Parameter Synthesis of Biological Models by Model Checking: A
Case Study

k 2017

Parameter Synthesis of Biological Models by Model Checking: A Case Study

BRIM, Luboš, David ŠAFRÁNEK, Nikola BENEŠ, Martin DEMKO, Samuel PASTVA et. al.

Basic information

Original name

Parameter Synthesis of Biological Models by Model Checking: A Case Study

Authors

BRIM, Luboš, David ŠAFRÁNEK, Nikola BENEŠ, Martin DEMKO, Samuel PASTVA and Matej HAJNAL

Edition

4th International Synthetic & Systems Biology Summer School. SSBSS 2017, 2017

Other information

Language

English

Type of outcome

Prezentace na konferencích

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Organization unit

Faculty of Informatics

Keywords in English

parameter synthesis; model checking; systems biology; dynamical systems; synthetic biology

Abstract

V originále

Biological systems often exhibit very interesting behaviour as a result of their complex dynamical nature. Every system could be described in terms of some model (e.g., differential equations), but some of its quantitative aspects are hard to be measured. We are talking about uncertain parameters which have direct impact on a particular system's behaviour. In fact, these parameters and their investigation are the main objectives of our study. In general, there are many approaches for investigation of biological systems properties and their parameters. Most of the parameters are mutually dependent and therefore it is hard and computationally demanding to find admissible parameter values with respect to constraints such as hypothesised properties or wet-lab measurements. We focus on verification of such properties by model checking, a formal technique originally designed for the analysis of computer systems. Examined properties are defined in terms of temporal logics allowing to describe system behaviour over time. Recently, we have developed several high-performance techniques for parameter synthesis that are based on parallel coloured model checking. In this presentation, we review the applicability of our techniques in the context of biological systems. In particular, in matter of issues such as parameters prediction, biffurcation analysis and model optimisation.

Links

GA15-11089S, research and development project

Name: Získávání parametrů biologických modelů pomocí techniky ověřování modelů

Investor: Czech Science Foundation

LM2015055, research and development project

Name: Centrum pro systémovou biologii (Acronym: C4SYS)

Investor: Ministry of Education, Youth and Sports of the CR

MUNI/A/0992/2016, interní kód MU

Name: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity (Acronym: SKOMU)

Investor: Masaryk University, Category A

Citovat

BRIM, Luboš, David ŠAFRÁNEK, Nikola BENEŠ, Martin DEMKO, Samuel PASTVA and Matej HAJNAL. Parameter Synthesis of Biological Models by Model Checking: A Case Study. In 4th International Synthetic & Systems Biology Summer School. SSBSS 2017. 2017.

@proceedings{1387861,
   author = {Brim, Luboš and Šafránek, David and Beneš, Nikola and Demko, Martin and Pastva, Samuel and Hajnal, Matej},
   booktitle = {4th International Synthetic & Systems Biology Summer School. SSBSS 2017},
   keywords = {parameter synthesis; model checking; systems biology; dynamical systems; synthetic biology},
   language = {eng},
   title = {Parameter Synthesis of Biological Models by Model Checking: A Case Study},
   url = {http://www.taosciences.it/ssbss/},
   year = {2017}
}

TY  - CONF
ID  - 1387861
AU  - Brim, Luboš - Šafránek, David - Beneš, Nikola - Demko, Martin - Pastva, Samuel - Hajnal, Matej
PY  - 2017
TI  - Parameter Synthesis of Biological Models by Model Checking: A Case Study
KW  - parameter synthesis
KW  - model checking
KW  - systems biology
KW  - dynamical systems
KW  - synthetic biology
UR  - http://www.taosciences.it/ssbss/
N2  - Biological systems often exhibit very interesting behaviour as a result of their complex dynamical nature. Every system could be described in terms of some model (e.g., differential equations), but some of its quantitative aspects are hard to be measured. We are talking about uncertain parameters which have direct impact on a particular system's behaviour. In fact, these parameters and their investigation are the main objectives of our study. In general, there are many approaches for investigation of biological systems properties and their parameters. Most of the parameters are mutually dependent and therefore it is hard and computationally demanding to find admissible parameter values with respect to constraints such as hypothesised properties or wet-lab measurements. We focus on verification of such properties by model checking, a formal technique originally designed for the analysis of computer systems. Examined properties are defined in terms of temporal logics allowing to describe system behaviour over time. Recently, we have developed several high-performance techniques for parameter synthesis that are based on parallel coloured model checking. In this presentation, we review the applicability of our techniques in the context of biological systems. In particular, in matter of issues such as parameters prediction, biffurcation analysis and model optimisation.
ER  -

BRIM, Luboš, David ŠAFRÁNEK, Nikola BENEŠ, Martin DEMKO, Samuel PASTVA and Matej HAJNAL. Parameter Synthesis of Biological Models by Model Checking: A Case Study. In \textit{4th International Synthetic \&{} Systems Biology Summer School. SSBSS 2017}. 2017.

Detailed Information on Publication Record