A Framework for Modelling and Simulating Networks of Cells

13 years 1 months ago

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Several complex biological phenomena are to be modelled in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events plays an essential role. Key examples are embryogenesis and morphogenesis processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. This paper introduces a practical framework for modelling and simulating these scenarios. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie's direct method. As an example of application of our framework, we model the first stages of Drosophila Melanogaste...

Sara Montagna, Mirko Viroli

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