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Maximal Reduction of Deterministic Semantics of Rule-Based Models : Syntax- Independent Setup

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2010

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Koeppl, Heinz

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NYKTER, Matti, ed. and others. Seventh International Workshop on Computational Systems Biology : WCSB 2010 : June 16–18 : 2010 : Luxembourg. Tampere: Tampere International Center for Signal Processing, 2010, pp. 83-86. TICSP series. ISSN 1456-2774

Zusammenfassung

We develop a syntax-independent rule-based specification in a set-theoretical framework. The reactants of rules are usually defined as partially defined objects, called patterns, to denote that we can apply a reaction by substituting a pattern with any species that contains the context described by the pattern. We choose a very general data structure to represent the patterns: we write a pattern as a set of species which comply the pattern, and we call it a macro-species. We define the deterministic (ODE) semantics on such a rule set, and we define its reduction imposed by aggregation of species. We characterize for which aggregations we can correctly compute the reduced ODE semantics directly from the rule set, ie which aggregations are self-consistent. Finally, we propose an algorithm that, given a set of initial aggregates, computes the least-refined self-consistent aggregation which contains the initial aggregates.

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WCSB 2010 : Seventh International Workshop on Computational Systems Biology, 16. Juni 2010 - 18. Juni 2010, Luxembourg
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ISO 690PETROV, Tatjana, Heinz KOEPPL, 2010. Maximal Reduction of Deterministic Semantics of Rule-Based Models : Syntax- Independent Setup. WCSB 2010 : Seventh International Workshop on Computational Systems Biology. Luxembourg, 16. Juni 2010 - 18. Juni 2010. In: NYKTER, Matti, ed. and others. Seventh International Workshop on Computational Systems Biology : WCSB 2010 : June 16–18 : 2010 : Luxembourg. Tampere: Tampere International Center for Signal Processing, 2010, pp. 83-86. TICSP series. ISSN 1456-2774
BibTex
@inproceedings{Petrov2010Maxim-42231,
  year={2010},
  title={Maximal Reduction of Deterministic Semantics of Rule-Based Models : Syntax- Independent Setup},
  issn={1456-2774},
  publisher={Tampere International Center for Signal Processing},
  address={Tampere},
  series={TICSP series},
  booktitle={Seventh International Workshop on Computational Systems Biology : WCSB 2010 : June 16–18 : 2010 : Luxembourg},
  pages={83--86},
  editor={Nykter, Matti},
  author={Petrov, Tatjana and Koeppl, Heinz}
}
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