Calzone Laurence, Fages François, Soliman Sylvain
Projet Contraintes, INRIA Rocquencourt, BP105, 78153 Le Chesnay Cedex, France.
Bioinformatics. 2006 Jul 15;22(14):1805-7. doi: 10.1093/bioinformatics/btl172. Epub 2006 May 3.
BIOCHAM (the BIOCHemical Abstract Machine) is a software environment for modeling biochemical systems. It is based on two aspects: (1) the analysis and simulation of boolean, kinetic and stochastic models and (2) the formalization of biological properties in temporal logic. BIOCHAM provides tools and languages for describing protein networks with a simple and straightforward syntax, and for integrating biological properties into the model. It then becomes possible to analyze, query, verify and maintain the model with respect to those properties. For kinetic models, BIOCHAM can search for appropriate parameter values in order to reproduce a specific behavior observed in experiments and formalized in temporal logic. Coupled with other methods such as bifurcation diagrams, this search assists the modeler/biologist in the modeling process.
BIOCHAM (v. 2.5) is a free software available for download, with example models, at http://contraintes.inria.fr/BIOCHAM/.
BIOCHAM（生化抽象机）是一个用于对生化系统进行建模的软件环境。它基于两个方面：（1）布尔、动力学和随机模型的分析与模拟，以及（2）生物属性在时态逻辑中的形式化。BIOCHAM提供了工具和语言，用于以简单直接的语法描述蛋白质网络，并将生物属性集成到模型中。这样就可以针对这些属性对模型进行分析、查询、验证和维护。对于动力学模型，BIOCHAM可以搜索合适的参数值，以便重现实验中观察到并在时态逻辑中形式化的特定行为。与诸如分岔图等其他方法相结合，这种搜索有助于建模人员/生物学家进行建模过程。
BIOCHAM（版本2.5）是一款免费软件，可在http://contraintes.inria.fr/BIOCHAM/下载，并带有示例模型。
