Simulation and database software for computational systems biology : PySCes and JWS Online

[摘要] ENGLISH ABSTRACT: Since their inception, biology and biochemistry have been spectacularly successful incharacterising the living cell and its components. As the volume of information aboutcellular components continues to increase, we need to ask how we should use this informationto understand the functioning of the living cell?Computational systems biology uses an integrative approach that combines theoreticalexploration, computer modelling and experimental research to answer this question.Central to this approach is the development of computational models, new modellingstrategies and computational tools. Against this background, this study aims to: (i) developa new modelling package: PySCeS, (ii) use PySCeS to study discontinuous behaviourin a metabolic pathway in a way that was very difficult, if not impossible, withexisting software, (iii) develop an interactive, web-based repository (JWS Online) of cellularsystem models.Three principles that, in our opinion, should form the basis of any new modellingsoftware were laid down: accessibility (there should be as few barriers as possible toPySCeS use and distribution), flexibility (pySCeS should be extendable by the user, notonly the developers) and usability (PySCeS should provide the tools we needed for ourresearch). After evaluating various alternatives we decided to base PySCeS on the freelyavailable programming language, Python, which, in combination with the large collectionof science and engineering algorithms in the SciPy libraries, would give us a powerfulmodern, interactive development environment.

[发布机构] Stellenbosch University