Generalizing Gillespie's direct method to enable network-free simulations

DOI10.1007/s11538-018-0418-2zbMath1422.92062arXiv1801.10227OpenAlexW2963472529WikidataQ52338294 ScholiaQ52338294MaRDI QIDQ2325562

William S. Hlavacek, Ryan Suderman, Keesha E. Erickson, Song Feng, Eshan D. Mitra, Yen Ting Lin

Publication date: 26 September 2019

Published in: Bulletin of Mathematical Biology (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1801.10227

zbMATH Keywords

combinatorial complexitystochastic simulationkinetic Monte Carlorule-based modeling

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Software, source code, etc. for problems pertaining to biology (92-04) Systems biology, networks (92C42)

Related Items (2)

Nonlinear pattern matching in rule-based modeling languages ⋮ Stochastic simulation of biochemical systems: in memory of Dan T. Gillespie's contributions

Uses Software

• BioNetGen
• BioModels
• NFsim
• GitHub
• STOCHSIM
• TRuML
• Spatkin
• KappaTools

Cites Work

• Unnamed Item
• Formal molecular biology
• A multiple time interval finite state projection algorithm for the solution to the chemical master equation
• Incremental Update for Graph Rewriting
• Rule-Based Modelling, Symmetries, Refinements
• Rule-Based Modelling of Cellular Signalling
• Equation of State Calculations by Fast Computing Machines
• Intrinsic information carriers in combinatorial dynamical systems
• A Guide to Numerical Modelling in Systems Biology
• Accurate Chemical Master Equation Solution Using Multi-Finite Buffers
• The Monte Carlo Method

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