{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T01:38:09Z","timestamp":1772501889039,"version":"3.50.1"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The Biochemical Simulation Environment (BISEN) is a suite of tools for generating equations and associated computer programs for simulating biochemical systems in the MATLAB\u00ae computing environment. This is the first package that can generate appropriate systems of differential equations for user-specified multi-compartment systems of enzymes and transporters accounting for detailed biochemical thermodynamics, rapid equilibria of multiple biochemical species and dynamic proton and metal ion buffering.<\/jats:p>\n               <jats:p>Availability: The software and a user manual (including several tutorial examples) are available at bbc.mcw.edu\/BISEN.<\/jats:p>\n               <jats:p>Contact: \u00a0dbeard@mcw.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp069","type":"journal-article","created":{"date-parts":[[2009,2,26]],"date-time":"2009-02-26T02:28:17Z","timestamp":1235615297000},"page":"836-837","source":"Crossref","is-referenced-by-count":13,"title":["BISEN: Biochemical Simulation Environment"],"prefix":"10.1093","volume":"25","author":[{"given":"J.","family":"Vanlier","sequence":"first","affiliation":[{"name":"1 BioModeling and Bioinformatics, BioMedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, 2Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA and 3Lilly-Singapore Centre for Drug Discovery Pte Ltd, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"F.","family":"Wu","sequence":"additional","affiliation":[{"name":"1 BioModeling and Bioinformatics, BioMedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, 2Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA and 3Lilly-Singapore Centre for Drug Discovery Pte Ltd, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"F.","family":"Qi","sequence":"additional","affiliation":[{"name":"1 BioModeling and Bioinformatics, BioMedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, 2Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA and 3Lilly-Singapore Centre for Drug Discovery Pte Ltd, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"K. C.","family":"Vinnakota","sequence":"additional","affiliation":[{"name":"1 BioModeling and Bioinformatics, BioMedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, 2Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA and 3Lilly-Singapore Centre for Drug Discovery Pte Ltd, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Y.","family":"Han","sequence":"additional","affiliation":[{"name":"1 BioModeling and Bioinformatics, BioMedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, 2Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA and 3Lilly-Singapore Centre for Drug Discovery Pte Ltd, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"R. K.","family":"Dash","sequence":"additional","affiliation":[{"name":"1 BioModeling and Bioinformatics, BioMedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, 2Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA and 3Lilly-Singapore Centre for Drug Discovery Pte Ltd, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"F.","family":"Yang","sequence":"additional","affiliation":[{"name":"1 BioModeling and Bioinformatics, BioMedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, 2Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA and 3Lilly-Singapore Centre for Drug Discovery Pte Ltd, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"D. A.","family":"Beard","sequence":"additional","affiliation":[{"name":"1 BioModeling and Bioinformatics, BioMedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, 2Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA and 3Lilly-Singapore Centre for Drug Discovery Pte Ltd, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,2,25]]},"reference":[{"key":"2023051209125366400_B1","article-title":"CellML metadata: standards, tools and repositories","author":"Beard","year":"2009","journal-title":"Trans. Roy. Soc."},{"key":"2023051209125366400_B2","first-page":"128","article-title":"Biochemical reaction networks. In Chemical Biophysics:","volume-title":"Quantitative Analysis of Cellular Processes.","author":"Beard","year":"2008"},{"key":"2023051209125366400_B3","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/S0076-6879(08)03802-0","article-title":"Multiple ion binding equilibria, reaction kinetics, and thermodynamics in dynamic models of biochemical pathways","volume":"454","author":"Vinnakota","year":"2009","journal-title":"Methods Enzymol."},{"key":"2023051209125366400_B4","doi-asserted-by":"crossref","first-page":"24525","DOI":"10.1074\/jbc.M701024200","article-title":"Computer modeling of mitochondrial tricarboxylic acid cycle, oxidative phosphorylation, metabolite transport, and electrophysiology","volume":"282","author":"Wu","year":"2007","journal-title":"J. Biol. Chem."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/6\/836\/50286731\/bioinformatics_25_6_836.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/6\/836\/50286731\/bioinformatics_25_6_836.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,12]],"date-time":"2023-05-12T09:13:34Z","timestamp":1683882814000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/6\/836\/252622"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,2,25]]},"references-count":4,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2009,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp069","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,3,15]]},"published":{"date-parts":[[2009,2,25]]}}}