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.
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:
- Download screencast recording from day 1 (WMV format). The groups you will see in the four quadrants at the beginning of the video are as follow:
- 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.)
- Download screencast recording from day 2 (WMV format). Due to a technical glitch, a significant amount of time (2-3 hours) was lost from the beginning of the session. This video picks up part-way.
Thursday, 6 December 2007
|13:00 GMT||Setting up connections and welcome of participants|
|Introduction to the meeting||M. Hucka|
|Summary of Finney's proposal, what's in L2v3, and needs to go in L3.||N. Le Novère|
|Implementation in SBMLEditor||N. Rodriguez|
|UCHC proposal||M. Blinov||PPT|
Friday, 7 December 2007
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.
- SBML Level 2 Version 3 Release 2 specification
- Le Novère and Oellrich's multistate components (06 December 2007)
- Finney's complex components (31 March 2004)
- Blinov's complex components (06 October 2004)
- Michael Blinov's slides from the last SBML Forum meeting (October 2007)
- Santa-Fe meeting on rule-based modelling
- Martin Meier-Schellersheim's summary slide from Santa Fe meeting
- Proposal for SBML L3 with hierarchical speciesTypes structure
- Proposal for SBML L3 with non-hierarchical speciesTypes structure
|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|
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.