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SBML Multicomponent & Multistate Workshop 2007

EBI, Hinxton, UK, 6-7 December 2007

Many models and modelers want to represent biochemical species that have internal structure or state properties. These may involve molecules that have multiple potential states, such as a protein that may be covalently modified, and molecules that combine to form heterogeneous complexes located among multiple compartments. The resulting system of reactions needs to be generated based on the combinatorial possibilities inherent in the definition of the species and on user-specified rules. The purpose of this meeting is to work on defining an extension to SBML that will support representing such models.


Meeting organization

Nicolas Le Novère and his EBI group organized the meeting. Attendees were distributed at four sites (EBI/Hinxton, VCell/UCHC, VBI, and U. Pittsburgh), and we used videoconferencing to hold the meeting. The actual number of groups involved was larger, but some of the group representatives travelled to the four main sites to reduce the number of connections and increase local interactions and discussions. See the table further below on this page for a list of the attendees and where they were joining from.


The EBI group acted as the lead. A live streaming feed and video recording were provided by the VCell group at UCHC during the meeting. Below are links to saved recordings of the feeds:

    • upper left: people at EBI
    • upper right: people at UCHC
    • lower left: Stefan Hoops at VBI
    • lower right: Jim Faeder at U. Pittsburgh
(Note: the locations of the feeds change whenever a feed is lost and reinstated, so later on, the groups are not be in the same quandrants on the screen.)


Thursday, 6 December 2007

Time Activity Who Files
13:00 GMT Setting up connections and welcome of participants
Introduction to the meeting M. Hucka PDF
Summary of Finney's proposal, what's in L2v3, and needs to go in L3. N. Le Novère PDF
Implementation in SBMLEditor N. Rodriguez PDF
UCHC proposal M. Blinov PPT
Simmune M. Meier-Schellersheim
16:00 Break
16:30 Discussion Everyone
19:00 End
19:30 Dinner

Friday, 7 December 2007

Time Activity Who Files
13:00 GMT Discussion Everyone
16:00 Break
16:30 Discussion Everyone
19:00 End
19:30 Dinner

Working materials/pages

Jim Faeder's Reaction+Rules Proposal.

Pre-meeting Background Information

The following is background reading material for the meeting. We asked people to read at least the Le Novère and Oellrich proposal, as well as the most recent proposal by Blinov/Faeder/Hlavacek/Moraru, and Martin M.-S.'s slide from the Santa Fe meeting.


Name Affiliation Relevant project Physical location
Nathan Addy Molecular Sciences Institute, California, USA E-Cell MSI
Michael Blinov Center for Cell Analysis and Modeling, Connecticut, USA BioNetGen UCHC
Emek Demir Sloan Kettering Cancer Center, New York, USA PAXtools UCHC
James Faeder University of Pittsburgh, Pennsylvania, USA BioNetGen UPitt
Stefan Hoops Virginia Bioinformatics Institute, Virginia, USA COPASI VBI
Michael Hucka Caltech CDS, California, USA SBML EBI
Nicolas Le Novère EMBL-EBI, Hinxton, UK StochSim EBI
Martin Meier-Schellersheim National Institute of Allergy and Infectious Diseases, Maryland, USA Simmune EBI
Ion Moraru Center for Cell Analysis and Modeling, Connecticut, USA The Virtual Cell UCHC
Anika Oellrich EMBL-EBI StochSim EBI
Nicolas Rodriguez EMBL-EBI SBMLeditor EBI

Note: Larry Lok was unable to participate in the telecon as originally hoped; in his place, Nathan Addy observed the event remotely using the video feed.

Other materials

Link to original meeting wiki pages at EBI

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