Workshop on the Development of Databases of Interacting Systems

Sponsored by the National Institute of General Medical Sciences
and the Office of the Director, NIH
The Cloister, NIH, Bethesda, Maryland
November 11-12, 1999

Goals of the Workshop

  1. To understand the extent and nature of efforts to develop databases of interacting systems.
  2. To understand the needs of the users of such databases.
  3. To reconcile goals 1 and 2.

Some specific issues that have been raised and that should be considered by the participants:

  1. To what extent is it desirable and possible to coordinate databases of interacting systems?
  2. Should there be a single submission site for categories of such data, e.g., protein-protein interactions?
  3. What are the data objects that are/will be commonly required, and how can they be represented? How can we be flexible about defining these so that future needs for both data inclusion and analysis can be accommodated?
  4. How will these databases be supported?

Agenda

Thursday, November 11
8:00Continental Breakfast
8:20-8:30Introduction: Tony Hunter and Tony Pawson
Morning Session
Chair: Tony Hunter, Salk Institute
8:30-9:10Bryan Ray, Science
  Science's Signal Transduction Environment: the "Connections Map," a Graphical Interface to a Database of Information on Signal Transduction
9:10-9:50Stephen Shaw, National Cancer Institute, NIH
9:50-10:30Minoru Kanehisa, Institute for Chemical Research, Kyoto University
 The Protein-Protein Interaction Network for Knowledge Representation of Cell Processes and for Integration with Genomic Information
10:30-10:50Break
10:50-11:30Christopher Hogue, Samuel Lunenfeld Research Institute, Mt. Sinai Hospital, Toronto
 BIND, the Biomolecular Interaction Network Database
11:30-12:10Peter Karp, Director, Bioinformatics Group, SRI International
  Pathway/Genome Databases and Software Tools [PDF] (related paper [PDF])
12:10-1:15Lunch
Afternoon Session
Chair: Tony Pawson, Mt. Sinai Hospital, Toronto
1:15-1:50Evgeni Selkov, Integrated Genomics, Inc.
 EMP and MPW Databases of Enzymes and Metabolic Pathways; Status and Outlook
1:50-2:30Les Loew, Center for Biomedical Imaging Technology, University of Connecticut Health Center
 The Virtual Cell Project
2:30-3:00Srinivas Ravi Iyengar, Department of Pharmacology, Mt. Sinai School of Medicine
 Databases for Modeling Signaling Networks
3:00-3:15Break
3:15-3:45Lewis Cantley, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School
 Predicting Protein-Protein Interactions from Primary Sequences
3:45-4:15William Gelbart, Department of Molecular and Cellular Biology, Harvard University
 Phenotypes, Genotypes, and Developmental Pathways
4:15-4:45Bernhard Palsson, Departments of Bioengineering and Medicine, University of California, San Diego
 Life on the Edge: Using Genome-Scale in silico Models of Microorganisms to Interpret and Predict Metabolic Phenotypes
4:45-5:30Wrap-up
Friday, November 12
Chair: Marvin Cassman, National Institute of General Medical Sciences, NIH
8:30-12:00Overview of Problems and Opportunities; Recommendations for Future Developments

Reports from the Workshop

PROW/KBTool: Building a Fabric of Biological Concepts and Relationships that is "Good, Simple, and Habit-Forming" (no longer available)
Stephen Shaw, National Cancer Institute, NIH

Pathway/Genome Databases and Software Tools [PDF] (related paper [PDF])
Peter Karp, Director, Bioinformatics Group, SRI International

The Virtual Cell Project
Les Loew, Center for Biomedical Imaging Technology, University of Connecticut Health Center

Useful Websites

Stephen Shawhttp://www.ncbi.nlm.nih.gov/prow/
Minoru Kanehisahttp://www.genome.ad.jp/kegg/​
Les Loewhttp://www.nrcam.uchc.edu
Christopher Hoguehttp://bioinfo.mshri.on.ca/
http://bioinfo.mshri.on.ca/discus/index.html
Bernhard Palssonhttp://www-bioeng.ucsd.edu/research/research_groups/gcrg
Michael Gribskovhttp://www.sdsc.edu/~gribskov
Peter Karphttp://ecocyc.PangeaSystems.com/ecocyc/
Shankar Subramanianhttp://biology.ncsa.uiuc.edu
Ulrike Wagnerhttp://histology.nih.gov
Brian Rayhttp://www.stke.org
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