New Biocham 3.0 major release with new graphical interface will be available soon.
New Biocham 2.9 is a temporary release available for Mac Os only. The new manual is available in pdf and html.
New Biocham 2.8 has been released in January 2009. This version includes a powerful method for searching parameter values from temporal logic specifications. Previous version was Biocham 2.7 from April 2008, more details in the file NEWS.

BIOCHAM was used (in synergy with Beta WB and GINsim) to win the Biological Modelling Competition of the Formal Methods in Molecular Biology Dagstuhl workshop in Feb. 2009.

Overview

BIOCHAM is a programming environment for modeling biochemical systems, making simulations and querying the model in temporal logic.

In its current version BIOCHAM is composed of :

• a rule-based language for modeling biochemical systems,
• a simple simulator (either boolean or numerical),
• a powerful query language based on temporal logic, CTL or LTL with arithmetic constraints over reals, for querying the temporal properties of the model,
  
• an interface to the NuSMV model checker for evaluating CTL queries,
• a machine learning system for correcting/completing a model, either by changing rules w.r.t. a CTL specification or by estimating parameters w.r.t. an LTL specification.

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 biological knowledge representation, research or teaching are particularly welcomed.

Documentation

• New v2.9 manual in html and pdf; old v2.8 manual in html;
  
• Tutorial PDF version for printing or downloading, or HTML version split in chapters for online viewing;
• Examples.

You can also try running some BIOCHAM commands through the online version. All commands acting on files (export_dot, add_biocham, load_sbml, etc.) are deactivated. Only one picture will be displayed (the last one produced with plot, dot, etc.).

Download

New version Biocham 2.9 binaries for Mac OS only.

Current version Biocham-2.8.tar.gz or Biocham-2.8.tar.bz2.

If you install from source, to be able to use all the features of Biocham, you need to install also:

• this patched version of the model checker NuSMV,
• and GNU Plot or Java (at least 1.5).

The file INSTALL explains the installation procedure for Windows, Linux and Mac OS X (at least 10.4).

The commands ./configure && make recompile BIOCHAM if necessary. If a recompilation is needed on your machine, you need to install also:

• a C compiler (preferably gcc),
• GNU Prolog (this patched snapshot of forthcoming version 1.3.1 is necessary)
• the GNU MP bignum library (version 4.1.3 or higher)
• the Parma Polyhedra Library (version 0.10 or more recent)

• Perl, to generate editor modes for vim and emacs,
• help2man to generate the man page.
• a Java compiler if you need to recompile the GUI.

make install can then be used to complete the installation of the program.

References:

See the corresponding section of the user's manual

Feedback and bug reports:

Mail to  biocham@inria.fr