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The 3rd Workshop on Software Platforms for Systems Biology

California Institute of Technology, Pasadena, California, USA
June 1–2, 2001

The 3rd workshop was held on the campus of the California Institute of Technology in Pasadena. It was organized by the Caltech ERATO Kitano group and supported by the ERATO Kitano Symbiotic Systems Project.

The following are the slides from individual presentations at the workshop. This page contains only the presentation materials from collaborating groups for the first day of the workshop. The second day consisted of presentations by the Caltech ERATO Kitano group and group discussions.

Speaker(s) Time Title
Hamid Bolouri 08:45–09:00 The Day's Agenda
Warren Hedley 09:00–09:45 Metadata Tutorial (discussion proposal available here)
Warren Hedley 09:45–10:30 CellML 1.0 Specification Summary,
CellML Future,
CellML ↔ SBML Translation
Break 10:30–11:00
Daniel Lucio 11:00–11:45 Geometry Description Standards?
Eric Mjolsness 11:45–12:30 XML for Multicellularity, Arrays and Interconnects (supporting article available here)
Lunch 12:30–14:00
Martin Ginkel and Jörg Stelling 14:00–14:45 XML Notation for Modularity (with example SBML Level 2 and pre-meeting proposal)
Nicolas Le Novère 14:45–15:15 Multistate molecules and complex objects
Break 15:00–15:30
Kouichi Takahashi 15:30–16:15 Mixed Mode and Large-Scale Simulation Issues
Igor Goryanin and Hugh Spence 16:15–17:00 Proposals for extensions to SBML


Additional materials: Andrew Finney had previously written a proposal for extensions to SBML that was the basis of much of the discussions at the workshop.

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