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SBML Composition Workshop 2007

University of Connecticut Health Center, Farmington, CT, USA, 9-10 September 2007

Model composition refers to the ability to include models as submodels inside other models. This requires defining the interfaces between the models and protocols for connecting parts of models together. One of the anticipated extensions for SBML Level 3 is to support model composition.

The Virtual Cell group at the University of Connecticut Health Center (UCHC), and in particular Ion Moraru, co-organized and hosted a mini-workshop on model composition in September 2007. The meeting was proposed by Ion Moraru and Michael Blinov to follow up on impromptu discussions about submodels/model composition during the Fifth SBML Hackathon earlier in 2007. The goal was to make further progress towards a draft SBML Level 3 extension. This set of wiki pages is based on those originally written and hosted on the VCell Web wiki at the time of the meeting.

Workshop results

The overall conclusion of the workshop was that 2 separate proposals will be developed. One will focus on the language elements required for the actual "model composition" (but brings also additional, initially unforeseen, functionality—such as encoding parameter sets and multiple related simulations). The other will focus on the mechanics of simply assembling SBML from bits and pieces (linking in multiple files and/or fragments thereof).

It is expected that the first proposal will be a bonafide L3 extension, wehereas the second will be (part of) L3 core enhancement(s). Links to the proposals are providede below, followed by the original materials/details/agenda, etc. of the workshop.

Other materials

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