person meeting of the 4DN-SC at the 2nd and 4th annual 4DN Network Investigator Meeting.  Other designated NIH program staff, 4DN-OH staff, 4DN-DCIC staff or external experts may attend the 4DN-SC meetings on a regular or ad-hoc basis, but will be ex officio (non-voting) members.
  • The 4DN-SC will be constituted at the 4DN Network kick-off meeting, and will meet at least quarterly, including at least once in-person during the annual 4DN Network Investigator Meeting.
  • The first meeting of the 4DN-SC will be chaired by the NIH representative on the 4DN-SC. Following that initial meeting, a Chairperson for the 4DN-SC will be chosen by the NIH amongst the 4DN-SC to serve a two-year term. The Chairperson is responsible for coordinating the 4DN-SC activities, for preparing meeting agendas and for chairing 4DN-SC meetings. After two years of service, NIH staff may ask the 4DN-SC Chairperson to serve a second 2-year term, or choose a replacement for that role. NIH staff may also choose to replace the 4DN-SC Chair at any time based on poor job performance or failure to follow the relevant procedures and guidelines.
  • All major scientific and policy decisions will be determined by voting policies as established by the 4DN-SC. Specific activities of the 4DN-SC will include, but are not limited to: developing collaborative protocols; identifying impediments to success and strategies to overcome them; developing shared tools for disseminating information about the 4DN Network projects; identifying opportunities for sharing techniques, materials, information and tools developed within each individual 4DN Network project; facilitating communication and fostering collaboration across the 4DN Network; reviewing progress of the 4DN Network towards meeting the overall Network goals; developing publication policies to facilitate collaborations and co-publications by consortium members; developing  data standards, metadata requirements, data quality standards, and submission and release policies; ensuring the 4DN Network leverages existing NIH resources and programs; making recommendations on the possible use of the “opportunity pool” of funds, such as topics for initiatives or tool/reagent-development projects  that can benefit the 4DN Network activities; reviewing the progress of applications or projects that will use "opportunity pool" funds; helping organize the scientific Agenda for the annual 4DN Network Investigator Meeting. 
  • Trans-4DN Network subcommittees and working groups may be constituted following recommendations and approval by the 4DN-SC, to help the 4DN-SC with scientific planning activities, development of common 4DN Network standards and policies, etc.
  • The 4DN-OH is responsible for providing and maintaining a record of minutes of all 4DN-SC meetings, which will be approved by the 4DN-SC.
  • The 4DN-SC activities and decisions will consider the advice of the NOFIC-SC, various trans-4DN Network subcommittees and working groups, and the 4DN-ESP.
  • NIH Project Scientists involved with the management of the 4DN Network will help the 4DN-SC develop and draft sharing and operating policies that are in accordance with NIH guidelines. NIH Project Scientists, in concert with the 4DN-SC, will also have the option to redirect activities or operations being pursued within the 4DN-OH and 4DN-DCIC if it is considered beneficial to the overall program.
  • The 4DN-OH PD/PI and 4DN-DCIC PD/PI will be responsible for accepting and implementing the goals, priorities, procedures, protocols, and policies agreed upon by the 4DN-SC. The 4DN-OH PD/PI, the 4DN-DCIC PD/PI, and the 4DN-SC Chair will jointly report progress with regard to overall 4DN Network activities and the development of new 4DN Network policies at the annual 4DN Investigator Meeting.
  • NOFIC Steering Committee (NOFIC-SC)

The main characteristics and functions of the NOFIC-SC are as follows:

  • The NOFIC-SC will be composed at a minimum of the following voting members: all NOFIC U54 PDs/PIs, one representative of the 4DN-DCIC and one NIH Project Scientist involved in the management of the NOFIC. A staff member of the 4DN-OH will facilitate NOFIC-SC meetings and teleconferences and generate minutes, that will need to be approved by the NOFIC-SC. Other individuals involved with the management of the 4DN Network could participate as Ex Officio (non-voting members) to the NOFIC-SC, in a permanent or ad hoc fashion, as needed and agreed upon by the voting members of the NOFIC-SC. These individuals could include various members of the 4DN-DCIC and the 4DN-OH, non-PI NOFIC investigators, or 4DN Network investigators who are not part of NOFIC. NIH staff and 4DN external experts will always be allowed to attend meetings and teleconferences of the NOFIC-SC as non-voting participants.
  • The NOFIC-SC will be constituted at the 4DN Network kick-off meeting, and will meet at least quarterly, including at least once in-person during the annual 4DN Network Investigator Meeting. The first meeting of the NOFIC-SC will be chaired by the NIH representative on the NOFIC-SC. Following that initial meeting, a Chairperson for the NOFIC-SC will be chosen by the NIH amongst NOFIC U54 PDs/PIs to serve a two-year term. The Chairperson is responsible for coordinating the NOFIC-SC activities, for preparing meeting agendas and for chairing NOFIC-SC meetings. After two years of  service, NIH staff may ask the NOFIC-SC Chairperson to serve a second 2-year term, or chose a replacement for that role. NIH staff may also choose to replace the NOFIC-SC Chair at any time based on poor job performance or failure to follow the relevant procedures and guidelines. During its initial meeting, the NOFIC-SC will also elect three NOFIC representatives to the 4DN-SC.
  • Specific activities of the NOFIC-SC will include, but are not limited to: facilitate communication and foster collaborations across the NOFIC; identify opportunities for sharing techniques, materials, information and tools developed by NOFIC investigators; develop  data standards, metadata requirements, data quality standards in close collaboration with the 4DN-DCIC; identify common cell types and/or biological systems to be used by all NOFIC investigators for the development of performance and reproducibility standards, NOFIC-wide “pilot mapping” efforts using combinations of mapping technologies, or the validation of models of structure/function relationships across NOFIC projects; review progress of the NOFIC towards meeting the overall goal of developing a set of complementary mapping strategies that can be combined to build comprehensive, whole-genome, and high-definition reference maps of the physical and functional organization of mammalian nuclear genomes and update NIH Staff regularly on the level of performance of the various NOFIC-supported mapping technologies, data analysis tools and computational modeling tools, to include metrics and measurements of reproducibility, accuracy, biological relevance and cost-effectiveness; help NIH assess when specific mapping technologies are sufficiently robust, validated and reliable to be used for the building of reference maps of genome organization in mammalian cells, at which point NIH staff may encourage NOFIC investigators to start producing a small set of such “reference maps” in specific cell types and/or tissues that will be chosen through consensus deliberations by the NOFIC-SC; make recommendations to the 4DN-SC on the possible use of the “opportunity pool” of funds, by proposing topics for initiatives or tool/reagent-development projects that can benefit NOFIC and 4DN Network activities;
  • NOFIC subcommittees and working groups may be constituted following recommendations and approval by the NOFIC-SC, to help the NOFIC-SC with strategic planning activities, development of standards and policies, etc.
  • The 4DN-OH is responsible for providing and maintaining a record of minutes of all NOFIC-SC meetings, which will be approved by the NOFIC-SC.
  • The NOFIC-SC activities and decisions will consider the advice of the 4DN-SC, various trans-4DN Network subcommittees and working groups, and the 4DN Network External Scientific Panel (4DN-ESP, defined below).
  • NIH Project Scientists involved with the management of the NOFIC will help the NOFIC-SC develop and draft sharing and operating policies that are in accordance with NIH guidelines. NIH Project Scientists, in concert with the NOFIC-SC, will also have the option to redirect activities or operations being pursued within the NOFIC and 4DN-DCIC if it is considered beneficial to the overall program.

