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Gordon Plotkin

Multi-Level Modelling via Stochastic Multi-Level Multiset Rewriting

Abstract. We present a simple stochastic rule-based approach to multilevel modelling for computational systems biology. Populations are modelled using multilevel multisets; these contain both species and agents, with the latter possibly containing further such multisets. Rules are pairs of such multisets, but now allowing variables to occur (as well as species and agents), together with an associated stochastic rate.

We give two illustrative examples. The first is an extracellular model of virus infection, coupled with an intracellular model of viral reproduction; this model can demonstrate successive waves of infection. The second is a model of cell division in which a repressor protein is diluted in successive generations, when repression no longer occurs.

This is joint work with Nicolas Oury.

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