Model Checking Approach to the Analysis of Biological Systems

2019 ◽  
pp. 3-35
Author(s):  
Nikola Beneš ◽  
Luboš Brim ◽  
Samuel Pastva ◽  
David Šafránek
Keyword(s):  
Model Checking ◽  
Biological Systems

scholarly journals Model Checking Biological Systems Described Using Ambient Calculus

2005 ◽  
pp. 85-103 ◽  
Author(s):  
Radu Mardare ◽  
Corrado Priami ◽  
Paola Quaglia ◽  
Oleksandr Vagin
Keyword(s):  
Model Checking ◽  
Biological Systems ◽  
Ambient Calculus

Model Checking of Biological Systems

2013 ◽  
pp. 63-112 ◽  
Author(s):  
Luboš Brim ◽  
Milan Češka ◽  
David Šafránek
Keyword(s):  
Model Checking ◽  
Biological Systems

Analyzing resilience properties in oscillatory biological systems using parametric model checking

Biosystems ◽  
2016 ◽  
Vol 149 ◽  
pp. 50-58 ◽  
Author(s):  
Alexander Andreychenko ◽  
Morgan Magnin ◽  
Katsumi Inoue
Keyword(s):  
Model Checking ◽  
Biological Systems ◽  
Parametric Model

scholarly journals A Bayesian Approach to Model Checking Biological Systems

2009 ◽  
pp. 218-234 ◽  
Author(s):  
Sumit K. Jha ◽  
Edmund M. Clarke ◽  
Christopher J. Langmead ◽  
Axel Legay ◽  
André Platzer ◽  
...  
Keyword(s):  
Model Checking ◽  
Bayesian Approach ◽  
Biological Systems

scholarly journals Probabilistic model checking of biological systems with uncertain kinetic rates

2012 ◽  
Vol 419 ◽  
pp. 2-16 ◽  
Author(s):  
Roberto Barbuti ◽  
Francesca Levi ◽  
Paolo Milazzo ◽  
Guido Scatena
Keyword(s):  
Model Checking ◽  
Probabilistic Model ◽  
Biological Systems ◽  
Probabilistic Model Checking ◽  
Kinetic Rates

Statistical model checking for biological systems

2014 ◽  
Vol 17 (3) ◽  
pp. 351-367 ◽  
Author(s):  
Alexandre David ◽  
Kim G. Larsen ◽  
Axel Legay ◽  
Marius Mikučionis ◽  
Danny Bøgsted Poulsen ◽  
...  
Keyword(s):  
Model Checking ◽  
Statistical Model ◽  
Biological Systems ◽  
Statistical Model Checking

MODELING AND ANALYZING BIOLOGICAL SYSTEMS USING COLORED HIERARCHICAL PETRI NETS ILLUSTRATED BYC. ELEGANSVULVAL DEVELOPMENT

2014 ◽  
Vol 22 (03) ◽  
pp. 463-493 ◽  
Author(s):  
FEI LIU ◽  
MONIKA HEINER ◽  
MING YANG
Keyword(s):  
Structural Analysis ◽  
Model Checking ◽  
Petri Nets ◽  
Petri Net ◽  
Large Scale ◽  
Biological Systems ◽  
Colored Petri Nets ◽  
Biological Models ◽  
Vulval Development ◽  
Continuous Simulation

Colored Petri nets allow compact, parameterizable and scalable representations of large-scale biological models by encoding, e.g., species as colored tokens, and offer a variety of analysis techniques, e.g., structural analysis, simulation and model checking to analyze biological models. However, so far colored Petri nets have not been widely used and well explored in systems biology. In this paper, we aim to present a systematic approach to modeling and analyzing complex biological systems using colored Petri nets in order to help biologists to easily use them. We first describe a framework comprising a family of related colored Petri nets: colored qualitative Petri net (𝒬𝒫𝒩𝒞), colored stochastic Petri net (𝒮𝒫𝒩𝒞) and colored continuous Petri net (𝒞𝒫𝒩𝒞). They share structure, but are specialized by their kinetic information. Based on this framework, we present our colored Petri net approach to modeling and analyzing complex biological systems. First a biological system is modeled as a hierarchical 𝒬𝒫𝒩𝒞model, animated and analyzed by structural analysis; then it is converted into a 𝒮𝒫𝒩𝒞or 𝒞𝒫𝒩𝒞model, to be further analyzed using stochastic or continuous simulation, and simulative or numerical model checking. We demonstrate this approach using a nontrivial example, Caenorhabditis elegans vulval development.

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