Systems biology Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological syst ...

relies heavily on building

mathematical models A mathematical model is a description of a system using mathematical concepts and language. The process of developing a mathematical model is termed mathematical modeling. Mathematical models are used in the natural sciences (such as physics, b ...

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 The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of use ...

, which is the de facto standard for exchanging models of biological cellular processes. Some tools also support

CellML CellML is an XML based markup language for describing mathematical models. Although it could theoretically describe any mathematical model, it was originally created with the Physiome Project in mind, and hence used primarily to describe models re ...

, 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 Reproducibility, also known as replicability and repeatability, is a major principle underpinning the scientific method. For the findings of a study to be reproducible means that results obtained by an experiment or an observational study or in a ...

long after the original publication of the work.

Actively supported open-source software applications

Legacy open-source software applications

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

References

{{Reflist Systems biology *

Bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

Science software

Systems A system is a group of interacting or interrelated elements that act according to a set of rules to form a unified whole. A system, surrounded and influenced by its environment, is described by its boundaries, structure and purpose and express ...