From species to pathway and tissue as process

Muffy Calder, Oana Andrei, Andrea Degasperi, Robin Donaldson
2010 Proceedings of the 8th International Conference on Computational Methods in Systems Biology - CMSB '10  
Process algebras were originally designed for modelling concurrent computations. Over the last decade, computer scientists have explored their application to modelling biomolecular processes, with considerable success. A predominant abstraction is molecule-as-process [RSS01, Car08], where each process represents a molecule. Analysis is by simulation and in a stochastic setting, there is a clear correspondence with stochastic simulation as proposed by Gillespie [Gil77]. An alternative
more » ... ernative abstraction is species-as-process [CGH06, CH09b], based on models that are continuous time Markov chains (CTMC) with levels of concentration. This populationbased abstraction allows control of the granularity of representation, at one end of the spectrum corresponding to Gillespie simulation and at the other end, ordinary differential equations. A key feature of this style is it permits a range of analysis techniques in addition to simulation, namely relations (e.g. bisimulation) and model-checking properties expressed in qualitative and quantitative logics. Within the species-as-process paradigm, a useful style has been reagent-centric models[CH09a], where all reagents in a reaction map to processes, whose variation reflect decrease through consumption and increase through product formation (consumers and producers). The reagent-centric style of modelling provides a distributed view of a system and is easily represented in a state-based formalism where state variables represent levels of concentration. An example is the language of reactive modules used in the PRISM modelchecker [KNP02] . Whilst this language is not strictly a process algebra: processes are represented by modules, there is process algebraic synchronisation between modules. Moreover, modules can be generic. This talk gives an overview of recent advances and applications of the reagent-centric modelling paradigm, extending
doi:10.1145/1839764.1839765 dblp:conf/cmsb/CalderADD10 fatcat:ajuwibewbncwhgrp7zgrhw7nvm