Report on the Computational Biology Workshop for the Genomes
to Life Program
U.S. Department of Energy, Germantown, Maryland
August 7–8, 2001
Introduction
A workshop was held August 7–8, 2001, at the U.S. Department of Energy (DOE) headquarters in Germantown, Maryland, to initiate detailed planning of the computational biology research component of the Genomes to Life (GTL) program. It is one in a series of program planning workshops being held to coordinate the program (see inside back cover). This workshop was supported by DOE’s Office of Advanced Scientific Computing Research and Office of Biological and Environmental Research. The goal of the workshop was to begin work towards the following objectives:
- Translate the GTL goals into requirements for computational biology and identify existing resources relevant to these goals;
- Describe the current state of capabilities in relevant computational and biological research areas;
- Identify needs for further development of computational methods, data repositories, data-analysis tools, and modeling and simulation of biological systems under the GTL umbrella;
- Identify high-performance computing infrastructure requirements to accomplish GTL goals; and
- Create a dialog among researchers in the computational and biological sciences.
The workshop included a diverse collection of scientists from DOE laboratories and other organizations (see Appendix A for a complete list of participants). The agenda (see Appendix B) was designed to facilitate discussions on the research and infrastructure needed to achieve the five computational biology aims stated in the GTL program roadmap (see Appendix C for an overview of the GTL program, including goals and expected payoffs):
Aim 1. Develop methods for high-throughput automated genome assembly and annotation
Aim 2. Develop computational tools to support high-throughput experimental measurements of protein-protein interactions and protein-expression profiles
Aim 3. Develop predictive models of microbial behavior using metabolic-network analysis and kinetic models of biochemical pathways
Aim 4. Develop and apply advanced molecular and structural modeling methods for biological systems
Aim 5. Develop the groundwork for large-scale biological computing infrastructure and applications
Breakout sessions during the second day, as well as lively discussions in plenary sessions, addressed three broad topical areas:
- Biological Data Management, Analysis, and Access
- Computational Prediction of Structure, Function, and Interactions
- High-Level Modeling of Metabolic Pathways and Signaling Networks for Cells and Microbial Communities
The above topics also were addressed through invited presentations. The breakout sessions and overview talks are summarized below. Specific findings and recommendations derived from these workshop sessions are presented in the Executive Summary at the beginning of this report.
