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Report on the Computational Biology Workshop for the Genomes to Life Program
U.S. Department of Energy, Germantown, Maryland
August 7–8, 2001

Appendix B: Agenda
Genomes to Life Program
August 7–8, 2001
Room A-410, DOE Germantown Headquarters
Germantown, Maryland

Tuesday, August 7, 2001
Goals and Computational Needs of the GTL Program
Moderator: John Wooley, UCSD
8:00 – 9:00 Arrival, Badging, Coffee and Pastries  
9:00 – 9:15 Welcome and Introduction Oliver, Patrinos
9:15 – 9:30 Review of Workshop Goals and Agenda  Johnson, Colvin, Mann
9:30 – 9:45  Overview of presentations    Wooley
9:45 – 10:15            High-throughput automated genome assembly and annotation Rokhsar
10:15 – 10:45  Discussion Uberbacher
10:45– 11:00 Break
11:00 – 11:30 Analysis of protein-protein interactions and protein-expression profiles  Cary
11:30 – 12:00 Discussion  Branscomb
12:00 – 1:00  Lunch  
1:00 – 1:30  Predictive models of microbial behavior, and models of biochemical pathways Palsson
1:30 – 2:00  Discussion    Wiley
2:00 – 2:30 Advanced molecular and structural modeling methods for biological systems  Dixon
2:30 – 3:00 Discussion  Heffelfinger
3:00 – 3:15 Break   
3:15 – 3:45  Large-scale biological computing infrastructure   Slezak
3:45 – 4:15     Discussion  Stevens
4:15 – 5:00  Charge to Breakout Groups  Johnson, Colvin, Mann
5:00  Adjourn  

 

Wednesday, August 8, 2001
GTL Computational Research Priorities and Infrastructure Needs
Moderator: Thom Dunning, NC SCC
8:30 – 10:30 

Breakout Group Discussions

Topics:

  1. Data analysis, management, validation, representation and integration, (e.g. genome  annotation, expression array analysis)
  2. Metabolic pathway reconstruction and simulations, and modeling cells and cell communities
  3. Methods predicting macromolecular structure, function, and interactions (including support of experimental. methods)

Guideline questions:

  1. What are the key next steps in this area to reaching the GTL goals?
  2. What are the highest research priorities in this field?
  3. What are the major technical roadblocks to achieving this goal?
  4. How far is the goal from the current state-of-the-art?
  5. What is the research effort necessary to achieve it?
  6. What is the mix of research disciplines needed to reach this goal?
  7. What other agencies and companies are sponsoring closely related research?
10:30 – 10:45  Break
10:45 – 12:00 Reports back from breakout groups
12:00 – 1:00 Lunch
1:00 – 2:00

Discussion of mathematics and computational research priorities for GTL
2:00 – 3:00 Discussion of GTL computational infrastructure requirements
3:00 – 3:30  Wrap-up
3:30  Adjourn