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 http://sbml.org/Documents and the sbml-discuss mailing list for questions of a more basic nature about SBML.)
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 National Institute of General Medical Sciences
(Grant #GM070923) USA - The Beckman Institute BNMC
California Institute of Technology
Pasadena, California, USA
Agenda
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 |
Fees
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.
Location
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.
Contacts
| Linda Taddeo | Michael Hucka |
|---|---|
| ltaddeo at caltech.edu | mhucka at caltech.edu |
| 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 USA | Biological Network Modeling Center The Beckman Institute at Caltech MC 139-74 Pasadena, California 91125 USA |



