HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks
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 availab...
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| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Wiley
2017-01-01
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| Series: | Complexity |
| Online Access: | http://dx.doi.org/10.1155/2017/1232868 |
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| _version_ | 1850232747549786112 |
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| author | Luca Marchetti Rosario Lombardo Corrado Priami |
| author_facet | Luca Marchetti Rosario Lombardo Corrado Priami |
| author_sort | Luca Marchetti |
| collection | DOAJ |
| description | 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). |
| format | Article |
| id | doaj-art-04c4bbb788ec4bfc8fa861a7a29e9702 |
| institution | OA Journals |
| issn | 1076-2787 1099-0526 |
| language | English |
| publishDate | 2017-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Complexity |
| spelling | doaj-art-04c4bbb788ec4bfc8fa861a7a29e97022025-08-20T02:03:05ZengWileyComplexity1076-27871099-05262017-01-01201710.1155/2017/12328681232868HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction NetworksLuca Marchetti0Rosario Lombardo1Corrado Priami2The Microsoft Research–University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, No. 1, 38068 Rovereto, ItalyThe Microsoft Research–University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, No. 1, 38068 Rovereto, ItalyThe Microsoft Research–University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, No. 1, 38068 Rovereto, ItalyHSimulator 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).http://dx.doi.org/10.1155/2017/1232868 |
| spellingShingle | Luca Marchetti Rosario Lombardo Corrado Priami HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks Complexity |
| title | HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks |
| title_full | HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks |
| title_fullStr | HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks |
| title_full_unstemmed | HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks |
| title_short | HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks |
| title_sort | hsimulator hybrid stochastic deterministic simulation of biochemical reaction networks |
| url | http://dx.doi.org/10.1155/2017/1232868 |
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