Agenda
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Monday
| 9:00-9:10 | "Welcome and Introduction" [PPT Peter D. Karp, SRI International |
| 9:10-10:00 | "It was the best of times, it was the worst of times: Caulobacter crescentus as a model for the study of bacterial cell cycle regulation." [PDF] Leticia Britos, Stanford University |
| 10:00-10:45 | "Regulator Network Visualization & Regulation Representation" [PPT] Mario Latendresse and Suzanne Paley, SRI International |
| 10:45-11:00 | BREAK |
| 11:00-11:30 | "The Ocelot Frame Knowledge Representation System System" [PPT] Peter D. Karp, SRI International |
| 11:30-12:00 | "NCBI Taxonomy Integration" Liviu Popescu, SRI International |
| 12:00-1:30 | LUNCH |
| 1:30-2:00 | "UniProt Feature Importer" [PPT] Tomer Altman, SRI International |
| 2:00-3:00 | "Introduction to Computing with Pathway/Genome Databases" [PPT] |
| 3:00-3:15 | BREAK |
| 3:15-3:35 | Running Lisp with SLIME Fred Gilham, SRI International |
| 3:35-5:00 | Breakout / Hackathon |
Tuesday
| 9:00-9:50 | "Hypothesis Generation Utilizing Genome-Scale Metabolic Modeling With BioCyc" Ranjan Srivastava, University of Connecticut-Storrs |
| 9:50-10:50 | "Pathway Tools and Synthetic Biology" [HTML] Drew Endy, Stanford University |
| 10:50-11 | BREAK |
| 11:00-11:30 | "Using PathwayTools and Matlab for Flux Balance Analysis" [PDF] Kent Peterson, SRI International |
| 11:30-12:00 | "Network Reachability Analysis" [PPT] Markus Krummenacker, SRI International |
| 12:00-1:30 | LUNCH |
| 1:30-2:30 | "Analyzing strains of Prochloroccocus marinus with Pathway Tools" [PPT] Jeremy Zucker, Broad Institute |
| 2:30-3:00 | "Curation and integration of biochemical pathways at the Saccharomyces Genome Database" [PDF] Eurie Hong, Stanford University |
| 3:00-3:15 | BREAK |
| 3:15-3:30 | "Auto-Protonation and Reaction-Balancing" [PPT] Tomer Altman, SRI International |
| 3:30-4:00 | "Pathway Tools and BioCyc: Progress and Future Directions" Peter D. Karp, SRI International |
| 4:00-5:00 | Breakout / Hackathon |
Wednesday
| 9:00-10:00 | "Symbolic Systems Biology: Using Formal Logics to Model and Reason About Biological Systems" [PDF] Carolyn Talcott, SRI International |
| 10:00-10:30 | "Biochemical characterization of metabolomic networks from GC-TOF mass spectrometry data" Oliver Fiehn, UC Davis |
| 10:30-10:45 | Break |
| 10:45-11:15 | Orphan Enzyme Research Alex Shearer, SRI International |
| 11:15-11:45 | The Pathway Tools Advanced Query Form and BioVelo Mario Latendresse, SRI International [PPT] |
| 11:45-12:00 | KEGG / MetaCyc Mapping Tomer Altman, SRI International [PPT] |
| 12:00-1:30 | LUNCH |
| 1:30-1:50 | Orthologs in Pathway Tools: Internals [PPT] Markus Krummenacker, SRI International |
| 1:50-5:00 | Breakout / Hackathon |
Thursday
| 9:00-10:00 | "Pathway / Genome Databases for Y. pestis, F. tularensis, and about a thousand more - tools and tricks of the trade" [PPT] Patrik D'haeseleer, Lawrence Livermore National Laboratory |
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| 10:00-11:00 | "The Archaeal Genome Database and Browser" Todd Lowe, UC Santa Cruz |
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| 11:00-11:15 | Break | |
| 11:15-12:00 | Website administration, customization & technology [PDF] Mario Latendresse and Suzanne Paley, SRI International |
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| 12:00-1:30 | LUNCH | |
| 1:30-2:00 | Machine Learning and PathoLogic [PDF] Joseph M. Dale and Liviu Popescu, SRI International |
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| 2:00-2:30 | GO Term Integration and Curation in Pathway Tools and EcoCyc [PPT] Ingrid Keseler, SRI International |
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| 2:30-2:45 | Gene Ontology in Pathway Tools: Internals [2:45-3:00 | Break |
| 3:00-3:30 | Electron Transfer Pathway / Reactions [PPT] Markus Krummenacker, SRI International |
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| 3:30-5:00 | Breakout / Hackathon |
Friday
| 9:00-9:20 | "CalbiCyc: Metabolic Pathways at the Candida Genome Database" [PPT] Martha Arnaud, Stanford University |
| 9:20-9:50 | BioWarehouse [PPT] Peter D. Karp, SRI International |
| 9:50-10:10 | Break |
| 10:10-10:30 | Pathway Tools Genome Browser: recent enhancements Markus Krummenacker, SRI International |
| 10:30-11:00 | Pathway Tools: Recent achievements and future directions Peter Karp, SRI International |
| 11:00-12:30 | Breakout / Hackathon |
| 12:30-2:00 | LUNCH |
| 2:00-2:30 | Enrichment Analysis Liviu Popescu, SRI International |
| 2:30-5:00 | Breakout / Hackathon |
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