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ENTCS
2010

A Framework for Modelling and Simulating Networks of Cells

10 years 1 months ago
A Framework for Modelling and Simulating Networks of Cells
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
Added 02 Mar 2011
Updated 02 Mar 2011
Type Journal
Year 2010
Where ENTCS
Authors Sara Montagna, Mirko Viroli
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