Cadbiom
Sources
Sources are released under MIT/GPLv3 licenses and are available on the INRIA Gitlab. You will find in the documentation a more detailed procedure than below to install Cadbiom in a proper virtual environment, or from the sources if you want to participate in its development. You will also find a troubleshooting section.
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
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 a Python interpreter:
pip install cadbiom-cmd cadbiom-gui
At this point 2 commands are available in your shell:
- cadbiom: Launch the GUI program.
- cadbiom_cmd: Launch the command line program.
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
At this point 1 command is available in your shell:
- biopax2cadbiom: Launch the command line program.
What to do next?
You can discover our workflow and follow the tutorials and examples available on the documentation.
Some small prebuilt models are available in the next chapter, but recent models built from large databases are presented here in the documentation.
Models available
We provide simple theoretical and biological pathways as examples.
Highly studied biological pathways (translated from NCI-PID database) are directly available in Cadbiom formalism:
- TGF beta pathway
- BMP pathway
- Circadian pathway
- Erbb1 receptor proximal pathway
- FOXO pathway
- Insulin pathway
- mTor pathway
- NFKappa b canonical pathway
- Notch pathway
- p53 downstream pathway
Whole NCI-PID database has been translated into Cadbiom formalism and is archived here since 2016:
- PID database in original format (xml)
- PID database in Cadbiom formalism from xml (v1 format, without annotations) (archived version from 2012)
Recently built models from large databases are presented here in the documentation.