PTools '10

Agenda
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Please note that schedule is subject to change

Monday

"Introduction"
Peter D. Karp, SRI International [PDF]
9 - 9:15 AM
"New Zoomable Web Metabolic Network and Regulatory Network Diagrams"
Mario Latendresse, SRI International [PPT]
9:15 - 9:45 AM
"Experimental evidence-based annotation and metabolic analysis of environmental microbes using MicrobesOnline"
Adam P. Arkin, Lawrence Berkeley National Laboratory
9:45 - 10:30 AM
Break 10:30 - 11 AM
Keynote Presentation: "Tryptophan Synthesis and Degradation: Regulatory and Evolutionary Features"
Charles Yanofsky, Stanford University [PPT]
11 AM - 12:15 PM
Lunch 12:15 - 1:30 PM
"Comparative and evolutionary analysis of genomes from Rickettsia-related endosymbionts"
B. Franz Lang, University of Montreal [PPT]
1:30 - 2:15 PM
"The IGS Annotation Engine and Manatee"
Michelle Gwinn Giglio, University of Maryland [PDF]
2:15 - 3 PM
"Annotation Error in Public Databases"
Alexandra Schnoes, University of California [PDF]
3 - 3:30 PM
Break 3:30 - 4 PM
"BsubCyc: A model organism database for Bacillus subtilis"
Ingrid Keseler, SRI International [PPT]
4 - 4:30 PM
"Importing GO terms from UniProt to a PGDB"
Markus Krummenacker, SRI International [PPT]
4:30 - 4:45 PM
"New Regulation Summary Diagram"
Suzanne Paley, SRI International [PPT]
4:45 - 5 PM
"Recent and Planned Enhancements to Pathway Tools and BioCyc"
Peter D. Karp, SRI International [PDF]
5 - 5:30 PM

Tuesday

"From genome sequences to metabolic flux models"
Jeremy Zucker, Broad Institute [PPT]
9 - 9:42 AM
"Towards a whole-cell model of Mycoplasma genitalium"
Markus Covert, Stanford University [PDF]
9:42 - 10:24 PM
Break 10:30 - 11 AM
"Integrating flux balance analysis of fungal genome-scale metabolic networks into metabolic engineering practice"
James R. Collett, Pacific Northwest National Laboratory [PDF]
11 - 11:42 AM
"Automated generation of flux-balance models from PGDBs"
Peter D. Karp, SRI International [PDF]
11:42 AM - 12:24 PM
"Finding dead-end metabolites"
Michael Travers, SRI International [PPT]
12:24 - 12:30 PM
Lunch 12:30 - 1:30 PM
"Cross-Linking BioCyc and KEGG"
Tomer Altman, SRI International [PDF]
1:30 - 1:45 PM
"EcoCyc on the iPhone"
Jerome Thomere, SRI International
1:45 - 2 PM
"Constraint-based Modeling of Metabolic Networks"
Radhakrishnan Mahadevan, University of Toronto
2 - 2:42 PM
"Recent Pathway Tools Performance Enhancements"
Mario Latendresse, SRI International [PPT]
2:42 - 2:57 PM
"Object Groups and Enrichment Analysis"
Suzanne Paley, SRI International [PPT]
3 - 3:20 PM
Break 3:20 - 3:50 PM
"Metabolic reconstructions from Global ocean sampling marine metagenome"
Mathangi Thiagarajan, J. Craig Venter Institute [PDF]
3:50 - 4:20 PM
"Orthology-Based Multi-PGDB Editor"
Suzanne Paley, SRI International [PPT]
4:20 - 4:40 PM
"Enzyme Commission Numbers"
Ron Caspi, SRI International [PDF]
4:40 - 5:10 PM
"Discovery of Novel Metabolic Pathways in PGDBs"
Luciana Ferrer, SRI International [PDF]
5:10 - 5:30 PM

Wednesday

"Acquisition and analysis of data in mass spectrometry based metabolomics"
Pavel Aronov, Stanford University [PPT]
9 - 9:42 AM
"Dealing With the Unknown: Metabolomics and Metabolite Atlases"
Ben Bowen, Lawrence Berkeley National Laboratory [PPT]
9:42 - 10:24 AM
Break 10:30 - 11 AM
"HumanCyc and the Metabolomics Network"
Miles Trupp, SRI International
11 - 11:30 AM
"Methanotrophic Bioplastic Production: Insights from Pathway / Genome Databases"
Katherine Rostkowski, Stanford University [PPT]
11:30 AM - 12:12 PM
Lunch 12:12 - 1:30 PM
"Strain engineering for advanced biofuels at Amyris"
Timothy Gardner, Amyris Biotechnologies [PDF]
1:30 - 2:12 PM
"The Model SEED Resource for High Throughput Reconstruction of Genome-scale Metabolic Models"
Christopher Henry, Argonne National Laboratory [PPT]
2:12 - 2:54 PM
"A BRG BioFuel Metabolic Engineering Project"
Mario Latendresse, SRI International [PPT]
2:54 - 3:09 PM
Break 3:09 - 3:30 PM
Panel Discussion: Automated Generation of Metabolic Flux Models 3:30 - 4:30 PM
"New Monoisotopic Mass Searches"
Markus Krummenacker, SRI International
4:30 - 4:45 PM
"New Support for Signaling Pathways in Pathway Tools"
Suzanne Paley, SRI International
4:45 - 5 PM
"Quantitative Proteomics: Approaches and Current Capabilities"
Chistopher Becker, SRI International [PPT]
5 - 5:20 PM
Blake Simmons, Sandia National Laboratory [PPT] 5:20 - 6:02 PM

Thursday

"ShewCyc and BeoCyc: discovery platforms for environmental and bioenergy research"
Tatiana Karpinets and Michael Leuze, Oak Ridge National Laboratory [PPT]
9 - 9:45 PM
"Orphan Enzymes"
Alexander Shearer, SRI International [PPT]
9:45 - 10:15 AM
"New Pathway Tools Web Services"
Suzanne Paley, SRI International
10:15 - 10:30 PM
Break 10:30 - 11 AM
"Overview of the Pathway Tools APIs"
Tomer Altman, SRI International
11 - 11:15 AM
"Memos and Author Crediting"
Markus Krummenacker, SRI International
11:15 - 11:30 AM
"The Protein Ontology (PRO)"
Natalia Roberts, Protein Information Resource [PPT]
11:30 AM - 12 PM
Lunch 12 - 1:30 PM
"JavaCycO: A polymorphic, object-oriented redesign of JavaCyc"
John Van Hemert, Iowa State University [ODP]
1:30 - 1:50 PM
Hackathon / Working Groups 1:50 - 5 PM

Friday

"Cytoscape and Pathway Tools Integration"
Scooter Morris, University of California [PPT] [Plugin JAR]
9 - 9:30 AM
"Challenges in creating and curating plant PGDBs: Lessons learned from AraCyc and PoplarCyc"
Peifen Zhang, Carnegie Institution [PPT]
9:30 - 10 AM
"Navigation to Related Objects"
Mario Latendresse, SRI International [PPT]
10 - 10:15 AM
Hackathon / Working Groups 10:15 AM - 12:30 PM
Lunch 12:30 - 1 PM
Catherine Ball, Stanford University 1 - 1:30 PM
Hackathon / Working Groups 1:30 - 5 PM


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