Conference on Predicting Cell Metabolism and Phenotypes

Sponsored by E & J Gallo Winery

Many research groups are interested in cell modeling, and models have begun to gain acceptance and proliferate. But are these models accurate and capable of making useful predictions of cell function? The last several years have seen significant improvements in computational methods for performing phenotypic predictions from metabolic network models. The speed with which such models can be assembled has also advanced. Similarly, experimental methods for high-throughput phenotypic characterization of cells have advanced during this time, and in particular, the use of Phenotype MicroArrays in challenging and improving models has become more widespread. This three-day workshop will bring together researchers in these and related areas to define current gaps and explore potential synergies between these computational and experimental approaches.

Conference topics include but are not limited to:

Advances in metabolic modeling, pathway bioinformatics, systems biology, metabolic engineering, metabolic evolution (both natural and man-made), genome annotation, and phenotype prediction and assessment.
Scientific results achieved with Pathway Tools, BioCyc, and Phenotype MicroArrays.
Development of metabolic flux models with Pathway Tools.
Extended capabilities developed for Pathway Tools.
SRI's recent and planned enhancements and improvements of Pathway Tools and BioCyc.
SRI's recent developments on software APIs and the database schema, to educate users on how to compute with PGDBs.
Biolog's PM analysis software and alternative software written by Biolog users.

We solicit submissions for oral presentations and posters. Please submit a proposed title and abstract to

"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 March 4-6, 2013 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 Closed]

Conference Organizers

Barry Bochner, Biolog, Inc. ()
Peter Karp, SRI International ()