The 11th SBML Forum Meeting
National Museum of Emerging Science and Innovation
October 12–13, 2006
The eleventh SBML Forum meeting was held as a satellite workshop of ICSB 2006 in Tokyo, Japan. We were once again in the Miraikan, a site where we have held meetings in the past, thanks to our local organizers' connections with the Japan Science and Technology Agency (who created the Miraikan). The local organizers were Akira Funahashi and Yukiko Matsuoka from Hiroaki Kitano's Systems Biology Institute.
We thank our generous sponsors for financial support of the meeting:
- The National Institute of General Medical Sciences (NIGMS), USA (grant R13 GM072439).
- The New Energy Development Organization (NEDO) of Japan
- Japan Science and Technology Agency (JST)
- Ministry of Education, Culture, Sports, Science and Technology (MEXT)
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 rest of this page contains the meeting agenda and links to people's presentation materials.
Day 1 (Thursday, October 12)
| Time | Speaker(s) | Title |
|---|---|---|
| 09:00–09:30 | Mike Hucka | Introductions and report on the state of SBML |
| 09:30–09:40 | Frank Bergmann | SBW |
| 09:40–09:50 | Nicolas Rodriguez | SBMLeditor |
| 09:50–10:00 | Brett Olivier | PySCeS |
| 10:00–10:10 | Lafras Uys | SBML in Berkeley DB |
| 10:10–10:20 | Aurélien Naldi | IBDML |
| 10:30–11:00 | Break | |
| 11:00–11:10 | Johannes Mandel | Narrator |
| 11:10–11:20 | Karthik Raman | PathwayAnalyzer |
| 11:20–11:30 | Akira Funahashi | CellDesigner Update |
| 11:30–11:40 | James Lu | Parameter Identification |
| 11:40–11:50 | Fedor Kolpakov | BioUML |
| 12:00–13:30 | Lunch | |
| 13:30–13:40 | Jean Peccoud | Hybrid stochastic modeling of gene networks |
| 13:40–13:50 | Sven Sahle | COPASI & SBML layout |
| 13:50–14:00 | Ralph Gauges | COPASI & SBML layout |
| 14:00–14:15 | Emek Demir | BioPAX |
| 14:15–14:30 | Eric Mjolsness | Developmental modeling in SBML |
| 14:30–14:50 | Break | |
| 14:50–15:05 | Fedor Kolpakov | Formal definitions of graphical notation |
| 15:05–15:20 | Karthik Raman | Flux annotations in SBML |
| 15:20–15:50 | Mike Hucka, Nicolas Le Novère, Andrew Finney | Final L2V2 Rev 1 debriefing |
| 15:50–17:30 | (Everyone) | Discussion about L2V2 |
| 17:30–18:00 | Final closing & dinner plans |
Day 2 (Friday, October 13)
| Time | Speaker(s) | Title |
|---|---|---|
| 09:00–09:20 | Mike Hucka | Introduction to second day |
| 09:20–09:30 | Nathan Addy | E-Cell |
| 09:30–09:50 | Nicolas Le Novère & Melanie Courtot | SBO |
| 09:50–10:05 | Chen Li & Nicolas Le Novère | BioModels Database |
| 10:05–10:15 | Nicolas Le Novère | MIRIAM & improving compliance |
| 10:15–10:35 | Break | |
| 10:35–10:50 | Mike Hucka | Restarting SBML L3 efforts + discussions |
| 10:50–11:10 | Eric Mjolsness | SBML Level 3: Arrays &/or sets |
| 11:10–11:20 | Bruce Shapiro | SBML Level 3: Sets &/or arrays |
| 11:30–12:00 | (Everyone) | SBML Level 3: Diagrammatic layout |
| 12:00–13:30 | Lunch | |
| 13:30–14:15 | Nicolas Le Novère | SBML Level 3: Spatial geometry |
| 14:15–15:00 | Andrew Finney & Nicolas Le Novère | SBML Level 3: Multicomponent species |
| 15:00–15:20 | Break | |
| 15:20–15:35 | Andrew Finney | SBML Level 3: Model composition |
| 15:35–15:50 | (Everyone) | SBML Level 3: Parameter sets |
| 15:50–16:05 | (Everyone) | SBML Level 3: Distributions |
| 16:05–16:30 | (Everyone) | Open discussion |
| 16:30–16:45 | Break | |
| 16:45–17:15 | (Everyone) | Modularization of SBML |
| 17:15–17:45 | (Everyone) | Open discussion |
| 17:45–18:00 | Mike Hucka | Summary of new SBML process |
| 18:00–18:30 | Mike Hucka | Planning next year's meetings |