Titlebook: Computational Methods in Systems Biology; International Confer Muffy Calder,Stephen Gilmore Conference proceedings 2007 Springer-Verlag Ber

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Expressive Models for Synaptic Plasticity,exploits process calculi as formal grounds, enjoys nice compositional properties, has a direct computational implementation that supports simulation trials, and, to our knowledge, represents the first process calculi based model of a presynaptic terminal. Simulation results have shown coherence with

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Digitalis

Reconstructing Metabolic Pathways by Bidirectional Chemical Search, in a specific organism. Current knowledge of biochemical pathways as stored in public databases such as KEGG, is based on carefully curated genomic evidence for the presence of specific metabolites and enzymes that activate particular biochemical reactions. In this paper, we present an efficient me

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Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus,ficiency. The algorithm is proved correct with respect to the calculus, and then used as a basis for implementing the latest version of the SPiM stochastic simulator. The algorithm is also suitable for generating graphical animations of simulations, in order to visualise system dynamics.

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https://doi.org/10.1007/978-1-4302-1605-6character and strength of interactions as well as time delays are context sensitive in the sense that they depend on the current state of the system. We propose an enhancement of the approach described above, integrating both structural and temporal context sensitivity.

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