{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T05:52:36Z","timestamp":1777441956293,"version":"3.51.4"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2017,6,28]],"date-time":"2017-06-28T00:00:00Z","timestamp":1498608000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB-1411482"],"award-info":[{"award-number":["MCB-1411482"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>A major barrier to the practical utilization of large, complex models of biochemical systems is the lack of open-source computational tools to evaluate model behaviors over high-dimensional parameter spaces. This is due to the high computational expense of performing thousands to millions of model simulations required for statistical analysis. To address this need, we have implemented a user-friendly interface between cupSODA, a GPU-powered kinetic simulator, and PySB, a Python-based modeling and simulation framework. For three example models of varying size, we show that for large numbers of simulations PySB\/cupSODA achieves order-of-magnitude speedups relative to a CPU-based ordinary differential equation integrator.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The PySB\/cupSODA interface has been integrated into the PySB modeling framework (version 1.4.0), which can be installed from the Python Package Index (PyPI) using a Python package manager such as pip. cupSODA source code and precompiled binaries (Linux, Mac OS\/X, Windows) are available at github.com\/aresio\/cupSODA (requires an Nvidia GPU; developer.nvidia.com\/cuda-gpus). Additional information about PySB is available at pysb.org.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx420","type":"journal-article","created":{"date-parts":[[2017,6,27]],"date-time":"2017-06-27T03:11:06Z","timestamp":1498533066000},"page":"3492-3494","source":"Crossref","is-referenced-by-count":13,"title":["GPU-powered model analysis with PySB\/cupSODA"],"prefix":"10.1093","volume":"33","author":[{"given":"Leonard A","family":"Harris","sequence":"first","affiliation":[{"name":"Department of Cancer Biology, Vanderbilt University, Nashville, TN, USA"},{"name":"Quantitative Systems Biology Center, Vanderbilt University, Nashville, TN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco S","family":"Nobile","sequence":"additional","affiliation":[{"name":"Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy"},{"name":"SYSBIO.IT Centre of Systems Biology, Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James C","family":"Pino","sequence":"additional","affiliation":[{"name":"Quantitative Systems Biology Center, Vanderbilt University, Nashville, TN, USA"},{"name":"Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, TN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander L R","family":"Lubbock","sequence":"additional","affiliation":[{"name":"Department of Cancer Biology, Vanderbilt University, Nashville, TN, USA"},{"name":"Quantitative Systems Biology Center, Vanderbilt University, Nashville, TN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniela","family":"Besozzi","sequence":"additional","affiliation":[{"name":"Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy"},{"name":"SYSBIO.IT Centre of Systems Biology, Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giancarlo","family":"Mauri","sequence":"additional","affiliation":[{"name":"Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy"},{"name":"SYSBIO.IT Centre of Systems Biology, Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paolo","family":"Cazzaniga","sequence":"additional","affiliation":[{"name":"SYSBIO.IT Centre of Systems Biology, Milan, Italy"},{"name":"Department of Human and Social Sciences, University of Bergamo, Bergamo, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3668-7468","authenticated-orcid":false,"given":"Carlos F","family":"Lopez","sequence":"additional","affiliation":[{"name":"Department of Cancer Biology, Vanderbilt University, Nashville, TN, USA"},{"name":"Quantitative Systems Biology Center, Vanderbilt University, Nashville, TN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,6,28]]},"reference":[{"key":"2023051506350619800_btx420-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1687-4153-2012-10","article-title":"The role of feedback control mechanisms on the establishment of oscillatory regimes in the Ras\/cAMP\/PKA pathway in S. cerevisiae","volume":"2012","author":"Besozzi","year":"2012","journal-title":"EURASIP J. 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