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 JST ERATO Kitano Symbiotic Systems Project
- The e-Science Initiative, BBSRC, UK
- The Biocomputation Group at the University of Hertfordshire, UK
This page contains the program and links to presentation materials and other documentation from the workshop. 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. 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.
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. The largest portion of time was devoted to discussing standards for interoperability, particularly the next generation of SBML, Level 3.
The rest of this page contains the meeting agenda.
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 |



