Hosted by the Bioinformatics Research Group at SRI International
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Teleconferencing options available
This workshop oriented around SRI's Pathway Tools software and BioCyc Database Collection will explore pathway bioinformatics and Pathway/Genome Databases.
The workshop will combine formal presentations by groups outside SRI International (invited speakers and speakers selected through an abstract-submission process), tutorials by SRI International staff, and a hackathon. Suggested topics include but are not limited to:
- Advances in pathway bioinformatics, model organism databases, genome annotation, and systems biology
- Scientific results achieved with Pathway Tools and BioCyc
- Share expertise on how to develop new organism-specific databases with Pathway Tools
- Share experiences on how to make the most of Pathway Tools
- Presentations by users on extensions they have developed to Pathway Tools
- Presentations by SRI International on recent and planned developments to the software, and on software APIs and the database schema, to educate users on how to compute with PGDBs
Presentations
We solicit submissions for presentations and posters. Please submit a proposed title and abstract toPlanned presentations: See the tentative agenda.
- "Tryptophan Synthesis and Degradation: Regulatory and Evolutionary
Features"
Charles Yanofsky, Stanford University - "Experimental evidence-based annotation and metabolic analysis
of environmental microbes using MicrobesOnline"
Adam P. Arkin, UC Berkeley - "Dealing With the Unknown: Metabolomics and Metabolite Atlases"
Ben Bowen, Lawrence Berkeley National Laboratory - "The Model SEED Resource for High Throughput Reconstruction of Genome-scaleMetabolic Models"
Christopher Henry, Argonne National Laboratory - "Microbial ecology and the application of Pathway Tools to
environmental genomics"
Simon Eng, University of British Columbia - "Comparative and evolutionary analysis of genomes from
Rickettsia-related endosymbionts"
B. Franz Lang, University of Montreal - "From genome sequences to metabolic flux models"
Jeremy Zucker, Broad Institute - "Integrating flux balance analysis of fungal genome-scale
metabolic networks into metabolic engineering practice."
James R. Collett, Pacific Northwest National Laboratory - "JavaCycO: A polymorphic, object-oriented redesign of JavaCyc"
John Van Hemert, Iowa State University - "Methanotrophic Bioplastic Production: Insights from Pathway /
Genome
Databases"
Katherine Rostkowski, Stanford University - "Towards a whole-cell model of Mycoplasma genitalium"
Markus Covert, Stanford - "The IGS Annotation Engine and Manatee"
Michelle Gwinn Giglio, University of Maryland - "The Protein Ontology (PRO)"
Natalia Roberts, Protein Information Resource - "Acquisition and analysis of data in mass spectrometry based metabolomics"
Pavel Aronov, Stanford - "Challenges in creating and curating plant PGDBs: Lessons learned from AraCyc and PoplarCyc"
Peifen Zhang, Carnegie Institution - "ShewCyc and BeoCyc: discovery platforms for environmental and bioenergy research"
Tatiana Karpinets and Michael Leuze, Oak Ridge National Lab - "Reasonably Random Synthetic Biology: Strain engineering for advanced biofuels at Amyris"
Timothy Gardner, Amyris Biotechnologies - "A Sneak Peak at EcoCyc on the iPhone"
Peter Karp, SRI International - "Constraint-based Modeling of Metabolic Networks"
Radhakrishnan Mahadevan, University of Toronto - "Signaling Pathways in Pathway Tools"
Suzanne Paley, SRI International - "Zoomable Cellular Network Overviews Using Modern Web Technologies"
Mario Latendresse, SRI International - "Linking MetaCyc Reactions and Compounds to KEGG"
Tomer Altman, SRI International
Registration and Travel Information
The workshop will be held at SRI International in Menlo Park, CA in the San Francisco Bay Area, with proximity to redwood forests, the Napa Valley wine country, Lake Tahoe, and Northern California beaches.
- Registration is now closed.
- Directions to the meeting at SRI International
- Hotels
