Overview of CADBIOM 0.3¶
CADBIOM (Computer Aided Design of Biological Models) is an open source modelling software. Based on Guarded transition semantic, it gives a formal framework to help the modelling of biological systems such as cell signalling networks.
- ability to study the behaviour of guarded transitions systems by generating scenarios (trajectory is a sequence of states of biomolecule);
- tools for the study of the structure and dynamics of biological networks;
- a command line and a graphical user interfaces to build and explore models, query the dynamics of these models, and work with the trajectories produced.
Cadbiom is freely available on cadbiom.genouest.org, distributed under the terms of the GNU General Public License. The website also provides a broad range of informations, model library and documentation.
The main repository is available on the INRIA Gitlab
Cadbiom packages are available on PyPI (Python Package Index), the official third-party software repository for Python language.
Cadbiom was born was born at the end of 2009. It has been extensively reviewed, rewritten and accompanied by technical documentation since 2016.
- System requirements
- Setting up a virtual environment
- Using Docker
- Install the development version
- Very outdated release (archived)
- Install a desktop shortcut
- Command line usage
- Named Arguments
- The modules
- Cadbiom GUI
- Workflow overview
- Characteristics of biopax ressources
- Query the Cadbiom model
- Search for molecules
- Processing of the generated files
- Avanced users - Creation of models
- Work with models
- Work with solutions
- Cadbiom File Format Specification
- Documentation for developers
- Developer overview
- Working with Cadbiom source code
- Technical documentation
- Command line package
- GUI package
- Graphical User Interface
- Graph Editor Design
- Library package
- Global settings
- Dynamical analysis