Precise parameter synthesis for stochastic biochemical systems

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26230%2F16%3APU121654" target="_blank" >RIV/00216305:26230/16:PU121654 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216224:14330/17:00094903

Výsledek na webu

<a href="http://link.springer.com/article/10.1007/s00236-016-0265-2" target="_blank" >http://link.springer.com/article/10.1007/s00236-016-0265-2</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/s00236-016-0265-2" target="_blank" >10.1007/s00236-016-0265-2</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Precise parameter synthesis for stochastic biochemical systems

Popis výsledku v původním jazyce

We consider the problem of synthesising rate parameters for stochastic biochemical networks so that a given time-bounded CSL property is guaranteed to hold, or, in the case of quantitative properties, the probability of satisfying the property is maximised or minimised. Our method is based on extending CSL model checking and standard uniformisation to parametric models, in order to compute safe bounds on the satisfaction probability of the property. We develop synthesis algorithms that yield answers that are precise to within an arbitrarily small tolerance value. The algorithms combine the computation of probability bounds with the refinement and sampling of the parameter space. Our methods are precise and efficient, and improve on existing approximate techniques that employ discretisation and refinement. We evaluate the usefulness of the methods by synthesising rates for three biologically motivated case studies: infection control for a SIR epidemic model; reliability analysis of molecular computation by a DNA walker; and bistability in the gene regulation of the mammalian cell cycle.

Název v anglickém jazyce

Precise parameter synthesis for stochastic biochemical systems

Popis výsledku anglicky

We consider the problem of synthesising rate parameters for stochastic biochemical networks so that a given time-bounded CSL property is guaranteed to hold, or, in the case of quantitative properties, the probability of satisfying the property is maximised or minimised. Our method is based on extending CSL model checking and standard uniformisation to parametric models, in order to compute safe bounds on the satisfaction probability of the property. We develop synthesis algorithms that yield answers that are precise to within an arbitrarily small tolerance value. The algorithms combine the computation of probability bounds with the refinement and sampling of the parameter space. Our methods are precise and efficient, and improve on existing approximate techniques that employ discretisation and refinement. We evaluate the usefulness of the methods by synthesising rates for three biologically motivated case studies: infection control for a SIR epidemic model; reliability analysis of molecular computation by a DNA walker; and bistability in the gene regulation of the mammalian cell cycle.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2016

Kód důvěrnosti údajů

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

Název periodika

Acta Informatica

ISSN

0001-5903

e-ISSN

1432-0525

Svazek periodika

54

Číslo periodika v rámci svazku

6

Stát vydavatele periodika

DE - Spolková republika Německo

Počet stran výsledku

35

Strana od-do

589-623

Kód UT WoS článku

000407713300003

EID výsledku v databázi Scopus

2-s2.0-84961655158