On Algorithmic Analysis of Transcriptional Regulation by LTL Model Checking

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F09%3A00029225" target="_blank" >RIV/00216224:14330/09:00029225 - isvavai.cz</a>

Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

On Algorithmic Analysis of Transcriptional Regulation by LTL Model Checking

Popis výsledku v původním jazyce

This paper is focused on the model checking approach for analysis of piecewise-linear deterministic models of genetic regulatory networks. Firstly, the qualitative simulation algorithm of de Jong et.al. that builds the heart of Genetic Network Analyzer (GNA) is revisited and its time complexity is studied in detail. Secondly, a novel algorithm that reduces the state space generation time is introduced. The new algorithm is developed as an abstraction of the original GNA algorithm. Finally, a fragment oflinear time temporal logic for which the provided abstraction is conservative is identified. Efficiency of the new algorithm when implemented in the parallel model checking environment is demonstrated on a set of experiments performed on randomly modified biological models. In general, the achieved results bring a new insight into the field of qualitative simulation emerging in the context of systems biology.

Název v anglickém jazyce

On Algorithmic Analysis of Transcriptional Regulation by LTL Model Checking

Popis výsledku anglicky

This paper is focused on the model checking approach for analysis of piecewise-linear deterministic models of genetic regulatory networks. Firstly, the qualitative simulation algorithm of de Jong et.al. that builds the heart of Genetic Network Analyzer (GNA) is revisited and its time complexity is studied in detail. Secondly, a novel algorithm that reduces the state space generation time is introduced. The new algorithm is developed as an abstraction of the original GNA algorithm. Finally, a fragment oflinear time temporal logic for which the provided abstraction is conservative is identified. Efficiency of the new algorithm when implemented in the parallel model checking environment is demonstrated on a set of experiments performed on randomly modified biological models. In general, the achieved results bring a new insight into the field of qualitative simulation emerging in the context of systems biology.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

IN - Informatika

OECD FORD obor

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Projekt

<a href="/cs/project/GA201%2F09%2F1389" target="_blank" >GA201/09/1389: Verifikace a analýza velmi velkých počítačových systémů</a><br>

Návaznosti

Z - Vyzkumny zamer (s odkazem do CEZ)<br>S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2009

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Theoretical Computer Science

ISSN

0304-3975

e-ISSN

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Svazek periodika

2009

Číslo periodika v rámci svazku

410

Stát vydavatele periodika

CZ - Česká republika

Počet stran výsledku

20

Strana od-do

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Kód UT WoS článku

000268921500007

EID výsledku v databázi Scopus

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