List of systems biology modeling software

Systems biology relies heavily on building mathematical models to help understand and make predictions of biological processes. Specialized software to assist in building models has been developed since the arrival of the first digital computers. The following list gives the currently supported software applications available to researchers.

The vast majority of modern systems biology modeling software support SBML, which is the de facto standard for exchanging models of biological cellular processes. Some tools also support CellML, a standard used for representing physiological processes. The advantage of using standard formats is that even though a particular software application may eventually become unsupported and even unusable, the models developed by that application can be easily transferred to more modern equivalents. This allows scientific research to be reproducible long after the original publication of the work.

To obtain more information about a particular tool, click on the name of the tool. This will direct you either to a peer-reviewed publication or, in some rare cases, to a dedicated Wikipedia page.