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.

Základní údaje

Originální název

PITHYA: High-Performance Parameter Synthesis for Biological Models

Autoři

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

Vydání

Intelligent Systems for Molecular Biology and European Conference on Computational Biology. ISMB/ECCB 2017, 2017

Další údaje

Jazyk

angličtina

Typ výsledku

Prezentace na konferencích

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Organizační jednotka

Fakulta informatiky

Klíčová slova anglicky

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

Příznaky

Mezinárodní význam

Změněno: 26. 2. 2018 10:31, prof. RNDr. Luboš Brim, CSc.

Anotace

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.

Návaznosti

GA15-11089S, projekt VaV

Název: Získávání parametrů biologických modelů pomocí techniky ověřování modelů

Investor: Grantová agentura ČR, Získávání parametrů biologických modelů pomocí techniky ověřování modelů

LM2015055, projekt VaV

Název: Centrum pro systémovou biologii (Akronym: C4SYS)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, The national infrastructure C4SYS - Centre for Systems Biology

MUNI/A/0945/2015, interní kód MU

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

Investor: Masarykova univerzita, Rozsáhlé výpočetní systémy: modely, aplikace a verifikace V., DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

BRIM, Luboš, Nikola BENEŠ, David ŠAFRÁNEK, Martin DEMKO, Samuel PASTVA a 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 a 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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