PITHYA: High-Performance Parameter Synthesis for Biological
Models

k 2017

PITHYA: High-Performance Parameter Synthesis for Biological Models

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

Basic information

Original name

PITHYA: High-Performance Parameter Synthesis for Biological Models

Authors

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

Edition

Intelligent Systems for Molecular Biology and European Conference on Computational Biology. ISMB/ECCB 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 exhibit complex behaviour emerging from non-linear interactions among system components. A system can be specified in terms of an ODE (ordinary differential equations) model typically containing parameters which can significantly affect system behaviour. In general, it is difficult to obtain exact parameters values from experimental data. The number of parameters and their interdependence make the identification of parameters values a hard task. A common approach is to use parameter estimation from time-series data. Such data might be of low resolution or even unavailable. Instead of estimating parameters from data, an alternative approach is to specify global hypotheses on system behaviour in terms of temporal properties and to use parameter synthesis methods based on model checking, a verification technique proven by decades of use in computer science. We present a new high-performance tool Pithya that implements state-of-the-art parameter synthesis methods. For a given ODE model, it allows to visually explore model behaviour with respect to different parameter values. Moreover, Pithya automatically synthesises parameter values satisfying a given property. Such property can specify various behaviour constraints, e.g., maximal reachable concentration, time ordering of events, characteristics of steady states, presence of limit cycles, etc.

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/0945/2015, interní kód MU

Name: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace V.

Investor: Masaryk University, Category A

Citovat

BRIM, Luboš, Nikola BENEŠ, David ŠAFRÁNEK, Martin DEMKO, Samuel PASTVA and Matej HAJNAL. PITHYA: High-Performance Parameter Synthesis for Biological Models. In Intelligent Systems for Molecular Biology and European Conference on Computational Biology. ISMB/ECCB 2017. 2017.

@proceedings{1387862,
   author = {Brim, Luboš and Beneš, Nikola and Šafránek, David and Demko, Martin and Pastva, Samuel and Hajnal, Matej},
   booktitle = {Intelligent Systems for Molecular Biology and European Conference on Computational Biology. ISMB/ECCB 2017},
   keywords = {parameter synthesis; model checking; systems biology; dynamical systems; synthetic biology},
   language = {eng},
   title = {PITHYA: High-Performance Parameter Synthesis for Biological Models},
   url = {https://www.iscb.org/ismbeccb2017},
   year = {2017}
}

TY  - CONF
ID  - 1387862
AU  - Brim, Luboš - Beneš, Nikola - Šafránek, David - Demko, Martin - Pastva, Samuel - Hajnal, Matej
PY  - 2017
TI  - PITHYA: High-Performance Parameter Synthesis for Biological Models
KW  - parameter synthesis
KW  - model checking
KW  - systems biology
KW  - dynamical systems
KW  - synthetic biology
UR  - https://www.iscb.org/ismbeccb2017
N2  - Biological systems exhibit complex behaviour emerging from non-linear interactions among system components. A system can be specified in terms of an ODE (ordinary differential equations) model typically containing parameters which can significantly affect system behaviour. In general, it is difficult to obtain exact parameters values from experimental data. The number of parameters and their interdependence make the identification of parameters values a hard task. A common approach is to use parameter estimation from time-series data. Such data might be of low resolution or even unavailable. Instead of estimating parameters from data, an alternative approach is to specify global hypotheses on system behaviour in terms of temporal properties and to use parameter synthesis methods based on model checking, a verification technique proven by decades of use in computer science. We present a new high-performance tool Pithya that implements state-of-the-art parameter synthesis methods. For a given ODE model, it allows to visually explore model behaviour with respect to different parameter values. Moreover, Pithya automatically synthesises parameter values satisfying a given property. Such property can specify various behaviour constraints, e.g., maximal reachable concentration, time ordering of events, characteristics of steady states, presence of limit cycles, etc.
ER  -

BRIM, Luboš, Nikola BENEŠ, David ŠAFRÁNEK, Martin DEMKO, Samuel PASTVA and Matej HAJNAL. PITHYA: High-Performance Parameter Synthesis for Biological Models. In \textit{Intelligent Systems for Molecular Biology and European Conference on Computational Biology. ISMB/ECCB 2017}. 2017.

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