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The 14th SBML Forum Meeting

Stanford University
September 3–4, 2009

The annual SBML Forum meeting is an opportunity for the SBML community to meet face-to-face and discuss developments in SBML as well as software systems for systems biology. The 2009 meeting included technical presentations by software developers, modelers and researchers on topics relevant to software for systems biology, as well as focused discussions about SBML itself. (There were no tutorials about SBML itself, however, and interested parties are referred to the documents at and the sbml-discuss mailing list for questions of a more basic nature about SBML.)

List of attendees

Photo album


There were times available during the meeting for people to give short presentations on the following topics: SBML-enabled applications, the use of SBML to integrate different applications, proposals for SBML extensions, proposals for standards that complement SBML, announcements of software or standards or events of interest to SBML users, and general experiences of using SBML "in the field".

We were grateful for support from the following organizations for the 2009 SBML Forum:


The meeting location was room 380-Y in building Jordan Hall #380.

Thursday, September 3

Time Topic Speaker/Leader Files Audio (MP3)
13:55–14:05 Introductions Mike Hucka Slides Audio
14:05–14:20 Brief summary of SBML news for 2009 Mike Hucka Slides Audio
14:20–14:30 libSBML update Sarah Keating Slides Audio
14:30–14:50 Antimony 1.2 Lucian Smith Slides Audio
14:50–15:00 SBW 2.7.10 Frank Bergmann Slides Audio
15:00–15:10 CaliBayes Darren Wilkinson Slides Audio
15:10–15:20 iBioSim 1.2 Chris Myers Slides Audio
15:20–15:30 CellDesigner 4.1 beta Akira Funahashi Slides Audio
15:30–15:40 ProcessDB Robert Phair Slides Audio
15:40–16:20 break
16:20–16:30 Cellucidate Ty Thomson Slides Audio
16:30–16:40 E-Cell IDE Takeshi Sakurada Slides Audio
16:40–16:50 BioNetGen rule-based modeling Bin Hu Slides Audio
16:50–18:00 SBML Level 3 Core draft specification Mike Hucka Slides Audio
18:00–19:30 Break and go to restaurant
19:30–22:00 Dinner at California Cafe

The California Cafe is on the Stanford campus, and attendees were able to walk to the meeting room or take the A-line Marguerite bus.

Friday, September 4

Time Topic Speaker/Leader Files Audio (MP3)
09:15–09:30 L3 conversions proposal status Lucian Smith Slides Audio
09:30–10:10 L3 FBA package discussion Brett Olivier Slides Audio
10:10–10:25 L3 Groups package discussion Mike Hucka Slides Audio
10:25–11:00 Break
11:00–11:50 L3 multicomponent/multistate species proposal status Anika Oellrich & Nicolas Le Novère Slides Audio
12:00–13:00 Lunch provided on-site
13:00–15:05 L3 spatial geometries proposal Jim Schaff Slides Audio
15:05–15:45 Break
15:45–16:25 L3 hierarchical composition review Stefan Hoops Web Audio
16:25–17:45 Revisiting Level 3 Core unsettled issues Mike Hucka Slides Audio
17:45–18:00 Wrap-up & discussion of future meetings Mike Hucka Slides Audio


The 2009 SBML Forum took place as a workshop of ICSB 2009. Participants were not required to attend ICSB 2009; however, if not, they stillĀ had to register with ICSB 2009 and indicate they were attending a workshop. A small fee of US $45 was charged by ICSB for workshop attendance to cover the costs of facilities and breaks.


The 14th SBML Forum was held as a satellite workshop of ICSB 2009 at Stanford University. The meeting room was in Jordan Hall (building #420) on the Stanford campus. Jordan Hall is located at the top of the main loop. The full address of the building is Jordan Hall, Building 420, Stanford, CA 94305.

The following maps show the buildings and parking facilities in the area:

Stanford University was founded in 1885 and is consistently ranked as one of the top institutions in the USA and in the world. Locals and members of the university community are known to refer to the school as The Farm, a nod to the fact that the university is located on the former site of founder Leland Stanford's horse farm. The Wikipedia page for Stanford provides more information about the university and its history, and debunks some famous myths about its origins.


Linda Taddeo Michael Hucka
ltaddeo at mhucka at
Tel: +1 626 395 3375
Fax: +1 636 395 3336
Tel: +1 626 395 8128
Biological Network Modeling Center
The Beckman Institute at Caltech
MC 139-74
Pasadena, California 91125
Biological Network Modeling Center
The Beckman Institute at Caltech
MC 139-74
Pasadena, California 91125

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