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Adelinde M Uhrmacher, Jan Himmelspach, Matthias Jeschke, Mathias John, Stefan Leye, Carsten Maus, Mathias Röhl, and Roland Ewald (2008)

One Modeling Formalism & Simulator is not enough! - A Perspective for Computational Biology Based on JAMES II

In: Proceedings of the 1st FMSB Workshop, ed. by Jasmin Fisher, vol. 5054/2008, pp. 123-138, Cambridge, UK, Springer. Lecture Notes of Computer Science, LNBI subseries.

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 II has 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 Pi, Beta Binders, DEVS, Space Pi), simulation algorithms (e.g. variants of Gillespie's algorithms (including Tau Leaping and NSM), Space Pi simulator, parallel Beta Binders simulator) 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.

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