The 13th SBML Forum Meeting
Wallenberg Conference Center at the University of Gothenburg
August 27–28, 2008
The annual SBML Forum meetings were an opportunity for the SBML community to meet face-to-face and discuss developments in SBML as well as software systems for systems biology. SBML Forum Meetings 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. (Attendees did not receive tutorials about SBML itself, but were 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 compliment SBML, announcements of software or standards or events of interest to SBML users, and general experiences of using SBML "in the field".
Agenda
Files and supplementary materials associated with people's presentations are available below.
Wednesday, August 27
Note: presentation times were 5 minutes plus 2 minutes for questions. Times in the schedule below have been adjusted post-hoc to account for schedule shifts due to ad-hoc discussions that arose during presentations.
| Time | Topic | Speaker/Leader | Files |
|---|---|---|---|
| 14:30–14:45 | Introductions | Mike Hucka | Slides |
| 14:45–14:55 | Recent SBML.org and SBML Team software news | Mike Hucka | Slides |
| 14:55–15:00 | Arcadia | Alice Villeger | Slides |
| 15:00–15:05 | BioModels Database version 3 | Chen Li | Slides |
| 15:05–15:15 | VCell recent developments | Ion Moraru | Slides |
| 15:15–15:25 | QBT | Eric Billings | Slides |
| 15:25–15:35 | SBW 2.7.8 | Frank Bergmann | Slides |
| 15:35–15:45 | SBToolbox2 | Henning Schmidt | Slides |
| 15:45–15:55 | iBioSim | Chris Myers | Slides |
| 16:00–16:20 | Break | ||
| 16:25–16:35 | SABIO-RK developments | Martin Golebiewski | Slides |
| 16:35–16:45 | PathText | Rune Saetre | Slides |
| 16:45–17:00 | BioUML recent developments | Fedor Kolpakov | Slides |
| 17:00–17:15 | Intro to SBML Level 3 activities | Mike Hucka | Slides |
| 17:15–17:25 | Report: SBML Level 3 Core | Sarah Keating | Slides |
| 17:25–17:45 | Report: Level 3 package for multiple components & states | Anika Oellrich | Slides, Example |
| 17:45–18:00 | Report: Level 3 package for layout & rendering | Sven Sahle | Slides, Example_PDF, Example_XML |
| 18:00–18:20 | Report: Level 3 package for qualitative modeling | Berenguier Duncan | Slides |
Thursday, August 28
In some cases, there are no associated slides because the presentation/discussion consisted either of visiting a web page or whiteboard interaction. The transcripts are accounts of the discussions, written by Mike Hucka from recordings taken during the meting.
| Time | Topic | Speaker/Leader | Files |
|---|---|---|---|
| 09:00–09:10 | Introduction to the day | Mike Hucka | |
| 09:10–09:25 | SED-ML | Nicolas Le Novère | Slides |
| 09:25–09:40 | Discussions after SED-ML presentation | Transcript | |
| 09:40–10:00 | SBRML | Joseph Dada | Slides |
| 10:00–10:10 | Discussions after SBRML presentation | Transcript | |
| 10:10–10:20 | Further discussions on SBRML & SED-ML | Transcript | |
| 10:20–10:45 | Break | ||
| 10:45–12:00 | SBML Level 2 Version 4 changes | Mike Hucka | |
| 12:00–13:30 | Lunch | ||
| 13:35–13:40 | Spatial modeling note | Ion Moraru | Slides |
| 13:40–13:55 | Hierarchical model ideas in BioUML | Fedor Kolpakov | Slides |
| 13:55–14:30 | In-depth: SBML Level 3 hierarchical composition | Stefan Hoops (+ use-case from Ion) | Slides, Use-case |
| 14:30–14:45 | Break | ||
| 14:45–15:30 | In-depth: SBML Level 3 Core (emerging proposal) | Stefan Hoops | Web page |
| 15:30–16:15 | In-depth: SBML Level 3 multicomponent & multistate | Anika Oellrich & Nicolas Le Novère | Web page |
| 16:15–16:30 | Break | ||
| 16:15–17:30 | Open discussion & perspectives | Everyone | |
| 17:30–18:00 | Picking 2009 Hackathon location & closing | Everyone |
Travel
The 2008 SBML Forum workshop took place in the Wallenberg Conference Centre of the Medicinaberget at the University of Gothenburg.
Please refer to the ICSB 2008 travel information page for more information about Göteborg and the convention center there. We regret that we had no travel support available for this meeting. We did, however, arrange for coffee breaks, a group dinner on August 27, and more.
The weather in Gothenburg at the end of August is mild with frequent chances of showers. Temperature ranges from 15–25 C (59–77 Fahrenheit) during the day and 10–15 C (50–59 Fahrenheit) during the night.
We recommended that if you were traveling from outside of Sweden, you brought an appropriate power plug converter for your laptop and all other electrical devices. Electric current in Sweden is 50 Hz, 220-240 V (the same as in central Europe). The plug types are depicted below. For more detailed information on the types of plugs that are used, as well as electrical standards in various countries, please visit http://users.pandora.be/worldstandards/electricity.htm .
| Type C Plug |
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| Type F Plug |
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Acknowledgments
This year's SBML Forum is supported by
- The National Institute of General Medical Sciences
(Grant #GM070923) USA - The Beckman Institute BNMC
California Institute of Technology
Pasadena, California, USA
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 |


