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dkNET Pilot Program
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Funding Opportunity Title:

dkNET New Investigator Pilot Program in Bioinformatics


Key Dates
Posted Date: November 01, 2019
Letter of Intent Due Date: January 14, 2020
Application Due Date: February 14, 2020
Scientific Review: March-April 2020
Start Date: May 2020
Expiration Date: February 15, 2020

Sections:

Section I. Funding Opportunity Purpose

As high throughput technologies become routine for individual laboratories in biomedical research, there is a growing need to develop a workforce that can use and further refine the computational approaches needed to interrogate complex data. This pilot program, through the NIDDK Information Network (dkNET), is designed to encourage new investigators to apply innovative bioinformatics approaches to important research problems in Diabetes, Endocrinology and Metabolic Diseases (DEMD). The dkNET New Investigator Pilot Program is designed to: (i) facilitate the ability of Early Stage and New Investigators with computational and bioinformatics expertise to pursue research questions in DEMD, or (ii) allow Early Stage and New PIs currently pursuing DEMD-related research to explore incorporating computational, statistical, and/or bioinformatics approaches into their research projects.

Section II. Funding Opportunity Description

Background

Contemporary biomedical research is increasingly dependent on high dimensional and high throughput technologies that generate vast amounts of complex data. Experimental approaches such as Genome Wide Association Studies (GWAS), whole genome sequencing, epigenomic mapping, transcriptomics, proteomics, metabolomics profiling, as well as an array of single cell high dimensional measures are increasingly being applied in NIDDK-relevant research. Extensive data and computational resources are also required to support modern image analysis and structural studies of proteins and chemical entities involved in biological processes. Accordingly, many NIDDK-supported research projects have already generated large datasets that are relevant to DEMD mission areas. Many of these datasets require complex analysis using sophisticated bioinformatics to reveal important characteristics related to disease incidence, onset, severity, and therapeutic responses. The ultimate goal of this pilot program is to increase the number of investigators that have the skill sets needed to apply modern computational approaches to important questions in DEMD research.

Objectives and Scope

Bioinformatics is an interdisciplinary field that applies quantitative sciences concepts and computational methods to advance our understanding of biological data and principles. Acquiring bioinformatics expertise will be important for many new DEMD investigators who need to manage large datasets and to use associated databases and analytical pipelines to solve contemporary biological problems. On the other hand, investigators with existing bioinformatics expertise will need to develop an in-depth knowledge of the biological systems that underlie the data to design relevant and practical approaches. In the future, having cross-disciplinary expertise in both laboratory and quantitative biology will be important for formulating relevant questions, for choosing the proper analytical techniques, and for presenting the outcomes in a meaningful and impactful way. The goal of the dkNET Pilot Award program is to provide support for Early Stage and New Investigators seeking to apply computationally-intensive methods to important questions in diabetes, endocrinology and metabolic diseases research. These awards will provide funding for preliminary studies that can serve as a foundation for the development of future grant applications in DEMD-focused topic areas.

dkNET Pilot Award applications should focus on applying computational and/or modeling approaches to compelling research problems in diabetes, endocrinology and related metabolic disorders. Consistent with these goals, this program will support projects focused on a wide array of topics including, but not limited to:
  • Metabolic modeling of known and unknown pathway kinetics and compartmentalization in diabetes and/or endocrine or metabolic disorders;
  • Network and systems biology of intra and intercellular regulation and inter-tissue and organ homeostasis focused on etiology, diagnosis, prognosis or responses to treatment, including computational approaches to identify biomarkers capable of tracking disease process or progress;
  • Structural biology/informatics and chemical informatics of endocrine and metabolic pathways in diabetes, endocrinology and related metabolic diseases;
  • High-throughput and/or high information content image analysis of organs or tissues of relevance to diabetes or metabolic disease;
  • Computational characterization of the normal or abnormal development of involved organs such as the formation of pancreatic islets.

