The Biochemical Abstract Machine BIOCHAM v4

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

developpers mailing list: biocham@inria.fr

Warning In the current period of alpha-test of Biocham 4.0.0, some Biocham commands may change and may be updated without notice, but they should be consistent with the online documentation, the online web server and the source distribution below.

New Biocham 4.0.0 has been released in January 2017. Biocham 4 is a complete rewriting of Biocham 3 for easier maintenance. It also integrates new features, in particular concerning influence systems and the synthesis of reaction systems, but also lacks some features of Biocham 3 concerning sensitivity analysis, robustness measures 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 For these reasons Biocham 3 is still active on http://lifeware.inria.fr/biocham3 but no longer maintained.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, with some unique features for static and dynamic analyses using temporal logic constraints.

Biocham is mainly composed of :

• a rule-based language for modeling biochemical systems with reactions (compatible with SBML) and/or influences (compatible with QualSBML)
• a hierarchy of semantics (differential, stochastic, Petri Net, Boolean) to interpret (and simulate) such models,
• a temporal logic based language to formalize the temporal behaviors of biochemical systems, and validate models with respect to such specifications,
  
• unique features for developing/analyzing/correcting/completing/calibrating/coupling/synthesizing reaction and influence systems with respect to formal specifications of their behaviour.
  

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 online

Try the last version of Biocham with its notebook online.

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

Feedback and bug reports:

Mail to biocham@inria.fr