Tools for System Biology

The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biological processes. It’s applicable to simulations of metabolism, cell-signaling, and many other topics.


CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML).

SBML squeezer: a CellDesigner plugin to generate kinetic rate equations for biochemical networks.

SBML2LaTeX: SBML2LaTeX is a tool to convert files in the System Biology Markup Language (SBML) format into LaTeX files.


Complex Pathway Simulator (COPASI) is a software application for simulation and analysis of biochemical networks.


Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.

BiNoM: Biological Network Manager, BiNoM is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out studies on the network structure. 

SBMLtoolbox for MATLAB

SBMLToolbox is built on top of libSBML and provides a set of basic functions allowing SBML models to be used in MATLAB.

Systems Biology Toolbox 2 for MATLAB