Getting poster data...
M.P. van Iersel, E.J. Gonçalves, C. Chaouiya, J. Saez-Rodriguez (EMBL-EBI, Wellcome Trust Genome Campus, Cambridge, UK)To get a better understanding of signaling pathways in the cell, and to understand how they go awry in diseases like cancer, we simulate them with logical models. Logic modeling is a particular type of formalism that is well-suited for signaling, and it can be applied even when the biomolecules are not completely understood. Using the CellNetOptimizer (CNO) tool, co-developed at the European Bioinformatics Institute, we can find out which parts of a signaling pathway is active under a given condition. Biological pathways tend to consist of a variety of processes, such as modification of biomolecules, transport of biomolecules around the cell, or binding between two proteins. This heterogeneity makes is hard to visualize pathway knowledge in an unambiguous and understandable manner. The Systems Biology Graphical Notation (SBGN) has been devised to tackle this problem. We are using the SBGN notation to visualize the output of the CNO program. The resulting software will take the form of a set of Cytoscape plug-ins, as part of a community effort called the Common Logical Modeling Toolbox (CoLoMoTo).