Alternative modeling frameworks 2008
EBI, Hinxton, UK, 12-13 August 2008
The subject of this meeting was how to extend SBML to support formal models. The purpose of the meeting was not to be a scientific workshop, but to produce practical solutions for specification documents.
The meeting was held as a teleconference. Attendees clustered at several sites: the EBI, Hinxton, University of Rostock, and SIB, Lausanne.
Tuesday, 12 August, 2008
|13:00 GMT||Setting up connections and welcome of participants||all|
|14:00||Introduction to SBML and the meeting||Nicolas Le Novère|
|14:15||Introduction to logical modeling||Denis Thieffry|
|14:30||GinSim. Native format and export||Aurélien Naldi|
|15:00||Squad. Native format and export||Ioannis Xenarios||Complementary Info|
|15:30||Chemchains. Native format and export||Tomas Helikar|
|16:30||Introduction to Petri Nets||Claudine Chaouiya|
|17:00||Pi-calculus and PiML||Mathias John|
|17:30||What should be the scope of this extension?||all|
|18:00||Proposal for an initial L3F extension||Duncan Berenguier|
Wednesday, 13 August 2008
On Wednesday morning we worked separately on trying out the proposal, extending it, finding examples, trying to break things, etc. Developers worked on implementation in libSBML, support in GinSIM, Squad and SBMLeditor. We reconvened online in the afternoon.
|13:00||Summary of Tuesday conclusions||all|
|13:15||Summary of the work done in the morning||all|
|Name||Affiliation||Relevant project||Physical location|
|Duncan Berenguier||EBI, UK||GinSim||Hinxton|
|Claudine Chaouiya||IBDM and IML, Luminy, France||GinSim, Petri Nets||Hinxton|
|Alessandro Di Cara||Merck-Serono, Geneva, Switzerland||SQUAD||Lausanne|
|Tomas Helikar||University of Nebraska, USA||ChemChains||Hinxton|
|Mathias John||University of Rostock, Germany||PiML||Rostock|
|Sarah Keating||Caltech, USA||libSBML||Hinxton|
|Dagmar Koehn||University of Rostock, Germany||PiML||Rostock|
|Nicolas Le Novère||EBI, UK||SBML||Hinxton|
|Aurélien Naldi||TAGC, INSERM ERM206, Université de la Méditerranée, Marseilles, France||GinSim||Hinxton|
|Nicolas Rodriguez||EBI, UK||SBMLeditor||Hinxton|
|Denis Thieffry||TAGC INSERM & Université de la Méditerranée, Marseille, France||GinSim||Hinxton|
|Ioannis Xenarios||Swiss Institute of Bioinformatics, Switzerland||SQUAD||Lausanne|
On another page, you can find links to different related projects and other background materials in preparation for the meeting. The various participants also put together this bibliography of papers relevant to the topic of the meeting.
People at the meeting discussed how to cover as many qualitative formalisms as possible. The notes from the meeting itself constituted an initial draft proposal for the package. Following the meeting, Duncan Berenguier and Nicolas Le Novère wrote a more formalized proposal. The proposal of September 19, 2008, is the result.