The 9th SBML Forum Meeting
Heidelberg, Germany
October 14–15, 2004
The ninth workshop was held at the NH Heidelberg in the lovely city of Heidelberg, Germany, as a satellite workshop of the 5th International Conference on Systems Biology (ICSB 2004). Over 40 people attended this productive two-day Forum meeting. The meeting was made possible by the sponsorship of:
- The International Joint Research Program of NEDO, Japan
- The National Institute of General Medical Sciences (NIGMS), USA (grant R13 GM072439)
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 14)
| Time | Speaker(s) | Title |
|---|---|---|
| 09:00–09:10 | Michael Hucka & Andrew Finney | Introduction and Overview |
| 09:10–09:20 | Michael Hucka & Andrew Finney | The State of SBML |
| 09:20–09:30 | Johan Elf and Johan Hattne | MesoRD: A Software for Stochastic Reaction Diffusion Simulation |
| 09:30–09:35 | Discussion | |
| 09:35–09:45 | Johann M. Rohwer, Brett G. Olivier and Jan–Hendrik S. Hofmeyr | PySCeS: Python Simulator for Cellular Systems |
| 09:45–09:50 | Discussion | |
| 09:50–10:00 | Akira Funahashi | CellDesigner and Hardware Accelerated Simulator |
| 10:00–10:05 | Discussion | |
| 10:05–10:15 | Fedor Kolpakov | BioUML: Open Source Extensible Workbench for Systems Biology and supplement 1 |
| 10:15–10:20 | Discussion | |
| 10:20–10:40 | Break | |
| 10:40–10:50 | Sarah M. Keating | SBMLToolbox Release 1.0 |
| 10:50–10:55 | Discussion | |
| 10:55–11:05 | Takeshi Sakurada | SBML support of E–Cell Simulation Environment version 3.1.103 |
| 11:05–11:10 | Discussion | |
| 11:10–11:20 | Bruce Shapiro | SBML Arrays in MathSBML and the Computable Plant Project |
| 11:20–11:25 | Discussion | |
| 11:25–11:35 | Claudine Chaouiya, Elisabeth Remy and Denis Thieffry (supplement 1) | From Logical Regulatory Networks to Petri Nets to SBML |
| 11:35–11:40 | Discussion | |
| 11:40–11:55 | Jeremy Zucker | Model Integration in SBML Using the BioPAX Ontology |
| 11:55–12:00 | Discussion | |
| 12:00–12:05 | Michael Blinov | BioNetGen: Software for Rule–Based Reaction Network Generation |
| 12:05–12:10 | Discussion | |
| 12:10–13:30 | Lunch | |
| 13:30–13:35 | Ralph Gauges/Sven Sahle | SBML Diagram Layout Proposal |
| 13:35–13:40 | Discussion | |
| 13:40–14:25 | Ben Bornstein | libSBML: Recent Developments and Future Directions |
| 14:25–14:40 | Discussion | |
| 14:40–15:15 | Andrew Finney | The SBML Semantic Test Suite |
| 15:15–15:30 | Break | |
| 15:30–16:30 | Continuing Discussion about SBML Validation | |
| 16:30 | Adjourn for the day |
Day 2 (Friday, October 15)
| Time | Speaker(s) | Title |
|---|---|---|
| 09:00–09:10 | Michael Hucka & Andrew Finney | Overview of the Day's Agenda |
| 09:10–09:20 | Karthik Raman and Nagasuma R. Chandra | Merging and Visualisation of SBML Models |
| 09:20–09:25 | Discussion | |
| 09:25–09:40 | David Schröder and Jörg R. Weimar | Modularization of SBML |
| 09:40–09:50 | Discussion | |
| 09:50–10:15 | General Discussion about SBML Modularization | |
| 10:15–10:35 | Break | |
| 10:35–10:55 | Michael Blinov | Graph–Based Rule–Based Approach to SBML Level 3 |
| 10:55–11:05 | Discussion | |
| 11:05–11:25 | Andrew Finney | Multicomponent Species: A Proposal for SBML Level 3 |
| 11:25–11:35 | Discussion | |
| 11:35–12:00 | General Discussion about Multicomponent Species Support in SBML | |
| 12:00–13:30 | Lunch | |
| 13:30–14:00 | SBML Level 2 Version 2 Proposals | |
| 14:00–15:00 | Discussion and Planning for SBML Level 2 Version 2 | |
| 15:00–15:15 | Break | |
| 15:15–16:45 | Discussion about Incorporating Extensions into SBML: Level 2, Level 3, other? | |
| 16:45–17:00 | Planning SBML Hackathon 2005 | |
| 17:00 | Adjourn |