Stochastic Semantics of Signaling as a Composition of Agent-view Automata

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2011
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Koeppl, Heinz
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Electronic Notes in Theoretical Computer Science. 2011, 272, pp. 3-17. ISSN 1571-0661. Available under: doi: 10.1016/j.entcs.2011.04.002
Zusammenfassung

In this paper we present a formalism based on stochastic automata to describe the stochastic dynamics of signal transduction networks that are specified by rule-sets. Our formalism gives a modular description of the underlying stochastic process, in the sense that it is a composition of smaller units, agent-views. The view of an agent is an automaton that identifies all local modification changes of that agent (internal state modifications, binding and unbinding), but also those of interacting agents, which are tested within the same rule. We show how to represent the generator matrix of the underlying Markov process of the whole rule-set as Kronecker sums of the rate matrices belonging to individual view-automata. In the absence of birth the automata are finite, since the number of different contexts in which one agent can appear in a rule-set is finite. We illustrate the framework by an example that is related to cellular signaling events.

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004 Informatik
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Cell signaling; Continuous-time Markov chain; Stochastic automata composition
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ISO 690KOEPPL, Heinz, Tatjana PETROV, 2011. Stochastic Semantics of Signaling as a Composition of Agent-view Automata. In: Electronic Notes in Theoretical Computer Science. 2011, 272, pp. 3-17. ISSN 1571-0661. Available under: doi: 10.1016/j.entcs.2011.04.002
BibTex
@article{Koeppl2011-05Stoch-42136,
  year={2011},
  doi={10.1016/j.entcs.2011.04.002},
  title={Stochastic Semantics of Signaling as a Composition of Agent-view Automata},
  volume={272},
  issn={1571-0661},
  journal={Electronic Notes in Theoretical Computer Science},
  pages={3--17},
  author={Koeppl, Heinz and Petrov, Tatjana}
}
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