Section: New Software and Platforms
Computer Aided Design of Biological Models
Keywords: Health - Biology - Biotechnology - Bioinformatics - Systems Biology
Functional Description: The Cadbiom software provides a formal framework to help the modeling of biological systems such as cell signaling network with Guarder Transition Semantics. It allows synchronization events to be investigated in biological networks among large-scale network in order to extract signature of controllers of a phenotype. Three modules are composing Cadbiom. 1) The Cadbiom graphical interface is useful to build and study moderate size models. It provides exploration, simulation and checking. For large-scale models, Cadbiom also allows to focus on specific nodes of interest. 2) The Cadbiom API allows a model to be loaded, performing static analysis and checking temporal properties on a finite horizon in the future or in the past. 3) Exploring large-scale knowledge repositories, since the translations of the large-scale PID repository (about 10,000 curated interactions) have been translated into the Cadbiom formalism.
News Of The Year: - Comprehensive command line to run the calculations and analyze the generated results. - Module designed to produce models through the interpretation of various databases or ontologies, formalized according to the BioPAX standard. - Update of the site and the documentation.
Participants: Geoffroy Andrieux, Michel Le Borgne, Nathalie Theret, Nolwenn Le Meur, Pierre Vignet and Anne Siegel