JigCell 7.1.0

JigCell is an effort to develop and maintain an open source modeling environment for computational biology. The goal of this project is to support building and testing models for studying complex biochemical regulatory systems in general, and the cell cycle control system in particular.


The JigCell applications are written in Java. You will need to install the Java Runtime Environment 1.4.2 or later if you do not already have it. After installing Java, make sure that it is available on your path.

For Linux/MacOSX run the JigCell installer (java -jar jigcell-7.1.0.jar) which will guide you through the installation process. Users on Linux need to go the xpp directory located where you installed JigCell and rename the XPP binary for your platform to xppaut. Users on other platforms need to download the XPP source code and built it to use XPP. Alternatively XPP binaries are available for MacOSX here.


Run the JigCell application from the installation directory.


JigCell Model Builder- Using, Manual, Analyzer
JigCell Comparator- Project page, Using, Changes, Analyzer, API
JigCell SBML Parser- Overview, API
JigCell Run File Library- API
JigCell Simulator API- API
JigCell XPP Wrapper- API


Tests for the Model Builder, Run Manager and Comparator.

Source Code

Source code is released under the DARPA BioCOMP Open Source License.

Released on October 11, 2009