Of particular interest are projects that can leverage and expand the utility of existing large datasets developed in NIDDK projects and programs. For examples, see the dkNET webpage at NIDDK-specific-repositories. Research designed to address important research questions through the development of new analytical tools, or through novel secondary analyses of existing datasets are encouraged.

Section III. Award Information

Funding Instrument:
Subcontract, awarded from the NIDDK Information Network (dkNET), University of California San Diego
Application Types Allowed:
New. Studies meeting the current NIH definition of Clinical Trials will NOT be eligible for support under this funding opportunity.
Funds Available:
dkNET intends to commit approximately $750,000 in FY2020 to fund up to 3 awards
Award Budget:
Awards are limited to $150,000 Direct Costs over the lifetime of the award (up to 2 years), plus applicable F&A costs to be determined at the time of award.
Project Period:
The maximum project period is 2 years.

Section IV. Eligibility Information

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 encouraged to apply for 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)

Non-profits Other Than Institutions of Higher Education
  • Non-profits with 501(c)(3) IRS Status (Other than Institutions of Higher Education)
  • Non-profits without 501(c)(3) IRS Status (Other than Institutions of Higher Education)
For‐Profit Organizations
  • Small Businesses
  • For‐Profit Organizations (Other than Small Businesses)
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 NIH Grants Policy, are NOT allowed.

Eligible Individuals (Program Director/Principal Investigator)

For the purposes of this FOA:

Multiple PD(s)/PI(s) are NOT allowed-although collaborations to bring in bioinformatics and/or DEMD expertise are encouraged.

In addition, applicants must meet the NIH definition of a New Investigator (NI) or Early Stage Investigator (ESI) at the time of application. A NI is defined by NIH as an applicant who has not yet competed successfully for a substantial, competing NIH research grant. An ESI is a new investigator who is within 10 years of completing his/her terminal research degree or end of post-graduate clinical training. See the office of NIH Extramural Research for a complete list of NIH grants that do not disqualify a PD/PI from being considered a New Investigator and for frequently asked questions about the NIH Early Stage Investigator (ESI) Policy.

Applicants also must hold an independent research position at a domestic (U.S.) institution at the time of submission of the application. For the purposes of this FOA, “independent research position” means a position that automatically confers eligibility, by the applicant’s institutional policy, for an investigator to apply for R01 grants, with an appropriate commitment of facilities to be used for the conduct of the proposed research. Investigators still in training or mentored status (e.g. postdoctoral fellows) are not eligible to apply unless they have a written commitment of an independent faculty position that is certified by the institution and provided as part of the application.

Applicants may submit or have an R01 grant application pending concurrently with their dkNET Bioinformatics Pilot Program award. However, if that pending R01 grant is awarded, the dkNET Bioinformatics Program Award will be terminated after the first year.

Section V. Application and Submission Information

Submitting an Application to the website

Content and Form of Application Submission

Application Forms: It is critical that applicants follow the instructions provided. Conformance to the requirements in the Application Guide is required and will be strictly enforced. Applications that are out of compliance with these instructions may be returned without review.

Letter of Intent: By the due date listed above (Jan 14, 2020), prospective applicants are asked to submit a letter of intent that includes the following information:
  • Descriptive title of proposed activity
  • Name, address and telephone number of the PD/PI
  • Names of other key personnel
  • Participating institution
The letter of intent should be sent in electronic form to: submissions@dknet.org

Budget: Budgets are limited to $150,000 direct costs. Applicants should budget for travel to an annual meeting of the dkNET Pilot Awardees each year of the award. Except in unusual circumstances, only the PD/PI may be supported by Pilot funds to travel to the dkNET Pilot Awardees meeting ($2000/year).

