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HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks

Author

Listed:
  • Luca Marchetti
  • Rosario Lombardo
  • Corrado Priami

Abstract

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).

Suggested Citation

  • Luca Marchetti & Rosario Lombardo & Corrado Priami, 2017. "HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks," Complexity, Hindawi, vol. 2017, pages 1-12, December.
    • Handle: RePEc:hin:complx:1232868
    DOI: 10.1155/2017/1232868
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    References listed on IDEAS

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    3. Leroy Hood & David Galas, 2003. "The digital code of DNA," Nature, Nature, vol. 421(6921), pages 444-448, January.
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