The Biochemical Abstract Machine BIOCHAM

version 4.1.5 March 2018

EP Lifeware, Inria Saclay - Ile de France
http://lifeware.inria.fr/biocham4/

developpers mailing list: biocham@inria.fr

Biocham logo

Biocham 4 was released in September 2017. Biocham 4 is a complete rewriting of Biocham 3 for easier maintenance. It integrates new features, in particular concerning influence systems, the synthesis of reaction systems, and robustness optimisation. It also lacks some features of Biocham 3 concerning model comparisons (by subgraph epimorphisms), sensitivity analyses and the graphical user interface. For these reasons Biocham 3 is still active on http://lifeware.inria.fr/biocham3 but no longer maintained.

Overview

The Biochemical Abstract Machine (Biocham) is a modelling environment for systems biology and synthetic biology.

Biocham is mainly composed of :

Biocham implements some unique features for:

Biocham is a free software protected by the GNU General Public License GPL version 2. This is an Open Source license that allows free usage of this software.

Feedback on the use of Biocham in applications, research or teaching are particularly welcomed.

Biocham notebook online

Try the tutorial notebook (presented at aSSB 2018) or the historical tutorial notebook (presented at CMSB 2017)

Try the other examples, or upload your own ones, on our online notebook.

Documentation

Reference manual in html

Download and Installation

Source version:  biocham.zip.

The installation then basically proceeds by using the Unix shell script
./install.sh

Previous versions:  biocham4.0.zip, biocham3.

Feedback and bug reports:

Mail to biocham@inria.fr