Application Guide

Include the following items as part of the application found here
  • Public Health Service Grant (PHS) 398: Face Page (form page 1)
  • Public Health Service Grant (PHS) 398: Detailed Budget for Initial Budget Period (form page 4)
  • Public Health Service Grant (PHS) 398: 2nd year budget and budget justification (form page 5)
  • Investigator Biographical Sketch (Biosketch) (5 page maximum) Biosketch form page
  • Other Key Personnel Biosketch (5 page maximum)
  • Research Plan (as detailed below) (5 page maximum)
  • Public Health Service Grant (PHS) 398: Checklist Form Page
Does the proposed research involve human specimens and/or data?
Select "Yes" or "No" on Question #4 of PHS 398 Face Page (form page 1) to indicate whether the proposed research involves human specimens and/or data. Applications involving the use of human specimens or data may not be considered to be research involving human subjects, depending on the details of the materials to be used. To help determine whether your research is classified as human subjects research, refer to the Research Involving Private Information or Biological Specimens flowchart.
If you answered “Yes” to the “Does the proposed research involve human specimens and/or data?” question, you must provide a justification for your claim that no human subjects are involved.
This justification should include:
  • information on who is providing the data/biological specimens and their role in the proposed research;
  • a description of the identifiers that will be associated with the human specimens and data;
  • a list of who has access to subjects’ identities; and
  • information about the manner in which the privacy of research participants and confidentiality of data will be protected.
Research Plan
The research plan should conform to the following instructions with careful attention to use of the headers and word limits outlined below:
Project Narrative (500 words): Applicants should describe how their objectives and research design will use innovative bioinformatics strategies to address an important research problem in the field of Diabetes, Endocrinology and/or Metabolic Diseases.

Project Description (up to 5 pages): Describe the scientific problem that you propose to address, its importance, and explain how it will allow you to either: 1) acquire bioinformatics expertise to solve biological problems related to diabetes, endocrinology or metabolic disease research; or 2) develop in-depth knowledge of DEM biological systems needed to apply bioinformatics techniques to current research questions. Describe your current expertise and how this will be used to address the research problem at hand. Explain how this pilot project will prepare you to have the cross-disciplinary expertise in bioinformatics and DEM research, allowing you to obtain preliminary data supporting a future R01 application focused on applying computationally-intensive approaches to DEM research questions. Briefly summarize the project Specific Aims, and describe the overall strategy, methodology, and analyses to be used to accomplish these aims. Describe the experimental design and methods proposed and how they will achieve robust and unbiased results. Explain necessary collaborations you will develop to provide scientific input outside of your expertise. Discuss potential problems, alternative strategies, and benchmarks for success anticipated to achieve the aims. Provide a brief overview of future directions and anticipated timeline for securing funding for continuation of the work at the end of the pilot award. A statement must be included that, if chosen to receive an award, the applicant will commit a minimum of 2 person‐months effort to the project supported by the this dkNET New Investigator Pilot Program in Bioinformatics.

Note: Bibliographic citations are not required but if included must fit within the page limit. Figures and illustrations may be included but must also fit within the page limit.

Resource Sharing Plan (2 page maximum): Individuals are required to comply with instructions for providing Resource Sharing Plans as found here NIH Grant Policy on Sharing Research Resources

The following modifications also apply:

If the application proposes the generation of a research resource, the application must provide a precise description of the resource to be generated. A resource could be something tangible such as biosamples, reagents, antibodies, cell lines, etc.; or could be datasets such as those generated by discovery research (e.g. RNAseq, omic profiles, epigenetic maps, etc). In this section, the applicant should detail timelines and methods to ensure project-generated resources are made available to the investigator community at-large; as well as plans to ensure resources remain available beyond the funding period of the Pilot Award. The NIDDK information network at dkNET provides a list of suggested Data Repositories and can provide assistance with the identification of appropriate resource repositories as well as finding and/or minting Research Resource Identifiers (RRIDs).

