{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T00:46:57Z","timestamp":1775954817633,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary We present a massively parallel stochastic simulation algorithm (SSA) for reaction-diffusion systems implemented on Graphics Processing Units (GPUs). These are designated chips optimized to process a high number of floating point operations in parallel, rendering them well-suited for a range of scientific high-performance computations. Newer GPU generations provide a high-level programming interface which turns them into General-Purpose Graphics Processing Units (GPGPUs). Our SSA exploits GPGPU architecture to achieve a performance gain of two orders of magnitude over the fastest existing implementations on conventional hardware.<\/jats:p>\n               <jats:p>Availability: The software is freely available at http:\/\/www.csse.monash.edu.au\/~berndm\/inchman\/.<\/jats:p>\n               <jats:p>Contact: \u00a0matthias.vigelius@monash.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq622","type":"journal-article","created":{"date-parts":[[2010,11,10]],"date-time":"2010-11-10T01:25:36Z","timestamp":1289352336000},"page":"288-290","source":"Crossref","is-referenced-by-count":34,"title":["Accelerating reaction\u2013diffusion simulations with general-purpose graphics processing units"],"prefix":"10.1093","volume":"27","author":[{"given":"Matthias","family":"Vigelius","sequence":"first","affiliation":[{"name":"FIT Centre for Research in Intelligent Systems, Monash University, Clayton Victoria 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aidan","family":"Lane","sequence":"additional","affiliation":[{"name":"FIT Centre for Research in Intelligent Systems, Monash University, Clayton Victoria 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bernd","family":"Meyer","sequence":"additional","affiliation":[{"name":"FIT Centre for Research in Intelligent Systems, Monash University, Clayton Victoria 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,11,8]]},"reference":[{"key":"2023012512172628200_B1","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1093\/bib\/bbp020","article-title":"Taming the complexity of biological pathways through parallel computing","volume":"10","author":"Ballarini","year":"2009","journal-title":"Brief Bioinform."},{"key":"2023012512172628200_B2","first-page":"1","article-title":"Episimdemics: an efficient algorithm for simulating the spread of infectious disease over large realistic social networks","volume-title":"SC '08: Proceedings of the 2008 ACM\/IEEE conference on Supercomputing","author":"Barrett","year":"2008"},{"key":"2023012512172628200_B3","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1159\/000106145","article-title":"The realistic modeling of biological systems: a workshop synopsis","volume":"3","author":"Broderick","year":"2006","journal-title":"Complexus"},{"key":"2023012512172628200_B4","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1142\/S0129183194000052","article-title":"Multiparticle lattice gas automata for reaction diffusion systems","volume":"5","author":"Chopard","year":"1994","journal-title":"Int. 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