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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:

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.

List of attendees


Supplementary Materials


Announcement page

Photo album

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

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