Hybrid representation and simulation of stiff biochemical networks

DOI10.1016/j.nahs.2012.05.004zbMath1269.93061OpenAlexW1974161639WikidataQ63241798 ScholiaQ63241798MaRDI QIDQ360624

Monika Heiner, Mostafa Herajy

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

Related Items (7)

HRSSA - efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks ⋮ Efficient modelling of yeast cell cycles based on multisite phosphorylation using coloured hybrid Petri nets with marking-dependent arc weights ⋮ HSimulator: hybrid stochastic/deterministic simulation of biochemical reaction networks ⋮ Analytic solutions for stochastic hybrid models of gene regulatory networks ⋮ Hybrid semantics for Bio-PEPA ⋮ Stochastic hybrid models of gene regulatory networks -- a PDE approach ⋮ Colouring fuzziness for systems biology

Uses Software

• SUNDIALS
• SNOOPY

Cites Work

• SUNDIALS
• 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
• Hybrid method for the chemical master equation
• From Petri Nets to Differential Equations – An Integrative Approach for Biochemical Network Analysis
• Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments
• Differential Petri nets: representing continuous systems in a discrete-event world
• Adaptive simulation of hybrid stochastic and deterministic models for biochemical systems

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