Cadbiom

Sources

Sources are available on the INRIA Gitlab. Here, you will find a more detailed procedure than below to install Cadbiom in a clean virtual environment, or from the sources and participate in its development.

System requirements

CADBIOM is mainly developed in Python 2.7. Before running Cadbiom, the following system packages have to be installed from the distribution packages library (or similar, depending on your operating system).
Most of these packages are already installed on basic GNU/Linux systems.

Debian-like systems (Ubuntu)

  • python2.7-dev
  • libxml2-dev
  • libxslt1-dev (Library providing the Gnome XSLT engine)
  • pkg-config (Fix errors when installing pygraphviz and when config is not loaded)
  • libgraphviz-dev (GUI layouts)
  • python-gtk2 (GUI)
  • python-glade2 (GUI)
  • python-gtksourceview2 (GUI)
  • python-tk (GUI)

You can install these dependencies with the following command :

sudo apt-get install python-gtksourceview2 python2.7-dev libxml2-dev libxslt1-dev \
libxslt1-dev libgraphviz-dev pkg-config python-glade2 python-gtk2 python-tk

To be solved: to use command line: pip install matplotlib==1.5

On some old systems you may have to install also `python-pip`.
When installing pygraphviz on some systems, you may have this error:

_graphviz.so: undefined symbol: Agundirected

...which is solved by:

pip install --upgrade pygraphviz --install-option="--include-path=/usr/include/graphviz" \
--install-option="--library-path=/usr/lib/graphviz/"

Red Hat-like systems (Fedora/CentOS)

  • python-devel
  • libxml-devel
  • redhat-rpm-config (lxml config)
  • libxslt-devel (Library providing the Gnome XSLT engine)
  • graphviz-devel (GUI layouts)
  • pygtk2 (GUI)
  • pygtk2-libglade (GUI)
  • pygtksourceview (GUI)

You can install these dependencies with the following command :

sudo dnf install python-devel libxml-devel redhat-rpm-config libxslt-devel graphviz-devel \
pygtk2 pygtk2-libglade pygtksourceview

Installation

Cadbiom package is available on PyPI (Python Package Index), the official third-party software repository for Python language.

You can install these packages with the following command on all systems that run Python interpreter :

pip install cadbiom-cmd cadbiom-gui

Very outdated release (archived)

To download Cadbiom on your Linux distribution, click on the following link : Download.
Please note that this version is still available on the INRIA Gitlab (branch 1.1.x).

You will have to install the following packages :

  • python-pygraphviz
  • python-lxml
  • python-networkx
  • python-gtksourceview2

If you encounter some problems with the precompiled solver (32bits or 64bits), we provide the sources of the 2.9 (recommended) and 2.7 versions.
The solver CryptoMiniSat is an LGPL-licenced SAT solver, more information on cryptominisat2.

BioPAX2Cadbiom add-on

biopax2cadbiom is a standalone module integrated in the Cadbiom GUI that converts BioPAX ontologies to Cabiom models.

Full help, command line options, tests and explained translations are available on the INRIA Gitlab.

You can install this package with the following command on all systems that run Python interpreter :

pip install biopax2cadbiom

Models available

We provide a simple theoretical examples to well understand Cadbiom features.

Hightly studied biological pathways (translated from NCI-PID database) are directly available in Cadbiom formalism:

Whole NCI-PID database has been translated into Cadbiom formalism :