Call for Participation
Pathway Tools Workshop
Emphasis on Microbiome Metabolic Modeling
September 13-15, 2017
This workshop will explore multiple topics related to SRI's Pathway Tools software, with an emphasis on metabolic modeling of the human microbiome.
There has been increasing interest recently in studying and engineering microbial communities for various applications, from biotechnology to health care. However, understanding the complexities of interspecies interactions remains a great challenge. In an effort to expedite advances in this area, SRI is starting a community initiative in modeling the human microbiome. One goal of this workshop is to create a community of researchers who will develop high quality, standardized microbial metabolic models as well as metabolic modeling tools to execute and analyze these models. How can we ensure that models developed by different researchers will plug-and-play with one another? This three-day workshop will bring together researchers to define current gaps and explore potential solutions to challenges in microbial community modeling and other areas in bioinformatics.
The workshop will also present new developments and applications of Pathway Tools.
Conference topics include but are not limited to:
- Advances in metabolic modeling, pathway bioinformatics, systems biology
- Development of metabolic and/or regulatory network models
- Microbial community modeling
- Coordinating the development of tens/hundreds of microbiome models
- Experimental methods for model validation
- Advances in high-throughput data visualization and management
- Genome annotation, and phenotype prediction and assessment
- Scientific results achieved with Pathway Tools and BioCyc
- SRI's recent and planned enhancements and improvements to Pathway Tools and BioCyc
- SRI's recent developments on software APIs and the database schema, to educate users on how to compute with PGDBs
We solicit submissions for oral presentations and posters. Please submit
a proposed title and abstract to
Stanford will be hosting a microbiome bioinformatics workshop in the two days before this SRI workshop. Registration for Stanford workshop Day 1 is at this page; registration for Day 2 will be available soon.
- "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 SRI workshop will be held Sept 13-15, 2017 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.
Conference Organizers
Peter Karp, SRI International ()
Wai Kit Ong, SRI International ()
R&D Divisions