Update: April 28, 2010 - Additional DBP Full Proposal FAQ was added
Update: April 27, 2010 - Additional DBP Full Proposal FAQ was added
Update: April 23, 2010 - Additional DBP Full Proposal FAQ was added
Update: April 21, 2010 - Additional DBP Full Proposal FAQ was added
Update: April 19, 2010 - Additional DBP Full Proposal FAQ was added
Update: April 8, 2010 - Additional DBP Full Proposal FAQ was added
Update: April 7, 2010 - Additional DBP Full Proposal FAQ was added
Update: April 6, 2010 - Additional DBP Full Proposal FAQs were added
Update: April 2, 2010 - DBP Full Proposal FAQs were added
Update: March 31, 2010 - Additional Instructions provided for Full Proposals
Update: March 5, 2010 - LOI Review and Full Proposal deadlines have changed
Update: March 2, 2010 - CLOSED - Submission deadline has passed
Update: February 18, 2010 - questions received and corresponding answers added to end of this page
Update: February 15, 2010 - to clarify submission and review process

PATRIC Request for Driving Biological Projects

- CLOSED FOR LOI SUBMISSION

Introduction

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The NIAID-funded PAThogen Resource Integration Center (PATRIC), a bacterial pathogen NIAID-funded Bioinformatics Resource Center (BRC) is seeking Driving Biological Projects (DBPs) that focus on infectious diseases research related to human bacterial pathogens.

DBPs must include research that uses high-throughput experimental technologies (HTP) to functionally characterize the genome, proteome or metabolome of bacterial organisms or host/pathogen interactions to help elucidate how genes, proteins and metabolites may be involved in pathogenesis, antimicrobial resistance or other biological processes of interest in the study of infectious diseases. HTP approaches to functional characterization of genes and proteins may include, for example, microarrays, mass spectrometry, two-hybrid screenings, RNAi experiments, Chip-Seq and RNA-Seq studies and bioassays.

All experimental results and data generated by DBPs awarded through PATRIC are to be released into the public domain according to the PATRIC Data Sharing/Release Policy.

Staff from the PATRIC BRC is required by the NIAID to assist with the bioinformatics aspect of the DBP project. Bioinformatics support may include performing the computational and statistical analysis of the experimental data, generating predictive models of the biological system under investigation, developing algorithms for the analysis or providing the data management system for the project, or all of the above.

For more information about the BRCs Program please visit the NIAID site

http://www3.niaid.nih.gov/LabsAndResources/resources/brc/

DBP Program Information

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  • Type of Award: Cost reimbursement subcontract
  • Number of Awards: 2
  • Duration of Each Award: up to 24 months
  • Maximum Total Cost per Award: $600,000 for 2 years
  • Anticipated Start Date: July 1, 2010
  • Letters of Intent (LOI) must be submitted electronically to patric-dbp@vbi.vt.edu by 5:00 PM Eastern Time, February 28, 2010. LOI are limited to two pages maximum, 11pt font or larger.
  • Full proposals will be solicited by invitation only, and must be submitted electronically to patric-dbp@vbi.vt.edu by 5:00 PM Eastern Time, March 31, 2010. [NOTE: LOI Review and Full Proposal deadlines have changed. Please see Addendum below for new schedule]. Full proposals are limited to fifteen pages maximum, 11 pt font or larger. Hardcopies with complete institutional signatures must be received by April 5, mailed to
    • Lisa Gunderman
      Virginia Bioinformatics Institute
      Washington Street, MC 0477
      Virginia Tech
      Blacksburg, VA 24061

Note: Please send any questions regarding the process to patric-dbp@vbi.vt.edu. Questions not already addressed herein will be posted with answers on this Website.

Another solicitation for DBPs is expected to occur in 2012.

Letter of Intent - CLOSED, LOI DEADLINE HAS PASSED

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Submission of a Letter of Intent is required. The LOI should be no longer than 2 pages, and should include the following components.

