Pathway Tools User Group Meeting

December 1, 2005

Geneva, Switzerland


9:00-9:15                     Introductions


9:15-9:45am                 “Introduction”, Peter Karp, SRI International, USA


9:45-10:15am               "Genome-wide studies using BioCyc"

Christos Ouzounis, European Bioinformatics Institute, United Kingdom


10:15-10:45am            "Study of Functional and Evolutionary Attributes through

the Analysis of Metabolic Pathways in Entire Genomes"

Sophia Tsoka, European Bioinformatics Institute, United Kingdom


10:45-11:00am Coffee Break


11:00-11:30am             "MaGe and BioCyc : putting together synteny and metabolic information to achieve relevant expert annotation of microbial genomes"

Claudine Medigue, Genoscope, France


11:30-12:00pm            "The construction of LacplantCyc and the use of physiological and genomics data to expand and rearrange the PGDB"

Christof Francke, Centre for Molecular and Biomolecular Informatics, The Netherlands


12:00-1:30pm              Lunch


1:30-2:00pm                "Debugging the bug:  Lessons learned from developing constraint-based  flux models of Buchnera"

Jeremy Zucker, Harvard University, USA


2:00-2:30pm                "Using BioCyc to work with FBA models : the "Metabolic Thesaurus" project"

Vincent Schachter, Genoscope, France


2:30-3:00pm                "Recent developments and future directions in Pathway Tools"

Peter Karp, SRI, USA


3:30-4:00pm                Coffee Break


4:00-4:30pm                "Writing Programs that Analyze Pathway/Genome Databases"

Markus Krummenacker, SRI International, USA


4:30-5:30pm                Roundtable Discussion