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.

General information
When an entry in the SBML column states "Yes, but only for reactions.", it means that the tool only supports the reaction component of SBML. For example, rules, events, etc. are not supported.

Specialist Tools
The following table lists specialist tools that cannot be grouped with the modeling tools.

Particle-based simulators
Particle based simulators treat each molecule of interest as an individual particle in continuous space, simulating molecular diffusion, molecule-membrane interactions and chemical reactions.

Comparison of particle-based simulators
The following list compares the features for several particle-based simulators. This table is edited from a version that was originally published in the Encyclopedia of Computational Neuroscience. System boundaries codes: R = reflecting, A = absorbing, T = transmitting, P = periodic, and I = interacting. * Algorithm is exact but software produced incorrect results at the time of original table compilation. † These benchmark run times are not comparable with others due to differing levels of detail.

Model calibration software
Model calibration is a key activity when developing systems biology models. This table highlights some of the current model calibration tools available to systems biology modelers. The first table list tools that are SBML compatible.

PEtab is a community standard for specifying model calibration runs.

Legacy open-source software applications
The following list some very early software for modeling biochemical systems that were developed pre-1980s There are listed for historical interest.

The following list shows some of the software modeling applications that were developed in the 1980s and 1990s. There are listed for historical interest.