  • PI name, affiliation and contact information
  • Project title
  • Bacterial pathogen involved
  • Project description
  • Description of how the project is expected to utilize as well as complement PATRIC BRC’s resources.

LOIs will be reviewed by the PATRIC Scientific Working Group (SWG), which is an external group of advisors to the PATRIC BRC. LOIs considered to be competitive by the SWG and by the NIAID will be invited to submit full proposals.

Full Proposal - Only selected LOIs are eligible for Full Proposal submission

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The DBP proposal will be structured as a white paper, and must clearly identify how the DBP will combine and apply high-throughput experimental and bioinformatics techniques to functionally characterize the genome, proteome or metabolome of bacterial organisms or host/pathogen interactions to help elucidate how genes, proteins and metabolites may be involved in pathogenesis, antimicrobial resistance or other biological processes of interest in the study of infectious diseases.

DBP white paper proposals should be no longer than 15 pages total (excluding budget and budget justification) and must include:

  • A description of the project's goals
  • Expected impact on scientific community served by BRC
  • A description of the HTP experimental technologies that are necessary to carry out the project and the facilities, equipment and other resources available to the project by the experimental lab
  • A description of the bioinformatics support services provided by the BRC and how the project will influence the development of new BRC features, in particular, how the project will drive the BRC infrastructure to deliver useful functionality to other researchers for similar data types. See note below regarding BRC Resource Utilization Plan.
  • A delineation of the project's milestones
  • Expected results and a data release/ data sharing plan for the project that is consistent with the data release guidelines of the BRC (see PATRIC Data Sharing/Release Plan)
  • A list of proposed scientific and technical personnel at the experimental laboratory, and a description of their qualifications, relevant experience and roles in the project. The DBP lead investigator must devote at least ten percent effort to the project
  • The budget proposed by the experimental laboratory, broken down into total costs for labor, materials, and other line items, as appropriate for the project. Use the NIH Budget and Budget Justification forms which can be downloaded from here (Budget Justification Budget Template)

BRC Resource Utilization Plan: The proposal must include a specific plan that describes the intended BRC integration with the project and bioinformatics support expected from the BRC. This section of the proposal must be submitted for review and evaluation at least one week before the proposal due date, submitted in MS Word format via email to patric-dbp@vbi.vt.edu. The response from the BRC will either be "Yes, we can support what you are proposing", or "No, we cannot support what you are proposing" with an indication of which part we will not be able to support and why. This information can be used by the proposer to modify their final proposal. At the time of final proposal submission the BRC will provide an official letter that includes a description of the the planned support from the BRC, that will be included with the proposal for SWG review.

Full proposals will be reviewed by the Scientific Working Group of the BRC, based on the following evaluation criteria:

  • Technical feasibility
  • Scientific merit
  • Impact on the scientific community served by the BRC
  • Impact on BRC’s development of new features

The NIAID will also review and provide the final approval of the DBPs proposed for award by the SWG. Final Proposals selected for submission to NIAID are subject to NIAID approval, NIAID supplemental award to the PATRIC prime contract, and successful subcontract negotiation between Virginia Tech and the potential awardee.

Questions and Answers: We will post questions received from submitters during the proposal preparation phase and our response on the public PATRIC website. If necessary, the question and answer will be re-phrased to make them generically relevant to all/other proposals.

Reporting Requirements

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Semi-annual and periodic ad hoc reports will be required to assist with the review of progress toward stated goals.

Eligibility

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All researchers with expertise and capabilities in the areas described above are invited to submit a Letter of Intent.

DBP Full Proposal FAQs

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Added April 28, 2010

Q: May we use the PHS 398 form for the budget instead of the Budget Template spreadsheet included in the instructions for the Full Proposal?
A: No. The selected DBPs will be submitted to NIAID as a prime contract modification request, with the DBP PI's organization listed as a subcontractor. Accordingly, NIH forms for contracts, and not forms for grants, must be used.

