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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