Publikation: Lumpability Abstractions of Rule-based Systems
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2010
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BEHRE, Jörn, ed. and others. Proceedings compendium of the Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi : MeCBIC2010 : and of the First Workshop on Applications of Membrane Computing : Concurrency : and Agent-based Modelling in Population Biology : AMCA-POP2010 : satellite events of the Eleventh International Conference on Membrane Computing : CMC11 : Friedrich Schiller University Jena : Germany 23 and 25 August 2010. Berlin: Pro Business, 2010, pp. 135-154. ISBN 978-3-86805-767-6
Zusammenfassung
The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the combinatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.
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MeCBIC 2010 : Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi 2010 and AMCA-POP2010 : First Workshop on Applications of Membrane Computing : Concurrency : and Agent-based Modelling in Population Biology, 23. Aug. 2010 - 25. Aug. 2010, Jena
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FERET, Jérôme, Thomas HENZINGER, Heinz KOEPPL, Tatjana PETROV, 2010. Lumpability Abstractions of Rule-based Systems. MeCBIC 2010 : Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi 2010 and AMCA-POP2010 : First Workshop on Applications of Membrane Computing : Concurrency : and Agent-based Modelling in Population Biology. Jena, 23. Aug. 2010 - 25. Aug. 2010. In: BEHRE, Jörn, ed. and others. Proceedings compendium of the Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi : MeCBIC2010 : and of the First Workshop on Applications of Membrane Computing : Concurrency : and Agent-based Modelling in Population Biology : AMCA-POP2010 : satellite events of the Eleventh International Conference on Membrane Computing : CMC11 : Friedrich Schiller University Jena : Germany 23 and 25 August 2010. Berlin: Pro Business, 2010, pp. 135-154. ISBN 978-3-86805-767-6BibTex
@inproceedings{Feret2010Lumpa-42230,
year={2010},
title={Lumpability Abstractions of Rule-based Systems},
isbn={978-3-86805-767-6},
publisher={Pro Business},
address={Berlin},
booktitle={Proceedings compendium of the Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi : MeCBIC2010 : and of the First Workshop on Applications of Membrane Computing : Concurrency : and Agent-based Modelling in Population Biology : AMCA-POP2010 : satellite events of the Eleventh International Conference on Membrane Computing : CMC11 : Friedrich Schiller University Jena : Germany 23 and 25 August 2010},
pages={135--154},
editor={Behre, Jörn},
author={Feret, Jérôme and Henzinger, Thomas and Koeppl, Heinz and Petrov, Tatjana}
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<dcterms:abstract xml:lang="eng">The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the combinatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.</dcterms:abstract>
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