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Section: New Software and Platforms
CADBIOM
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.
We recently developed a framework that integrates an updated version of the CADBIOM core software and visualization tools. We provided a command line interface allowing users to translate the interactions between biomolecules described in data sources in BioPAX format into the formalism based on the guarded transitions used by CADBIOM. The command line also makes it easy to search for scenarios based on the constraints of a model, to compare scenarios with each other and to visualize interaction graphs facilitating the biologist’s expertise (Vignet et al 2019 JOBIM)