The Biochemical Abstract Machine BIOCHAM 3

Warning: Biocham 3 is deprecated and no longer maintained. The new version of Biocham 4.0 was released in Sep 2017. It is available here and online.

The last version of Biocham 3, version 3.7 is available online. Warning: if you encounter a problem mentioning access with https, delete your HSTS setting for the site lifeware.inria.fr in your browser (for Chrome connect to chrome://net-internals/#HSTS and delete the url lifeware.inria.fr, for Safari delete the file ~/Local/Cookies/HSTS.plist)

Biocham 3.7 was released in July 2015. See what's new

Biocham 3.7 is also available as a REST web service.

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 :

• a rule-based language for modeling biochemical systems (compatible with SBML)
• several simulators (boolean, differential, stochastic),
• a temporal logic based language to formalize the temporal properties of a biological system and validate models with respect to such specifications,
  
• unique features for developing/correcting/completing/coupling models, including the inference of kinetic parameters in high dimension from temporal logic constraints.
  

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

• Reference manual in html and pdf (including a bibliography and changes with previous versions)
  
• Examples
• Tutorial (corresponding to older version 2.4) in html and pdf.
  
• Video tutorials: Working with an existing model , or Creating a new model

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:

• Windows XP binary version
• Windows 7 binary version
• Mac OS X (x86_64) binary version (tested on SnowLeopard)
• Linux (x86_64) binary version (theoretically standalone, built on Ubuntu 12.04)
  
  Some third-party librairies are required for the Linux binary distribution to run. Here are the commands to install them on Ubuntu 12.04:
  • Open MPI: dpkg -s libopenmpi1.3 >/dev/null 2>&1 || sudo apt-get install libopenmpi1.3
  • GNU MP Bignum Library: dpkg -s libgmp3c2 >/dev/null 2>&1 || sudo apt-get install libgmp3c2
  • Parma Polyhedra Library: dpkg -s libppl-c4 >/dev/null 2>&1 || sudo apt-get install libppl-c4
  Then, extract archive contents to {dest} location:
  tar xC {dest} -f Biocham_x86_64.tar.gz
  Run biocham:
  {dest}/biocham

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:

• Java (at least 1.5)
• the NuSMV model checker,
• GNU Plot
  
• Graphviz
  

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

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

• a C compiler (preferably gcc) and a Java compiler,
  
• GNU Prolog (version 1.3.2 or later)
• 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.

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