AEON: attractor bifurcation analysis of parametrised Boolean networks

N Beneš, L Brim, J Kadlecaj, S Pastva… - … Aided Verification: 32nd …, 2020 - Springer
Boolean networks (BNs) provide an effective modelling tool for various phenomena from
science and engineering. Any long-term behaviour of a BN eventually converges to a so …

Detecting attractors in biological models with uncertain parameters

J Barnat, N Beneš, L Brim, M Demko, M Hajnal… - … Methods in Systems …, 2017 - Springer
Complex behaviour arising in biological systems is typically characterised by various kinds
of attractors. An important problem in this area is to determine these attractors. Biological …

Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway

M Demko, L Chrást, P Dvořák, J Damborský… - Microorganisms, 2019 - mdpi.com
In our previous work, we designed and implemented a synthetic metabolic pathway for 1, 2,
3-trichloropropane (TCP) biodegradation in Escherichia coli. Significant effects of metabolic …

Pithya: a parallel tool for parameter synthesis of piecewise multi-affine dynamical systems

N Beneš, L Brim, M Demko, S Pastva… - … Aided Verification: 29th …, 2017 - Springer
We present a novel tool for parameter synthesis of piecewise multi-affine dynamical systems
from specifications expressed in a hybrid branching-time temporal logic. The tool is based …

A large-scale assessment of exact lumping of quantitative models in the BioModels repository

IC Perez-Verona, M Tribastone, A Vandin - Theoretical Computer Science, 2021 - Elsevier
Chemical reaction networks are a popular formalism for modeling biological processes
which supports both a deterministic and a stochastic interpretation based on ordinary …

[HTML][HTML] Parallel parameter synthesis algorithm for hybrid CTL

N Beneš, L Brim, S Pastva, D Šafránek - Science of Computer …, 2020 - Elsevier
Parametrised models of dynamical systems arise in various areas of science. In this work,
we focus on models described as parametrised Kripke structures with properties formulated …

Bifurcation manifolds in predator–prey models computed by Gröbner basis method

V Hajnová, L Přibylová - Mathematical Biosciences, 2019 - Elsevier
Many natural processes studied in population biology, systems biology, biochemistry,
chemistry or physics are modeled by dynamical systems with polynomial or rational right …

Model checking approach to the analysis of biological systems

N Beneš, L Brim, S Pastva, D Šafránek - Automated Reasoning for …, 2019 - Springer
Formal verification techniques together with other computer science formal methods have
been recently tailored for applications to biological and biomedical systems. In contrast to …

BNClassifier: Classifying Boolean Models by Dynamic Properties

N Beneš, L Brim, O Huvar, S Pastva… - … Computational Methods in …, 2024 - Springer
Abstract Partially Specified Boolean Networks (PSBNs) represent a family of Boolean
models resulting from possible interpretations of unknown update logics. Hybrid extension of …

[图书][B] Computer aided cerification

R Majumdar, V Kuncak - 2017 - Springer
It has been our privilege to serve as the program chairs for CAV 2017, the 29th International
Conference on Computer-Aided Verification. CAV 2017 was held in beautiful Heidelberg …