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The 12th SBML Forum Meeting

Hyatt Regency Hotel, room Seaview C
October 5–6, 2007

List of attendees

Announcement page

The twelfth SBML Forum was held at the Long Beach Hyatt hotel in Long Beach, California, as a satellite workshop of the 8th International Conference on Systems Biology (ICSB 2007). It was organized by the Caltech SBML Team, and was made possible thanks to support from the following organizations:

This page contains the program and links to presentation materials and other documentation from the workshop.

Day 1 (Friday, October 5, 2007)

Time Speaker(s) Title
09:00–09:45 M. Hucka Introduction & review of status of SBML
09:45–10:00 M. Goliebwieski SABIO-RK
10:00–10:10 F. Bergmann SBW
10:10–10:20 S. Sahle COPASI
10:20–10:40 J. Schaff Virtual Cell
10:40–10:55 Break
10:55–11:10 F. Kolpakov BioUML
11:10–11:20 N. Rodriguez SBMLeditor
11:20–11:30 M. Pedersen LBS
11:30–11:45 D. Kell (a) Workflows for systems biology and (b) Issues in representing parameter uncertainty
11:45–12:05 N. Le Novère MIRIAM, SBO, Teddy
12:05–12:15 D. Köhn Guidelines for Annotating Simulation Runs
12:15–12:20 R. Phair ProcessDB
12:20–12:30 R. Phair Issues in loss of info caused by non-unique species names
12:30–12:40 S. Hoops Issues in handling changing compartment volumes
12:40–14:15 Lunch
02:30–15:05 Everyone Further discussion of issues raised before lunch
03:05–15:30 Break
03:30–15:40 M. Hucka SBML Level 3 orientation
03:40–16:00 N. Le Novère Modifying SBML Level 2 to be Level 3 Core
04:00–16:20 S. Hoops SBML Level 3 Core enhancements: a report
04:20–16:40 I. Moraru SBML Model Composition: a report
04:40–17:00 S. Hoops SBML Hiearchical Models: syntax proposal
05:00–17:15 J. Schaff Spatial modeling in SBML
05:15–18:00 Everyone Open discussions & planning day 2
06:00–19:00 Wine & cheese reception

Day 2 (Saturday, October 6, 2007)

Time Speaker(s) Title
09:05–09:10 M. Hucka Introduction to day 2
09:10–09:45 S. Hoops What’s fixed when volumes are changing? What changes are needed in SBML?
09:45–10:20 N. Le Novère Proposed MathML changes in Level 3
10:20–10:45 Break
10:45–11:05 N. Le Novère SBML Level 3 multistate variables
11:05–11:30 M. Blinov Rule-based modeling in SBML
11:30–11:50 F. Kolpakov Embedding formal graphic notations into SBML models
11:50–12:05 Everyone Additional discussions
12:05–12:15 B. Olivier Plans for the next Hackathon
12:15–14:00 Lunch
02:00–15:15 M. Hucka The SBML Development Process
03:15–15:30 F. Kolpakov Process for developing SBML extensions
03:30–16:00 Break
04:00–17:15 Everyone More discussions of SBML Level 3 Core
05:15–17:30 Everyone Final discussions and closing


The 2007 SBML Forum was supported by

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