The Biochemical Abstract Machine BIOCHAM

EPI Lifeware, INRIA Paris-Rocquencourt, France
http://lifeware.inria.fr/Biocham/

developpers mailing list: biocham@inria.fr

New Biocham 3.7 has been released in July 2014. See what's new

New The latest version of Biocham is available online. Try it now!

New Biocham is also available as a REST web service.

Let's assume a test.bc file with the following contents:
add(tyson91).
list_ODE.
(Note: The quit. command will be automatically appended to the file if it's not present.)

Assuming tyson91 refers to the tyson91.bc file located in the Biocham examples directory, you will be able to call the Biocham web service using the test.bc file with the following command:
curl -X POST -F 'file=@test.bc' -F 'ref=@${BIOCHAM_PATH}/EXAMPLES/cell_cycle_Tyson_6Var/tyson91.bc' http://lifeware.inria.fr/biocham/online/rest/call > out.json

Overview

The Biochemical Abstract Machine (Biocham) is a modelling environment for systems biology, with some unique features for static analysis or for inferring unknown model parameters from temporal logic constraints.

Biocham is mainly composed of :

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.

Documentation

You can also try running some Biocham commands through the online version.

Biocham-web

Try the last version of Biocham online.

Download and Installation

Binary versions:

We recommend that you have already installed first Java version >= 1.5 for using the GUI of BIOCHAM.

Then you just need to execute and follow the instructions of the setup program.

Source version:  Biocham-3.7.tar.bz2.

To install from source (which may be difficult on some platforms), and to be able to use all the features of Biocham, you need to install also:

The installation then basically proceeds by
./configure
make
make install

If a recompilation is needed on your machine, you may need to install also:

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

References:

See the bibliography of the user's manual

Feedback and bug reports:

Mail to  biocham@inria.fr