Q: If we are unfamiliar with the DHHS/NIH Proposal Summary and Data Record form, may we use a PHS 398 Face Page or other form?
A: The DHHS/NIH Proposal Summary and Data Record form must be used instead of a PHS 398 Face Page because this is a contract, not a grant. Blocks which are not applicable, such as ERRATA, "OFFEROR'S ACKNOWLEDGEMENT OF AMENDMENTS TO THE RFP," "DOLLAR VOLUME OF BUSINESS PER ANUM," and "THIS OFFER EXPIRES..." may be left blank.

Added April 27, 2010

Q: What contract number should we use for the proposal cover sheet?
A: The prime contract number for PATRIC, HHSN272200900040C.

Q: Is the cover page included in the 15 page limit?
A: No, the cover page is not included in the 15 page limit.

Q: The cover page asks for the "DOLLAR VOLUME OF BUSINESS PER ANNUM". Does this item need to be answered?
A: No, the "DOLLAR VOLUME OF BUSINESS PER ANNUM" field does not need to be filled in.

Added April 23, 2010

Q: Should we include a standard NIH face page for the DBP application? If not, where should the institutional signatures go?
A: Please use the form found here for subcontracts.

Q: When will we receive a letter confirming the approval of our BRC Utilization Plan to accompany our proposal?
A: We will begin distributing them shortly. When your BRC Utilization Plan has been approved, you will first receive an email from us confirming the approval. We will follow up with a letter confirming PATRIC’s capability to support the bioinformatics work you proposed. You may submit this letter along with your final proposal. It will not count against the 15-page limit. We will also keep a copy of the letter on file.

Added April 21, 2010

Q: Is PI salary allowable in the budget?
A: Yes (up to the NIH salary limit, if applicable). The PI (DBP Lead) is expected to devote at least 10% effort to the project, as stated in the April 2 FAQ update below.

Q: Who is the sponsor? Is this proposal to Virginia Tech or NIAID?
A: The selected DBP projects will be submitted to NIAID as a prime contract modification request, with the DBP PI's organization listed as a subcontractor. Thus, the successful awardees will be subcontractors to Virginia Tech.

Q: What precisely is "PATRIC" in relation to NIH and Virginia Tech?
A: PATRIC is the Pathosystems Resource Integration Center project, which is a NIH/NIAID-funded Bioinformatics Center. The PATRIC project was awarded to Bruno Sobral, PI, through a contract to Virginia Tech.

Added April 19, 2010

Q: Item G in the white paper, a list of Personnel, seems redundant. Is this listing in addition to the biosketches and Personnel justifications?
A: It is not necessary to provide both a personnel listing and biosketches in the white paper. Either will suffice in that section of the document. Include the personnel in the budget justification.

Added April 8, 2010.

Q: What project start date should we use in the proposal and budget?
A: Assume a start date of July 16, 2010.

Added April 7, 2010.

Q: Who to contact at the BRC to discuss computational/bioinformatic support for the DBP proposal?
A: Use the process described in the BRC Resource Utilization Plan above. The draft of this plan should be submitted to patric-dbp@vbi.vt.edu for review and approval/modification at least one week before the proposal due date.

Added April 6, 2010.

Q: Is this funding deemed federal or foundation?
A: This is federal funding.

Q: Is this proposal is one time term or will resubmission be allowed?
A: No resubmission allowed.

Q: The Excel budget forms include a page for "materials". How much detail is needed here? For example, is it sufficient to list "basic molecular biology supplies", or should we give a detailed, itemized list, e.g. "gloves", "restriction enzymes", "pipette tips"?
A: For this example, it is sufficient to say “basic molecular biology supplies”.

Q: What indirect cost (IDC) rate should we use? (Clarification of response from NIAID Program)
A: You can use your institution's indirect rate. However, the total cost cannot exceed $600,000 for the 2-year budget - which is the total budget inclusive of indirect costs.

Q: How many preliminary DBP proposals were submitted, and how many were selected to go forward to the next round?
A: There are no plans to publish this information.

