Publikation: Stochastic Semantics of Signaling as a Composition of Agent-view Automata
Dateien
Datum
Autor:innen
Herausgeber:innen
ISSN der Zeitschrift
Electronic ISSN
ISBN
Bibliografische Daten
Verlag
Schriftenreihe
Auflagebezeichnung
URI (zitierfähiger Link)
DOI (zitierfähiger Link)
Internationale Patentnummer
Link zur Lizenz
Angaben zur Forschungsförderung
Projekt
Open Access-Veröffentlichung
Core Facility der Universität Konstanz
Titel in einer weiteren Sprache
Publikationstyp
Publikationsstatus
Erschienen in
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.
Zusammenfassung in einer weiteren Sprache
Fachgebiet (DDC)
Schlagwörter
Konferenz
Rezension
Zitieren
ISO 690
KOEPPL, 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.2011.04.002BibTex
@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} }
RDF
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:void="http://rdfs.org/ns/void#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/42136"> <dc:contributor>Koeppl, Heinz</dc:contributor> <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/> <dcterms:issued>2011-05</dcterms:issued> <dcterms:title>Stochastic Semantics of Signaling as a Composition of Agent-view Automata</dcterms:title> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-04-23T11:45:32Z</dcterms:available> <foaf:homepage rdf:resource="http://localhost:8080/"/> <dc:creator>Petrov, Tatjana</dc:creator> <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/36"/> <dc:rights>Attribution-NonCommercial-NoDerivs 3.0 Unported</dc:rights> <dcterms:abstract xml:lang="eng">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.</dcterms:abstract> <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/42136/1/Koeppl_2-ry7dtqss5ela4.pdf"/> <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/36"/> <dc:creator>Koeppl, Heinz</dc:creator> <dc:contributor>Petrov, Tatjana</dc:contributor> <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/42136/1/Koeppl_2-ry7dtqss5ela4.pdf"/> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-04-23T11:45:32Z</dc:date> <dc:language>eng</dc:language> <dcterms:rights rdf:resource="http://creativecommons.org/licenses/by-nc-nd/3.0/"/> <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/42136"/> </rdf:Description> </rdf:RDF>