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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.

Meeting Organization

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

Time Activity Who Files
13:00 GMT Setting up connections and welcome of participants all
14:00 Introduction to SBML and the meeting Nicolas Le Novère PDF
14:15 Introduction to logical modeling Denis Thieffry PDF
14:30 GinSim. Native format and export Aurélien Naldi PDF
15:00 Squad. Native format and export Ioannis Xenarios Complementary Info
15:30 Chemchains. Native format and export Tomas Helikar PDF
16:00 coffee break all
16:30 Introduction to Petri Nets Claudine Chaouiya PDF
17:00 Pi-calculus and PiML Mathias John PDF
17:30 What should be the scope of this extension? all
18:00 Proposal for an initial L3F extension Duncan Berenguier PDF
19:00 dinner all

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.

Time Activity Who
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

Pre-meeting materials

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.

Meeting outcomes

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.

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