One Modelling Formalism & Simulator Is Not Enough! A Perspective for Computational Biology Based on James II

  • Authors:

  • Adelinde M. Uhrmacher;Jan Himmelspach;Matthias Jeschke;Mathias John;Stefan Leye;Carsten Maus;Mathias Röhl;Roland Ewald

  • Affiliations:

  • University of Rostock, Rostock, Germany D-18059;University of Rostock, Rostock, Germany D-18059;University of Rostock, Rostock, Germany D-18059;University of Rostock, Rostock, Germany D-18059;University of Rostock, Rostock, Germany D-18059;University of Rostock, Rostock, Germany D-18059;University of Rostock, Rostock, Germany D-18059;University of Rostock, Rostock, Germany D-18059

  • Venue:
  • FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
  • Year:
  • 2008

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Abstract

Diverse modelling formalisms are applied in Computational Biology. Some describe the biological system in a continuous manner, others focus on discrete-event systems, or on a combination of continuous and discrete descriptions. Similarly, there are many simulators that support different formalisms and execution types (e.g. sequential, parallel-distributed) of one and the same model. The latter is often done to increase efficiency, sometimes at the cost of accuracy and level of detail. James IIhas been developed to support different modelling formalisms and different simulators and their combinations. It is based on a plug-in concept which enables developers to integrate spatial and non-spatial modelling formalisms (e.g. stochastic茂戮驴calculus, Beta binders, Devs, space-茂戮驴), simulation algorithms (e.g. variants of Gillespie's algorithms (including Tau Leaping and Next Subvolume Method),space-茂戮驴simulator, parallel Beta binderssimulator) and supporting technologies (e.g. partitioning algorithms, data collection mechanisms, data structures, random number generators) into an existing framework. This eases method development and result evaluation in applied modelling and simulation as well as in modelling and simulation research.