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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.)


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 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


Type F Plug

Acknowledgments

This year's SBML Forum is supported by

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

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