The 5th Workshop on Software Platforms for Systems Biology
University of Hertfordshire, UK
July 8–10, 2002
The fifth workshop was held at the Hatfield Campus of the University of Hertfordshire, UK. It was organized by Hamid Bolouri's group at the University. Attendance was overwhelming (more than would fit in the room!). This page contains the agenda and (where available) presentation materials from the two day workshop. It also contains links to the SBW Programmer's Manual documentation issued to all delegates attending the Forum, and used at the tutorial session on day 3.
Day 1 (Monday, July 8)
| Speaker(s) | Time | Title |
|---|---|---|
| Hiroaki Kitano | 09:00–09:10 | Welcome and introduction |
| Akira Funahashi | 09:10–09:30 | Diagram proposal: a proposal for SBEdit's extension of SBML Level 1 |
| 09:30–09:55 | Discussion | |
| Martin Ginkel | 09:55–10:15 | Modular SBML: Proposal for an extension of SBML towards Level 2 |
| 10:15–10:30 | Discussion | |
| Break | 10:30–11:00 | |
| Daniel Lucio | 11:00–11:20 | Ion channel/membrane potential proposal |
| 11:20–11:45 | Discussion | |
| Nicolas Le Novère | 11:45–12:05 | SBML Level 2 Proposal: Multistate Features |
| 12:05–12:30 | Discussion | |
| Lunch | 12:30–14:00 | |
| Andrew Finney | 14:00–14:20 | SBML Level 2 Proposal: Miscellaneous Features ("Other" functions and conditional expressions proposal) |
| 14:20–14:45 | Discussion | |
| Andrew Finney | 14:45–15:05 | SBML Level 2 Proposal: Array Features |
| 15:05–15:30 | Discussion | |
| Break | 15:30–16:00 | |
| 16:00–17:45 | Parallel break-out groups |
Additional material: A proposal for a minimal SBML Level 2 definition by Mike Hucka and Herbert Sauro. Additional materials included the SBML Level 1 specification document.
Day 2 (Tuesday, July 9)
| Speaker(s) | Time | Title |
|---|---|---|
| Daniel Lucio | 09:00–09:20 | Experiences with SBML Level 1 in the Virtual Cell |
| 09:20–09:25 | Discussion | |
| Pedro Mendes | 09:25–09:45 | Experiences with SBML Level 1 in Gepasi and elsewhere |
| 09:45–09:50 | Discussion | |
| Mike Hucka | 09:50–9:55 | SBML Level 1 errata and clarifications |
| 09:55–10:00 | Discussion | |
| 10:00–10:30 | Discussion about implementation issues with SBML Level 1 | |
| Break | 10:30–11:00 | |
| Mike Hucka and David Morley | 11:00–11:20 | Overview of SBML Level 1.5 |
| 11:20–11:45 | Discussion | |
| 11:45–12:30 | Discussion: planning (1) the feature set of SBML Level 1.5, (2) documenting the SBML Level 1.5 standard, (3) deadline for comments on SBML Level 1.5, and (4) organizing Level 2 development. | |
| Lunch | 12:30–14:00 | |
| Andrew Finney | 14:00–14:05 | Overview of SBW developments |
| Mike Hucka | 14:05–14:30 | Distributed computing with SBW |
| 14:30–14:40 | Discussion | |
| Andrew Finney | 14:40–14:50 | Perl and CORBA with SBW |
| 14:50–15:00 | Discussion | |
| Herbert Sauro | 15:00–15:20 | New SBW-enabled modules (with demo) |
| 15:20–15:30 | Discussion | |
| Break | 15:30–16:00 | |
| Daniel Lucio | 16:00–16:20 | Recent developments in VCell |
| 16:20–16:30 | Discussion | |
| Pedro Mendes | 16:30–16:40 | The latest version of Gepasi and Metabolite Neighbourhoods |
| 16:40–16:45 | Discussion | |
| Claudine Chaouiya | 16:45–16:55 | Gene Interaction Network software |
| 16:55–17:00 | Discussion | |
| Akira Funahashi | 17:00–17:10 | SBML and KEGG |
| 17:10–17:15 | Discussion | |
| 17:15–17:45 | Organization of collaborations/Any Other Business | |
| Break | 17:45–19:30 | |
| 19:30–22:45 | Optional evening outing: Elizabethan Banquet at The Old Palace, Hatfield House, Old Hatfield, Hertfordshire |
Day 3 (Wednesday, July 10)
| Speaker(s) | Time | Title |
|---|---|---|
| 09:00– | SBW tutorials: • Download and set up SBW installation • Download and set up full range of available modules • Run through a pre-worked example in which the user exercises the full range of SBW and its modules • Implement a simple new module (in C, C++, Java, or Python), link it to SBW and "exercise" it. |
Additional materials (SBW programmer's manuals and other documentation):