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The 8th SBML Forum Meeting

St. Louis, Missouri, USA
November 10, 2003

The eighth workshop was held at the Chase Park Plaza Hotel in St. Louis, Missouri, as a satellite workshop of the 4th International Conference on Systems Biology (ICSB 2003). It was organized by the Caltech ERATO Kitano team and the Biocomputation Group at the University of Hertfordshire, UK, and was made possible thanks to generous support from the following organizations:

The workshop was a working meeting and did not include any introductory presentations about SBML or related technologies. Attendees had the opportunity to announce developments of software and standards in the field. A large part of the meeting consisted of open discussion of organizational and technical issues surrounding the development of systems biology software and associated standards, and standards for interoperability, particularly in relation to the next generation of SBML, Level 3. The remaining portions of the meeting were devoted to presentations on proposals for standards, as well as technical developments such as new features of a given simulation system.


List of attendees


Minutes


This page contains the meeting agenda and links to presentation materials and other documentation from the workshop

Monday, November 10

Time Speaker(s) Title
08:30–09:00 Continental breakfast
09:00–09:05 Mike Hucka & Andrew Finney Introduction and Overview of the Day’s Agenda
09:05–09:10 Ben Kovitz Introduction fo new facilities at SBML.org
09:10–09:15 Discussion
09:15–09:20 Jo Mathews Active web pages supporting SBML
09:20–09:25 Discussion
09:25–09:30 Sarah Keating SBML MATLAB toolkit and future
09:30–09:35 Discussion
09:35–09:40 Ben Bornstein libSBML developments
09:40–09:45 Discussion
09:45–09:50 Stephen Ramsey Dizzy, a simulator for chemical kinetics of complex systems
09:50–09:55 Discussion
09:55–10:00 Ute Platzer Gene-O-Matic
10:00–10:05 Discussion
10:05–10:15 Bruce E. Shapiro MathSBML
10:15–10:20 Discussion
10:20–10:40 break
10:40–11:00 Zheng Li TeraSim
11:00–11:05 Discussion
11:05–11:10 Shai Sachs The STKE Connections Map and SBML
11:10–11:15 Discussion
11:15–11:20 Developments in CellML ontologies
11:20–11:25 Discussion
11:25–11:30 Ben Kovitz Review of recent Working Group progress
11:30–11:35 Discussion
11:35–11:45 Herbert Sauro Diagram Layout support in SBML
11:45–11:50 Discussion
11:50–12:20 Sven Sahle Diagram Layout Proposal
12:20–12:40 Discussion of Diagram Layout standardization
12:40–14:00 lunch (on your own)
14:00–14:40 Planning future development of Diagram Layout
14:40–14:45 Andrew Finney SBML Level 2 features requested
14:45–14:55 Discussion
14:55–15:05 Andrew Finney Outline of Sets proposal + an Arrays reference implementation
15:05–15:10 Discussion
15:10–15:30 break
15:30–16:00 Establishing an SBML compliance/validation model suite
16:00–16:10 Mike Hucka SBML Level 2 errata
16:10–16:20 Discussion
16:20–16:50 Planning SBML development
16:50–17:20 Additional discussions
17:20–17:30 Discussion about the location of the next SBML Forum meeting
17:30 Adjourn for the day

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