PTools 06

Home | Agenda | Directions | Hotels


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


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


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


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
10:00-11:00 "The Archaeal Genome Database and Browser"
Todd Lowe, UC Santa Cruz
11:00-11:15 Break
11:15-12:00 Website administration, customization & technology [PDF]
Mario Latendresse and Suzanne Paley, SRI International
12:00-1:30 LUNCH
1:30-2:00 Machine Learning and PathoLogic [PDF]
Joseph M. Dale and Liviu Popescu, SRI International
2:00-2:30 GO Term Integration and Curation in Pathway Tools and EcoCyc [PPT]
Ingrid Keseler, SRI International
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
3:30-5:00 Breakout / Hackathon


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

About SRI International   Vertical divider   R&D Divisions  Divider   Careers  Divider   Newsroom  Divider   Contact Us
©2006 SRI International 333 Ravenswood Avenue, Menlo Park, CA 94025-3493
SRI International is an independent, nonprofit corporation. Privacy policy