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The 11th SBML Forum Meeting

National Museum of Emerging Science and Innovation
October 12–13, 2006

The eleventh SBML Forum meeting was held as a satellite workshop of ICSB 2006 in Tokyo, Japan. We were once again in the Miraikan, a site where we have held meetings in the past, thanks to our local organizers' connections with the Japan Science and Technology Agency (who created the Miraikan). The local organizers were Akira Funahashi and Yukiko Matsuoka from Hiroaki Kitano's Systems Biology Institute.


List of attendees


Meeting wiki


Announcement page


Photo album


We thank our generous sponsors for financial support of the meeting:

This page contains the program and links to presentation materials and other documentation from the workshop. A large part of the meeting consisted of open discussion of organizational and technical issues surrounding the development of systems biology software and associated standards. The remaining portions of the meeting were devoted to presentations on proposals for standards, as well as technical developments such as new features of a given simulation system.

The rest of this page contains the meeting agenda and links to people's presentation materials.

Day 1 (Thursday, October 12)

Time Speaker(s) Title
09:00–09:30 Mike Hucka Introductions and report on the state of SBML
09:30–09:40 Frank Bergmann SBW
09:40–09:50 Nicolas Rodriguez SBMLeditor
09:50–10:00 Brett Olivier PySCeS
10:00–10:10 Lafras Uys SBML in Berkeley DB
10:10–10:20 Aurélien Naldi IBDML
10:30–11:00 Break
11:00–11:10 Johannes Mandel Narrator
11:10–11:20 Karthik Raman PathwayAnalyzer
11:20–11:30 Akira Funahashi CellDesigner Update
11:30–11:40 James Lu Parameter Identification
11:40–11:50 Fedor Kolpakov BioUML
12:00–13:30 Lunch
13:30–13:40 Jean Peccoud Hybrid stochastic modeling of gene networks
13:40–13:50 Sven Sahle COPASI & SBML layout
13:50–14:00 Ralph Gauges COPASI & SBML layout
14:00–14:15 Emek Demir BioPAX
14:15–14:30 Eric Mjolsness Developmental modeling in SBML
14:30–14:50 Break
14:50–15:05 Fedor Kolpakov Formal definitions of graphical notation
15:05–15:20 Karthik Raman Flux annotations in SBML
15:20–15:50 Mike Hucka, Nicolas Le Novère, Andrew Finney Final L2V2 Rev 1 debriefing
15:50–17:30 (Everyone) Discussion about L2V2
17:30–18:00 Final closing & dinner plans

Day 2 (Friday, October 13)

Time Speaker(s) Title
09:00–09:20 Mike Hucka Introduction to second day
09:20–09:30 Nathan Addy E-Cell
09:30–09:50 Nicolas Le Novère & Melanie Courtot SBO
09:50–10:05 Chen Li & Nicolas Le Novère BioModels Database
10:05–10:15 Nicolas Le Novère MIRIAM & improving compliance
10:15–10:35 Break
10:35–10:50 Mike Hucka Restarting SBML L3 efforts + discussions
10:50–11:10 Eric Mjolsness SBML Level 3: Arrays &/or sets
11:10–11:20 Bruce Shapiro SBML Level 3: Sets &/or arrays
11:30–12:00 (Everyone) SBML Level 3: Diagrammatic layout
12:00–13:30 Lunch
13:30–14:15 Nicolas Le Novère SBML Level 3: Spatial geometry
14:15–15:00 Andrew Finney & Nicolas Le Novère SBML Level 3: Multicomponent species
15:00–15:20 Break
15:20–15:35 Andrew Finney SBML Level 3: Model composition
15:35–15:50 (Everyone) SBML Level 3: Parameter sets
15:50–16:05 (Everyone) SBML Level 3: Distributions
16:05–16:30 (Everyone) Open discussion
16:30–16:45 Break
16:45–17:15 (Everyone) Modularization of SBML
17:15–17:45 (Everyone) Open discussion
17:45–18:00 Mike Hucka Summary of new SBML process
18:00–18:30 Mike Hucka Planning next year's meetings

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