Kiran Mariam, Coakley Simon, Walkinshaw Neil, McMinn Phil, Holcombe Mike
University of Sheffield, Department of Computer Science, Regent Court, 211 Portobello Street, Sheffield S1 4DP, United Kingdom.
Biosystems. 2008 Jul-Aug;93(1-2):141-50. doi: 10.1016/j.biosystems.2008.03.010. Epub 2008 Apr 11.
Simulation software is often a fundamental component in systems biology projects and provides a key aspect of the integration of experimental and analytical techniques in the search for greater understanding and prediction of biology at the systems level. It is important that the modelling and analysis software is reliable and that techniques exist for automating the analysis of the vast amounts of data which such simulation environments generate. A rigorous approach to the development of complex modelling software is needed. Such a framework is presented here together with techniques for the automated analysis of such models and a process for the automatic discovery of biological phenomena from large simulation data sets. Illustrations are taken from a major systems biology research project involving the in vitro investigation, modelling and simulation of epithelial tissue.
模拟软件通常是系统生物学项目中的一个基本组成部分，并且在寻求从系统层面更好地理解和预测生物学的过程中，为实验技术与分析技术的整合提供了一个关键要素。建模与分析软件的可靠性以及用于自动分析此类模拟环境所生成的大量数据的技术至关重要。需要一种严谨的方法来开发复杂的建模软件。本文介绍了这样一个框架，以及对此类模型进行自动分析的技术，还有从大型模拟数据集中自动发现生物学现象的过程。示例取自一个涉及上皮组织体外研究、建模与模拟的大型系统生物学研究项目。
