The 12th SBML Forum Meeting
Hyatt Regency Hotel, room Seaview C
October 5–6, 2007
The twelfth SBML Forum was held at the Long Beach Hyatt hotel in Long Beach, California, as a satellite workshop of the 8th International Conference on Systems Biology (ICSB 2007). It was organized by the Caltech SBML Team, and was made possible thanks to support from the following organizations:
- The National Institute of General Medical Sciences (NIGMS), USA (grant R01 GM070923)
- The Beckman Institute BNMC, California Institute of Technology, Pasadena, California, USA
This page contains the program and links to presentation materials and other documentation from the workshop.
Day 1 (Friday, October 5, 2007)
| Time | Speaker(s) | Title |
|---|---|---|
| 09:00–09:45 | M. Hucka | Introduction & review of status of SBML |
| 09:45–10:00 | M. Goliebwieski | SABIO-RK |
| 10:00–10:10 | F. Bergmann | SBW |
| 10:10–10:20 | S. Sahle | COPASI |
| 10:20–10:40 | J. Schaff | Virtual Cell |
| 10:40–10:55 | Break | |
| 10:55–11:10 | F. Kolpakov | BioUML |
| 11:10–11:20 | N. Rodriguez | SBMLeditor |
| 11:20–11:30 | M. Pedersen | LBS |
| 11:30–11:45 | D. Kell | (a) Workflows for systems biology and (b) Issues in representing parameter uncertainty |
| 11:45–12:05 | N. Le Novère | MIRIAM, SBO, Teddy |
| 12:05–12:15 | D. Köhn | Guidelines for Annotating Simulation Runs |
| 12:15–12:20 | R. Phair | ProcessDB |
| 12:20–12:30 | R. Phair | Issues in loss of info caused by non-unique species names |
| 12:30–12:40 | S. Hoops | Issues in handling changing compartment volumes |
| 12:40–14:15 | Lunch | |
| 02:30–15:05 | Everyone | Further discussion of issues raised before lunch |
| 03:05–15:30 | Break | |
| 03:30–15:40 | M. Hucka | SBML Level 3 orientation |
| 03:40–16:00 | N. Le Novère | Modifying SBML Level 2 to be Level 3 Core |
| 04:00–16:20 | S. Hoops | SBML Level 3 Core enhancements: a report |
| 04:20–16:40 | I. Moraru | SBML Model Composition: a report |
| 04:40–17:00 | S. Hoops | SBML Hiearchical Models: syntax proposal |
| 05:00–17:15 | J. Schaff | Spatial modeling in SBML |
| 05:15–18:00 | Everyone | Open discussions & planning day 2 |
| 06:00–19:00 | Wine & cheese reception |
Day 2 (Saturday, October 6, 2007)
| Time | Speaker(s) | Title |
|---|---|---|
| 09:05–09:10 | M. Hucka | Introduction to day 2 |
| 09:10–09:45 | S. Hoops | What’s fixed when volumes are changing? What changes are needed in SBML? |
| 09:45–10:20 | N. Le Novère | Proposed MathML changes in Level 3 |
| 10:20–10:45 | Break | |
| 10:45–11:05 | N. Le Novère | SBML Level 3 multistate variables |
| 11:05–11:30 | M. Blinov | Rule-based modeling in SBML |
| 11:30–11:50 | F. Kolpakov | Embedding formal graphic notations into SBML models |
| 11:50–12:05 | Everyone | Additional discussions |
| 12:05–12:15 | B. Olivier | Plans for the next Hackathon |
| 12:15–14:00 | Lunch | |
| 02:00–15:15 | M. Hucka | The SBML Development Process |
| 03:15–15:30 | F. Kolpakov | Process for developing SBML extensions |
| 03:30–16:00 | Break | |
| 04:00–17:15 | Everyone | More discussions of SBML Level 3 Core |
| 05:15–17:30 | Everyone | Final discussions and closing |