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

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


Useful Web Sites

Stephen Shaw http://www.ncbi.nlm.nih.gov/prow/
 
Minoru Kanehisa http://www.genome.ad.jp/kegg/ Link to external Web site
 
Les Loew http://www.nrcam.uchc.edu Link to external Web site
 
Christopher Hogue http://bioinfo.mshri.on.ca/
http://bioinfo.mshri.on.ca/discus/index.html
 
Bernhard Palsson http://www-bioeng.ucsd.edu/research/research_groups/gcrg Link to external Web site
 
Michael Gribskov http://www.sdsc.edu/~gribskov 
 
Peter Karp http://ecocyc.PangeaSystems.com/ecocyc/
 
Shankar Subramanian http://biology.ncsa.uiuc.edu
 
Ulrike Wagner http://histology.nih.gov
 
Brian Ray http://www.stke.org Link to external Web site


This page last reviewed on December 30, 2015