HSimulator: hybrid stochastic/deterministic simulation of biochemical reaction networks (Q1693768): Difference between revisions
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Property / full work available at URL: https://doi.org/10.1155/2017/1232868 / rank | |||
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Property / cites work: Computational challenges in systems biology / rank | |||
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Property / cites work: Numerical Methods for Ordinary Differential Equations / rank | |||
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Property / cites work: Computational Methods in Systems Biology / rank | |||
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Property / cites work: Hybrid representation and simulation of stiff biochemical networks / rank | |||
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Property / cites work: HRSSA - efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks / rank | |||
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Latest revision as of 01:49, 15 July 2024
scientific article
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English | HSimulator: hybrid stochastic/deterministic simulation of biochemical reaction networks |
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HSimulator: hybrid stochastic/deterministic simulation of biochemical reaction networks (English)
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31 January 2018
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Summary: HSimulator is a multithread simulator for mass-action biochemical reaction systems placed in a well-mixed environment. HSimulator provides optimized implementation of a set of widespread state-of-the-art stochastic, deterministic, and hybrid simulation strategies including the first publicly available implementation of the Hybrid Rejection-based Stochastic Simulation Algorithm (HRSSA). HRSSA, the fastest hybrid algorithm to date, allows for an efficient simulation of the models while ensuring the exact simulation of a subset of the reaction network modeling slow reactions. Benchmarks show that HSimulator is often considerably faster than the other considered simulators. The software, running on Java v6.0 or higher, offers a simulation GUI for modeling and visually exploring biological processes and a Javadoc-documented Java library to support the development of custom applications. HSimulator is released under the COSBI Shared Source license agreement (COSBI-SSLA).
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hybrid stochastic/deterministic simulation
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biochemical reaction networks
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Hybrid Rejection-based Stochastic Simulation Algorithm (HRSSA)
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