If the project proposes the generation of dataset(s) and new data-based resources such as molecular signatures and knowledgebases, the applicant should include a Data Management and Sharing Plan. NIDDK supports the concept that data produced using NIDDK funds should strive to conform to “FAIR” principles (be Findable, Accessible, Interoperable and Reusable) as articulated in the NIH Strategic Plan for Data Science released on June 4, 2018 (NIH Strategic Plan for Data Science). In support of this goal, the plan should precisely describe: 1) the data types and file formats generated, the amount of data, and any related tools and software to be generated, along with standards, unique identifiers, and metadata concepts to be applied (the data files and tools need to be generated/transformed into formats that can be easily accessed by the research community); 2) where the data will be deposited, using established data repositories whenever possible and if established repositories do not exist for the data types to be generated, the plan should describe where the data will be held, how it will be maintained, and how it will be made accessible and advertised to the research community; 3) a precise timeline for deposition of data (within 1 year of validation or upon publication, whichever is first) as well as who will be responsible for the deposition and for maintaining records of data that have been transferred into public repositories; 4) any terms and conditions for re-use and redistribution of data to the research community, including any projected limitations on data access (including de-identification processes needed for human participants or specimens); and 5) plans for oversight of data management as well as for preserving data beyond the project period.

Details of NIH Sharing Policies and related guidance are found here: NIH Sharing Policies

Prior to funding, NIH Program Staff may negotiate modifications to the Resource Sharing Plan with the applicant.

Appendix: Letters from Collaborators should be submitted in the Appendix.

Section VI. Application Review Information

Criteria

Only the review criteria described below will be considered in the review process. All applications submitted will be evaluated for scientific and technical merit using external peer review.

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? Is there a strong scientific premise for the project? If the aims of the project are achieved, how will scientific knowledge and technical capability be improved? How will successful completion of the aims change the concepts, methods, technologies, treatments, services, or preventative interventions that drive this field? Is the project an appropriate vehicle for a New Investigator? Is the scope of activities proposed appropriate to meet those needs? Will successful completion of the aims bring about unique advantages or capabilities regarding the application of computational and/or modeling approaches to compelling research problems in diabetes, endocrinology and related metabolic disorders?
  • Investigator(s): Does the New Investigator have appropriate experience and training to carry out the experiments proposed? Is the New Investigator, collaborators, and other researchers well suited to the project? Are appropriate collaborations necessary to apply bioinformatics approaches to biological problems in place? Upon completion of this pilot project, will the New Investigator obtain the interdisciplinary expertise needed to incorporate computational and bioinformatics approaches into their biomedical research programs?
  • Innovation: Does the application challenge and seek to shift current research 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?
  • Approach: Are the overall strategy, methodology, and analyses well‐reasoned and appropriate to accomplish the specific aims of the project? Has the investigator presented strategies to ensure a robust and unbiased approach, as appropriate for the work proposed? 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? Are rigorous bioinformatics approaches used to address a research problem relevant to the field of Diabetes, Endocrinology and Metabolic Diseases?
  • 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 investigator adequate for the project proposed?

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.

Vertebrate Animals:
When relevant, reviewers will evaluate the involvement of live vertebrate animals as part of the scientific assessment according to the following criteria: (1) description of proposed procedures involving animals, including species, strains, ages, sex, and total number to be used; (2) justifications for the use of animals versus alternative models and for the appropriateness of the species proposed; (3) interventions to minimize discomfort, distress, pain and injury; and (4) justification for euthanasia method if NOT consistent with the AVMA Guidelines for the Euthanasia of Animals.

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

Review and Selection Process

Applications will be evaluated for scientific and technical merit by external peer reviewers convened by dkNET using the stated review criteria.

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 peer review will NOT be accepted for applications submitted in response to this funding opportunity.
Applications will compete for available funds with all other recommended applications submitted in response to this funding opportunity. Following initial peer review, recommended applications will receive a second level of review by an ad hoc group of dkNET External Science Panel members. NIH staff affiliated with dkNET will make final funding decisions, with consideration of the following:
  • 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.

Anticipated Announcement and Award Dates

After peer review and secondary review of the applications are complete, the PD/PI will be notified by dkNET as to funding decisions by March 2020

Contact Information

Corinne M. Silva, Ph.D.
DDEM/NIDDK/NIH
Tel: 301-451-7335
silvacm@mail.nih.gov * Preferred method of contact

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