Valentina Di Francesco Senior Program Officer for

1. Valentina Di Francesco Senior Program Officer for Bioinformatics, Structural Genomics and Systems Biology email: vdifrancesco@niaid.nih.gov Microbial Genomics and Advanced Technologies DMID, NIAID, NIH

2. Outline • Goals of the Systems Biology program and how it fits with other ongoing Genomics Initiatives • Overview of the NIAID’s expectations for the Systems Biology Working Group. • Start to address some of the initial input and feedback received from the SBWG during the November meeting in Seattle

3. Systems Biology for Infectious Diseases Research Goals: To establish large scale, coordinated Systems Biology Programs that utilize a combination of computational and experimental methodologies To conduct research projects to analyze, quantify, model and predict the interacting networks of cellular molecular components of microbial organisms and their interactions with the host cells. To utilize the existing high-throughput “-omics” technologies, such as functional genomics, proteomics, metabolomics, lipidomics. To make research data, analysis tools, modeling algorithms, reagents and experimental protocols publicly and freely accessible to the scientific community in publicly available repositories.

4. “Omics” Programs Systems Biology Metabolomics Lipidomics Functional & Clinical Genomics Structural Genomics Centers Genomics Proteomics Sequencing Centers Pathogen Functional Genomics Center Structural Genomics Centers Clinical Proteomics Centers Systems Biology Centers Human Microbiome Project Bioinformatics Resource Centers http://www3.niaid.nih.gov/research/resources/dmid/data.htm

5. Data Release Requirements • The release to the scientific community within four (4) weeks from publication, or within one (1) year of generation, whichever comes first of contract-generated resources, such as • experimental and computationally generated research data • metadata, • statistical models, • experimental protocols, • novel reagents • database schema • computational algorithms and data analysis tools.

6. Data Release Requirements • Contract-generated data and software shall be made available through publicly accessible web and database sites, including • Systems Biology Centers’ Web Portals • the NIAID funded Bioinformatics Resource Centers and Influenza Research Database • BEI Resources repository • and/or other public repositories, as identified by the Centers in consultation with the NIAID

7. Systems Biology Working Group (SBWG) • 1 SBWG for the entire program with 13 members http://www3.niaid.nih.gov/LabsAndResources/resources/sb/sbwg.htm • Members with a variety of scientific expertise • Drs. Reid Townsend and Thomas Braciale are the SBWG co-Chairs • SBWG members are expected to participate in 1 meeting in person and 1 conference call per year. • After meetings in person, write a report for the Centers with SBWG’s recommendations

8. SBWG • The SBWG is expected to provide advice to the Centers and not to the NIAID on the operations, scientific progress and data release guidelines of all the contracts awarded under this program and to make recommendations regarding future directions. • The SBWG acts in concert with the centers and is a partner in the Systems Biology Program

9. SBWG Members are expected to become familiar with: • the centers programs and their specific aims • Share centers’ Statement of Work, deliverables and milestones with the SBWG? • Centers could encourage attendance of some of their meetings by SBWG members • the technical objectives and requirements of the NIAID Program • Collaboration among centers is encouraged but it is not a requirement by the NIAID

10. How to assess the impact of a systems biology approach to infection diseases versus a traditional R01 type of research? • Short-term progress is measured by depositing data and resources in the public domain (by NIAID’s contract requirement) • Are there other measures of short-term progress? • How to measure long-term progress?