Section: Application Domains

Modeling software for systems biology and synthetic biology

Since 2002, we develop an open-source software environment for modeling and analyzing biochemical reaction systems. This software, called the Biochemical Abstract Machine (BIOCHAM ), is compatible with SBML for importing and exporting models from repositories such as BioModels. It can perform a variety of static analyses, specify behaviors in Boolean or quantitative temporal logics, search parameter values satisfying temporal constraints, and make various simulations. While the primary reason of this development effort is to be able to implement our ideas and experiment them quickly on a large scale, BIOCHAM is used by other groups either for building models, for comparing techniques, or for teaching (see statistics in software section). BIOCHAM-web is a web application which makes it possible to use BIOCHAM without any installation. We plan to continue developing BIOCHAM for these different purposes and improve the software quality.