MAGNet Driving Biological Projects (DBPs) - Request for Applications

What?

Request for Applications (RFA) for new DBPs (August 01, 2008 - July 31, 2010)
Center for the Multiscale Analysis of Genomic and Cellular Networks (MAGNet)
1130 St. Nicholas Ave., 8th Floor
Columbia University Medical Center
New York, NY 10032

Program Summary

Cellular processes are determined by the concerted activity of thousands of genes, their products, and a variety of other molecules. This activity is coordinated by a complex network of biochemical interactions largely determined by molecular structures and physiochemical properties which control common intra and inter-cellular functions over a wide range of scales. At an increasing level of granularity, these may range from the formation/activation of transcriptional complexes, to the availability of a signaling pathway, all the way to complex, macroscopic cellular processes, such as cell adhesion. Understanding this organization is crucial for the elucidation of biological function and for framing associated health related applications in a quantitative, molecular context. Additionally, the emerging complexity of these molecular interactions in the cell calls for a new level of sophistication in the design of genome-wide computational approaches.

The National Center for the Multiscale Analysis of Genomic and Cellular Networks (MAGNet) addresses this challenge through the application of both knowledge-based and physics-based methods. The Center provides an integrative computational framework to organize molecular interactions in the cell into manageable context dependent components. Furthermore, it is developing a variety of interoperable computational models and tools that can leverage such a map of cellular interactions to elucidate important biological processes and to address a variety of biomedical applications.

The aim of this request for applications (RFA) is to solicit outstanding proposals that will (1) make use of the already extensive infrastructure that has been developed and/or (2) provide new, exciting and challenging biomedical problems and applications to validate and/or motivate the further development of novel computational methods and tools within the MAGNet Center. Specific areas of current interest can be reviewed at https://magnet.c2b2.columbia.edu/overview.php, and include:

• Evidence integration to collect and fuse a variety of diverse cellular interaction clues based on their statistical relevance.
• Physics- and knowledge-based methodologies to provide computational and experimental clues about specific molecular interactions, including
  • (a) protein-protein interactions, as revealed by sequence and structure analysis
  • (b) interactions, discovered by a variety of novel reverse engineering algorithms
  • (c) interactions discovered by literature data mining
  • (d) experimental interactions from a variety of existing databases
• Methodologies and filters, anchored in formal domain ontologies, to associate specific interactions to an organism, tissue, molecular, and cellular context (phenotype).

Eligibility

Any individual(s) with the skills, knowledge, and resources necessary to carry out the proposed research as the PD/PI is invited to work with his/her organization to develop an application for support. Additional eligibility criteria include:

• Project must be aligned with the driving goals of the MAGNet Center.
• Project must provide a driving biological problem, one which can serve to motivate continued advances in algorithms and/or technology

Important Notes

• Useful background information on the objectives of the NCBC program are available in the NIH/NCBC RFA (http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-04-022.html).
• A detailed discussion of the research goals of the MAGNet Center, including a description of the currently funded DBPs, can be found at the Center's web site: http://magnet.c2b2.columbia.edu/.
• As a result of this RFA, 2-3 additional DBPs will be funded, for a duration of 2 years. Proposals with research plans that extend pas this time frame are also eligible, as long as the applicant(s) provide a clear plan for pursuing funding past the first 2 years. Their funding is contingent on the renewal of the MAGNet Center in Year 5.
• Successful applications will be funded directly by the MAGNet Center.
• Annual direct costs cannot exceed $150,000.
• NIH R01 proposal format must be used for all applications. The full applications should be submitted using the PHS 398 Form.
• Applicants should clearly indicate one or more MAGNet Investigator liaisons who will be the target collaborators (see the "People" section of the MAGNet web site).

How to Apply

• Pre-proposal: The potential applicant should accurately review the aims and challenges addressed by the MAGNet Center. Then the applicant should contact a MAGNet Investigator 6-8 weeks before the initial pre-proposal is due. The Investigator must be carefully chosen so that she/he is an expert in the proposed field of research, interested and willing to serve as local MAGNet liaisons for this proposal. Once this initial contact is established, the applicant must submit a 3-5 page pre-proposal summarizing the proposed research. Although there is no particular format to use, the pre-proposal should address the following topics:
  1. What scientific question(s) are you addressing.
  2. Anticipated specific aims.
  3. Background.
  4. Statement of relevance, i.e., how you see your work and ours would be complementary.
  5. Summary of your existing resources/expertise.
  6. Specific resources you would imagine requiring from us.
     
• Full proposals will be submitted by invitation only and must be based on the pre-proposals. These must include:
  • What to submit? As with a regular PHS 398 grant application http://grants.nih.gov/grants/funding/phs398/phs398.html, you must submit a complete proposal, including Face Page, Form Page 2, Table of Contents, Budget Forms, Budget Justification, Biosketches, Resources, Research Plan, Checklist, Targeted/Planned Enrollment Table & Inclusion Enrollment Report if there are human subjects involved in the project, and publications for the appendix. The research plan should not exceed 15 pages. In addition, you must submit your Statement of Work and a copy of your institution's F-&-A Costs Agreement for setup of the subcontract at Columbia. If there are human subjects or animal subjects involved in the project, please work on your human or animal protocol ASAP. List MAGNet as the primary funding source, Grant # U54 CA121852-01A1 in your protocol. Once you obtain approval from your own institution, please send all the related documents to us, as we must obtain approval from Columbia as well.
  • Send the final proposal (PDF copy) directly to Dr. Aris Floratos at: A hardcopy of the signed first page must be mailed to Dr. Floratos at the address provided at the bottom of this page. Institutional signature is needed on the Face Page for proposal processing.
  • For administrative purposes, Columbia University should be listed as the sponsor, not NIH. As with a regular subcontract submission, the primary site (Columbia University) is your sponsor, not NIH.

Timeline

• Scientific merit.
• Relevance of the proposal to the aims of MAGNet.
• Approach & innovation.
• PI & environment.
• Plans to obtain support for the DBPs research after July 31, 2010.
  

The DBP applications review committee includes the MAGNet Principals with feedback from the MAGNet NIH Science/Program Officers.

For more information please contact

Aris Floratos
Executive Director, MAGNet Center
Columbia University Medical Center
1130 St. Nicholas Avenue
New York, NY, 10032