Dec 20, 2011: Stefano Schivo: ANIMO: Analysis of Networks by Interactive MOdeling

December 20, 2011ANIMO: Analysis of Networks by Interactive MOdeling
Room: Zi 5126Stefano Schivo
12:30-13:30

When analyzing the complex interactions occurring in a cell, a biologist needs to make use of computational methods in order to understand most of the non-trivial effects of external signals. ANIMO (Analysis of Networks by Interactive Modeling) is a tool that allows the user to create and explore executable models of biological networks, helping to derive hypotheses and plan wet-lab experiments. The tool is based on Timed Automata, which allow to have a formal definition of the interaction networks and obtain an answer to some useful queries thanks to the model checker UPPAAL. Moreover, to allow the biologist to work in a familiar and visually appealing environment, the user interface is implemented as a plugin to the biological network modeling tool Cytoscape. The flexibility of ANIMO allows its user to model different kinds of networks, from signaling pathways to metabolic pathways to gene networks, defining granularity and precision settings for each modelled reactant and reaction.
In my presentation I will explain the foundations of the ANIMO tool, display its main features and show some example applications to the modeling of biological networks.