4DN Network External Scientific Panel (4DN-ESP)

An independent panel of 3-6 External Experts will be appointed by NIH and meet by teleconference with the 4DN-SC at least once a year. The 4DN-ESP will be updated on progress and provide feedback to NIH on adjustments and future directions for the 4DN Network activities.  NIH staff will appoint a 4DN-ESP Chair who will attend the annual 4DN Network Investigator Scientific Retreat and be invited to participate ex officio in 4DN-SC meetings.  All members of the 4DN-ESP will be given the opportunity to listen to 4DN-SC meetings and to attend the annual 4DN Network Investigator Scientific Retreat. The 4DN-OH will support costs for 4DN-ESP members to participate in the 4DN Network Investigator Annual Meeting.

Dispute Resolution:

Disagreements that may arise in scientific/technical matters, publication/authorship matters or programmatic matters (within the scope of the award) between award recipients, or between award recipients and the NIH, may be brought to arbitration after first attempting to resolve the issue through the 4DN-SC or its subcommittees, as appropriate. An Arbitration Panel composed of three members will be convened.  The Panel will be composed of: a designee of the 4DN-SC 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 members; in the case of individual disagreement, the first member may be chosen by the individual awardee. This special dispute resolution procedure in no way affects the awardee's right to appeal an adverse action in accordance with PHS regulations at 42 CFR Part 50, Subpart D, and HHS regulations at 45 CFR Part 16.

3. Reporting

When multiple years are involved, awardees will be required to submit the annual Non-Competing Progress Report (PHS 2590 or RPPR) and financial statements as required in the NIH Grants Policy Statement.

A final progress report, invention statement, and the expenditure data portion of the Federal Financial Report are required for closeout of an award, as described in the NIH Grants Policy Statement.

The Federal Funding Accountability and Transparency Act of 2006 (Transparency Act), includes a requirement for awardees of Federal grants to report information about first-tier subawards and executive compensation under Federal assistance awards issued in FY2011 or later.  All awardees of applicable NIH grants and cooperative agreements are required to report to the Federal Subaward Reporting System (FSRS) available at www.fsrs.gov on all subawards over $25,000.  See the NIH Grants Policy Statement for additional information on this reporting requirement. 

Section VII. Agency Contacts

We encourage inquiries concerning this funding opportunity and welcome the opportunity to answer questions from potential applicants.

Application Submission Contacts

eRA Commons Help Desk (Questions regarding eRA Commons registration, submitting and tracking an application, documenting system problems that threaten submission by the due date, post submission issues)
Telephone: 301-402-7469 or 866-504-9552 (Toll Free)
Finding Help Online: https://grants.nih.gov/support/index.html
Email: commons@od.nih.gov

Grants.gov Customer Support (Questions regarding Grants.gov registration and submission, downloading forms and application packages)
Contact CenterTelephone: 800-518-4726
Email: support@grants.gov

GrantsInfo (Questions regarding application instructions and process, finding NIH grant resources)
Telephone: 301-710-0267
Email: GrantsInfo@nih.gov

Scientific/Research Contact(s)

Sean E. Hanlon, Ph.D.
National Cancer Institute (NCI)
Telephone: 240-276-5061
Email: sean.hanlon@nih.gov

Peer Review Contact(s)

David Balasundaram, Ph.D.
Center for Scientific Review (CSR)
Telephone: 301-435-1022
Email: balasundaramd@csr.nih.gov    

Financial/Grants Management Contact(s)

Crystal Wolfrey
National Cancer Institute (NCI)
Telephone: 240-276-6277
Email: wolfreyc@mail.nih.gov

Section VIII. Other Information

Recently issued trans-NIH policy notices may affect your application submission. A full list of policy notices published by NIH is provided in the NIH Guide for Grants and Contracts. All awards are subject to the terms and conditions, cost principles, and other considerations described in the NIH Grants Policy Statement.

Authority and Regulations

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 Part 52 and 45 CFR Parts 74 and 92.

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