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Simon Bartels (2011)

The integration of software to compute BioPEPA models in JAMES II

Bachelorthesis, Universität Rostock.

There exist many simulation systems that have been developed from scratch to support only a single modelling formalism [HU07]. Developing a new simulation system requires implementation e orts for already existing functionality, e.g. visualization, random number generation, ... The re-implementation of these functionalities demands time that can not be spent for innovation. To alleviate these circumstances general purpose modelling and simulation frameworks like JAMES II [HU07] or the systems biology workbench [SHF+03] have been developed. They allow to easily integrate and exchange their components which bene fits software reuse. This Bachelor's dissertation shows exemplary how to integrate software for the computation of Bio-PEPA models [DGG+] in JAMES II.

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