Agenda
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Monday
| 9:00-9:15 | "Welcome and Introduction" Peter Karp, SRI International |
| 9:15-10:15 | "Use of Pathway Tools to Aid Comparative and Functional
Genomics" [PDF] Keynote presentation by Ian Paulsen, TIGR |
| 10:15-10:45 | "Mapping the Metabolome with Pathway Tools" Bart Weimer, University of Utah |
| 10:45-11:15 | BREAK |
| 11:15-11:25 | "The Cell Component Ontology" [PDF] Peifen Zhang, Carnegie Institution |
| 11:25-12:05 | "Recent Developments in the MetaCyc Database" [PDF] Ron Caspi, SRI International |
| 12:05-1:30 | LUNCH |
| 1:30-2:00 | "The Yeast Biochemical Pathway Tool" [PDF] Rama Balakrishnan, Cynthia Krieger, Anita Grover, Christopher Lane, Eurie L. Hong, Mike J. Cherry and SGD Project Saccharomyces Genome Database |
| 2:00-2:30 | "Using genome context data to identify missing enzymes in PGDBs" [PDF] Michelle Green, SRI International |
| 2:30-3:00 | "Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests" [PDF] Jing Shi, Stanford University |
| 3:00-3:30 | BREAK |
| 3:30-4:00 | "AraCyc -- birth and growth of the Arabidopsis Pathway/Genome Database" [PDF] Peifen Zhang, Carnegie Institution |
| 4:00-4:30 | "Finding Drug Targets for Malaria Using PlasmoCyc" Iwei Yeh, Stanford University |
| 4:30-5:00 | "Pathway Tools and BioCyc: Progress and Future Directions" [PDF] Peter Karp, SRI International |
Tuesday
| 9-9:30 | "Comparative Analyses in Pathway Tools" Alex Shearer, SRI International |
| 9:30-10 | "Computing with PGDBs" [PDF] Markus Krummenacker, SRI International |
| 10-10:30 | "PerlCyc: computing with Pathway Tools using Perl" [PDF] Lukas Mueller, Cornell University |
| 10:30-11 | BREAK |
| 11-11:30 | "Debugging the Bug: Lessons learned from integrating EcoCyc and iJR904" [PDF] Jeremy Zucker, Harvard University |
| 11:30-12 | "An Introduction to Flux Balance Analysis Using Pathway/Genome Databases" [PDF] Ranjan Srivastava, University of Connecticut-Storrs |
| 12:00-1:30 | LUNCH |
| 1:30-2 | "Conceptual differences between BioCyc and KEGG and their implications for computational biologists" [PDF] Michelle Green, SRI International |
| 2-3:30 | Tutorial and Discussion: "Pathway Tools Schema and Semantic Inference Layer: Genes, Operons, and Replicons" [PDF] Peter Karp, SRI International |
| 3:30-5:00 | Hackathon / Group discussions |
Wednesday
| 9:00-9:30 | "Community-assisted genome annotation: The Pseudomonas example" [PDF] Geoff Winsor, Simon Fraser University |
| 9:30-10:00 | "The EcoCyc Curation Process" [PDF] Ingrid Keseler, SRI International |
| 11:00-12:00 | Panel: "Funding an Organism-Specific Database Project" Michael Cherry, Stanford University [PDF] Gavin Sherlock, Stanford University [PDF] Bart Weimer, Utah State University Geoff Winsor, Simon Fraser University |
| 12:00-1:30 | LUNCH |
| 2-3:30 | Tutorial and Discussion: "Pathway Tools Schema and Semantic Inference Layer: Reactions, Compounds, Proteins/RNAs" [PDF] Pallavi Kaipa and Alex Shearer, SRI International |
| 3:30-5:00 | Hackathon / Group discussions |
Thursday
| 9:00-9:30 | "The Pathway Tools Advanced Query Form" [PDF] Mario Latendresse, SRI International |
| 9:30-10:00 | "The Pathway Tools Genome Browser" [PDF] Markus Krummenacker, SRI International |
| 10:00-10:30 | "How to administer a PGDB" [PDF] Suzanne Paley, SRI International |
| 10:30-12:00 | Hackathon / Group discussions |
| 12:00-1:30 | LUNCH |
| 2-3:30 | Tutorial and Discussion: "Pathway Tools Schema and Semantic Inference Layer: Pathways and the Overview" [PDF] Suzanne Paley, SRI International |
| 3:30-5:00 | Hackathon / Group discussions |
Friday
| 9-12:00 | Hackathon / Group discussions |
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