Added April 2, 2010.

Q: How many LOI applicants were asked to submit full proposals?
A: There are no plans to publish this information.

Q: For the full proposal, is it encouraged to include co-PIs or collaborators from other research institutions who may request cost sharing/subcontracts? Or a single PI from a single institution is preferred?
A: Propose what you believe is best for the project. There must a single PI for the proposal.

Q: The full proposal will be structured as a white paper with less than 15 pages. Do you have a general proposal template to share?
A: No, we do not have a proposal template, , but the following is a suggested format:

  • Executive summary of the project's goals, including the pathogen(s) involved, information to be produced, and the expected impact on scientific communities served by the BRC.
  • Description of the data to be produced, including methods used to generate this information and possible obstacles. The proposal should also review any relevant datasets that are currently available, and discuss their relationship to the proposed project.
  • Details of high throughput experimental technologies necessary to carry out the project, noting currently available reagents, facilities, equipment and other resources.
  • Discussion of computational and/or statistical analyses, noting those to be provided by the applicant, and those required from the BRC (see below).
  • Assessment of impact, including how these data are likely to influence development of new BRC features, and how they will be used by relevant research communities.
  • BRC Utilization Plan, as described above.
  • Project timeline, including specific milestones and deliverables.
  • Data release / data sharing plan, consistent with NIAID and BRC data release guide¬lines (see below).
  • List of proposed scientific and technical personnel, detailing qualifications, experience, and role(s) in the project. The DBP lead must devote at least 10% effort to this project. Note: full CVs are not required.

Q: Does the 15 page limit include references and biosketchs?
A: Yes, the 15 pages includes references, biosketches, and all other parts of the proposal with the exception of the budget and budget justification.

Q: Is it appropriate to contact PATRIC staff informally while preparing the application to determine how best to use their expertise? If so, who is the best person to contact initially?
A: No, the process for interaction is described in the BRC Resource Utilization Plan, provided in the Full Proposal section above.

Q: Is it possible to send the BRC Resource Utilization Plan more than a week before the deadline?
A: Yes, we encourage submission of the BRC Resource Utilization Plan as soon as possible, but at least one week before the deadline.

Q: What indirect cost (IDC) rate should we use?
A: Use the indirect rate your institute has negotiated with the NIH. Remember that TOTAL COSTS (direct plus indirect) are limited to $600,000 over two years.

Letter of Intent FAQs

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The following questions have been received regarding the DBP request, and the corresponding answers are shown:

Q: Is the DBP Program open to labs outside the U.S.?
A: Yes. Final Proposals selected for submission to NIAID are subject to NIAID approval, NIAID supplemental award to the PATRIC prime contract, and successful subcontract negotiation between Virginia Tech and the potential awardee.

Q: Would a proposal based on bioinformatics analysis of existing data sets be appropriate?
A: Purely bioinformatics DBPs are not encouraged. DBPs should be about high-throughput experimental methods.

Q: Are DBPs seeking novel bioinformatics approaches for emerging high-throughput profiling datasets or methods to obtain these data?
A: The DBPs should propose projects that deliver comprehensive data sets of community interest that push PATRIC to develop novel informatics infrastructure in support of those data. The PATRIC team would do the informatics and deploy the analysis, storage and visualization capabilities in support of the DBP generated data and the DBP team would generate the data and deposit it in PATRIC.

Addendum - March 5, 2010:

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Due to the delay in release of the original request for proposals for Bioinformatics Resource Centers (BRC) Driving Biological Projects (DBP), the following change to the review and submission timelines will be used:

Letter of Intent (LOI) submission February 28, 2010 (no change)
LOI review March 1 – 30
PI notification of LOI acceptance March 31
DBP full proposal submission April 30, 5:00 PM Eastern Daylight Time
Full proposal hardcopy May 5
DBP proposal review May 1 – 21
DBP recommendations sent to NIAID May 24
PI notification of award May 31
DBP subcontract start deadline July 16 or earlier