Multicellular spatial models have become an essential tool in quantitative biology and multiple model formalisms and simulation frameworks coexist. Progress towards software interoperability and reproducibility requires a novel model description language and conversion library, complementing SBML. Building on the community‘s practical experiences with multiple formalisms and simulators, we aim at (1) defining the concept for a multicellular language while simultaneously (2) exploring automated model conversion between (closely related, e.g. CPM-supporting) simulators using the language prototype. This defines two tracks (1. Language and 2. Converter) with joint talks and parallel sessions.
The workshop at the start will present lessons learnt from SBML, recent advances in simulators, efforts to reproduce simulation studies as well as declarative model interfaces in specific simulators.
The subsequent hackathon combines joint cross-track discussions with parallel working sessions for drafting the language concept and specification in the Language track as well as hands on coding and applying software in the Converter track. Please bring your laptop with your simulator installed.
Confirmed speakers (frameworks)
- James A. Glazier (CompuCell3D), Indiana University, USA
- Tim Johann (TiSim), IfADo, Germany
- Matthias König (SBML), Humboldt-University Berlin, Germany
- Jochen Kursawe (Chaste), University of St Andrews, UK
- Andy Somogyi (Mechanica), Indiana University, USA
- Jörn Starruß and Walter de Back (Morpheus), Technische Universität Dresden, Germany
Lutz Brusch (TU Dresden)
Martin Golebiewski (HITS Heidelberg)
SEEK ID: https://fairdomhub.org/events/194
Projects: COMBINE Multicellular Modelling
1st Sep 2019 at 12:00
4th Sep 2019 at 20:00
Technische Universität Dresden
Nöthnitzer Str. 46