Analysing biochemical oscillation through probabilistic model checking

DOI10.1016/J.ENTCS.2009.02.002MaRDI QIDQ5404071zbMATH OpenOpenAlexFDO

Authors P. Ballarini, Radu Mardare, Ivan Mura

Publication date 21 March 2014

Published in Electronic Notes in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.entcs.2009.02.002

zbMATH Keywords

Markov modelssimulationordinary differential equationsbiological oscillatorsstochastic model checking

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Specification and verification (program logics, model checking, etc.) (68Q60)

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Cites work

• scientific article; zbMATH DE number 729460 (Why is no real title available?)
• scientific article; zbMATH DE number 2080040 (Why is no real title available?)
• scientific article; zbMATH DE number 763717 (Why is no real title available?)
• Analysing biochemical oscillation through probabilistic model checking
• Automatic verification of finite-state concurrent systems using temporal logic specifications
• Bio-PEPA: an extension of the process algebra PEPA for biochemical networks
• Evolving BlenX programs to simulate the evolution of biological networks
• Membrane systems with peripheral proteins: transport and evolution
• Probabilistic model checking of complex biological pathways

Cited in

(16)

• Analyzing oscillatory behavior with formal methods
• Multiple verification in complex biological systems: the bone remodelling case study
• Automata-based CSL model checking
• Analysing biochemical oscillation through probabilistic model checking
• Model checking biological oscillators
• Modelling biological compartments in bio-PEPA
• On-the-fly verification and optimization of DTA-properties for large Markov chains
• A model and analysis of the AKAP scaffold
• Analysis of multimodal stochastic oscillations in a biochemical reaction model
• A Ticking Clock: Performance Analysis of a Circadian Rhythm with Stochastic Process Algebra
• End-to-end statistical model checking for parameterization and stability analysis of ODE models
• On the qualitative behaviour of oscillating biochemical systems: the stochastic approach
• Detecting synchronisation of biological oscillators by model checking
• Applications of an expressive statistical model checking approach to the analysis of genetic circuits
• Query-based verification of qualitative trends and oscillations in biochemical systems
• A formal approach for tuning stochastic oscillators

Describes a project that uses

Uses Software

• Cyto-Sim
• BlenX
• COPASI
• Bio-PEPA

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