{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T07:20:41Z","timestamp":1761895241196},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,4,15]]},"abstract":"Abstract<\/jats:title>\n Motivation: The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological\/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB.<\/jats:p>\n Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user's models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2.<\/jats:p>\n Availability: The software is open source under the GPL v3 and available at http:\/\/www.maths.ox.ac.uk\/cmb\/STOCHSIMGPU. The web site also contains supplementary information.<\/jats:p>\n Contact: \u00a0klingbeil@maths.ox.ac.uk<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr068","type":"journal-article","created":{"date-parts":[[2011,2,27]],"date-time":"2011-02-27T01:13:12Z","timestamp":1298769192000},"page":"1170-1171","source":"Crossref","is-referenced-by-count":28,"title":["STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB"],"prefix":"10.1093","volume":"27","author":[{"given":"Guido","family":"Klingbeil","sequence":"first","affiliation":[{"name":"1 Centre for Mathematical Biology, 2Oxford Centre for Collaborative Applied Mathematics, 3Oxford-Man Institute of Quantitative Finance, Mathematical Institute, University of Oxford, Oxford OX1 3LB and 4Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK"}]},{"given":"Radek","family":"Erban","sequence":"additional","affiliation":[{"name":"1 Centre for Mathematical Biology, 2Oxford Centre for Collaborative Applied Mathematics, 3Oxford-Man Institute of Quantitative Finance, Mathematical Institute, University of Oxford, Oxford OX1 3LB and 4Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK"}]},{"given":"Mike","family":"Giles","sequence":"additional","affiliation":[{"name":"1 Centre for Mathematical Biology, 2Oxford Centre for Collaborative Applied Mathematics, 3Oxford-Man Institute of Quantitative Finance, Mathematical Institute, University of Oxford, Oxford OX1 3LB and 4Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK"}]},{"given":"Philip K.","family":"Maini","sequence":"additional","affiliation":[{"name":"1 Centre for Mathematical Biology, 2Oxford Centre for Collaborative Applied Mathematics, 3Oxford-Man Institute of Quantitative Finance, Mathematical Institute, University of Oxford, Oxford OX1 3LB and 4Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK"},{"name":"1 Centre for Mathematical Biology, 2Oxford Centre for Collaborative Applied Mathematics, 3Oxford-Man Institute of Quantitative Finance, Mathematical Institute, University of Oxford, Oxford OX1 3LB and 4Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK"}]}],"member":"286","published-online":{"date-parts":[[2011,2,25]]},"reference":[{"key":"2023061311473560900_B1","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1093\/genetics\/149.4.1633","article-title":"Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells","volume":"149","author":"Arkin","year":"1998","journal-title":"Genetics"},{"key":"2023061311473560900_B2","doi-asserted-by":"crossref","first-page":"046001","DOI":"10.1088\/1478-3975\/6\/4\/046001","article-title":"Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions","volume":"6","author":"Erban","year":"2009","journal-title":"Phys. Biol."},{"key":"2023061311473560900_B3","doi-asserted-by":"crossref","first-page":"1876","DOI":"10.1021\/jp993732q","article-title":"Efficient exact stochastic simulation of chemical systems with many species and many channels","volume":"104","author":"Gibson","year":"2000","journal-title":"J. Phy. Chem. A"},{"key":"2023061311473560900_B4","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1021\/j100540a008","article-title":"Exact stochastic simulation of coupled chemical reactions","volume":"81","author":"Gillespie","year":"1977","journal-title":"J. Phy. Chem."},{"key":"2023061311473560900_B5","doi-asserted-by":"crossref","first-page":"2923","DOI":"10.1093\/bioinformatics\/bti431","article-title":"Stochastic reaction-diffusion simulation with mesord","volume":"21","author":"Hattne","year":"2005","journal-title":"Bioinformatics"},{"key":"2023061311473560900_B6","article-title":"Fat vs. thin threading approach on GPUs: application to stochastic simulation of chemical reactions","author":"Klingbeil","year":"2011","journal-title":"IEEE Trans. Parallel Distributed Syst."},{"key":"2023061311473560900_B7","volume-title":"Logarithmic direct method for discrete stochastic simulation of chemically reacting systems.","author":"Li","year":"2006"},{"key":"2023061311473560900_B8","first-page":"39","article-title":"NVIDIA Tesla: A unified graphics and computing architecture","volume":"28","author":"Lindholm","year":"2008","journal-title":"IEEE Comput. Soc. Hot Chips"},{"key":"2023061311473560900_B9","doi-asserted-by":"crossref","first-page":"2289","DOI":"10.1093\/bioinformatics\/btp387","article-title":"Efficient stochastic simulation of reaction-diffusion processes via direct compilation","volume":"25","author":"Lis","year":"2009","journal-title":"Bioinformatics"},{"key":"2023061311473560900_B10","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1093\/bioinformatics\/bti799","article-title":"Systems Biology Toolbox for MATLAB: a computational platform for research in Systems Biology","volume":"22","author":"Schmidt","year":"2006","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/8\/1170\/50580130\/bioinformatics_27_8_1170.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/8\/1170\/50580130\/bioinformatics_27_8_1170.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,13]],"date-time":"2023-06-13T11:47:56Z","timestamp":1686656876000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/8\/1170\/227011"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,2,25]]},"references-count":10,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2011,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr068","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,4,15]]},"published":{"date-parts":[[2011,2,25]]}}}