Hybrid representation and simulation of stiff biochemical networks

DOI10.1016/J.NAHS.2012.05.004MaRDI QIDQ360624zbMATH OpenOpenAlexWikidataFDO

Authors Mostafa Herajy, Monika Heiner

Publication date 27 August 2013

Published in Nonlinear Analysis. Hybrid Systems (Search for Journal in Brave)

Full work available at URL http://www.sciencedirect.com/science/article/pii/S1751570X12000192

zbMATH Keywords

hybrid simulationdynamic partitioninggeneralised hybrid Petri netsstiff biochemical networks

Mathematics Subject Classification ID

Adaptive control/observation systems (93C40) Discrete event control/observation systems (93C65)

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Cites work

• Adaptive simulation of hybrid stochastic and deterministic models for biochemical systems
• Differential Petri nets: representing continuous systems in a discrete-event world
• Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments
• Formal methods for computational systems biology. 8th international school on formal methods for the design of computer, communication, and software systems, SFM 2008 Bertinoro, Italy, June 2--7, 2008. Advanced lectures
• From Petri Nets to Differential Equations – An Integrative Approach for Biochemical Network Analysis
• Hybrid method for the chemical master equation
• SUNDIALS

Cited in

(15)

• A critical comparison of rejection-based algorithms for simulation of large biochemical reaction networks
• HRSSA - efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks
• Analytic solutions for stochastic hybrid models of gene regulatory networks
• Colouring fuzziness for systems biology
• Hybrid semantics for Bio-PEPA
• Computational and experimental approaches to determining the structure and interaction potentials of prototypical biological systems
• scientific article; zbMATH DE number 5494031 (Why is no real title available?)
• Implementing biological hybrid systems: allowing composition and avoiding stiffness
• scientific article; zbMATH DE number 1794358 (Why is no real title available?)
• Efficient modelling of yeast cell cycles based on multisite phosphorylation using coloured hybrid Petri nets with marking-dependent arc weights
• Accelerated simulation of hybrid biological models with quasi-disjoint deterministic and stochastic subnets
• Adaptive simulation of hybrid stochastic and deterministic models for biochemical systems
• scientific article; zbMATH DE number 6769232 (Why is no real title available?)
• HSimulator: hybrid stochastic/deterministic simulation of biochemical reaction networks
• Stochastic hybrid models of gene regulatory networks -- a PDE approach

Describes a project that uses

Uses Software

• SNOOPY
• SUNDIALS

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