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Section: Software

Data integration: actors involved in the response of a living system

The goal is to offer a toolbox for the reconstruction of networks from genome, literature and large-scale observation data (expression data, metabolomics...) in order to elucidate the main regulators of an observed phenotype.

  • Mobyle@GenOuest network portal We are developing a web service (http://mobyle.genouest.org/cgi-bin/Mobyle/portal.py ) to use several tools to confront knowledge and data towards the correction of large-scale networks, based either on decision diagrams or on answer set programming. BioQuali (http://www.irisa.fr/symbiose/bioquali/ ) (http://www.irisa.fr/symbiose/projects/bioqualiCytoscapePlugin/ ) allows one to confront model and data, localize errors and, when model and data are consistent, to predict the variation of non observed nodes [6] . BioASP (http://www.cs.uni-potsdam.de/bioasp/ ) was developed in Potsdam and allows one to perform prediction even if model and observations are contradictory, by considering all possible repairs of data and models and computing the common predictions of all repaired models [5] . The portal also include tools for the completion of metabolic networks [32] .

  • Combined set of key actors in reaction-based networks: Cadbiom (http://cadbiom.genouest.org/ ). This tool is based on state-chart like graphical language. It allows investigating synchronization events in biological networks. It is applied to cancer signaling networks [10] .