{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,3]],"date-time":"2023-02-03T05:25:13Z","timestamp":1675401913489},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We present In silico Biochemical Reaction Network Analysis (IBRENA), a software package which facilitates multiple functions including cellular reaction network simulation and sensitivity analysis (both forward and adjoint methods), coupled with principal component analysis, singular-value decomposition and model reduction. The software features a graphical user interface that aids simulation and plotting of in silico results. While the primary focus is to aid formulation, testing and reduction of theoretical biochemical reaction networks, the program can also be used for analysis of high-throughput genomic and proteomic data.<\/jats:p>\n               <jats:p>Availability: The software package, manual and examples are available at http:\/\/www.eng.buffalo.edu\/~neel\/ibrena<\/jats:p>\n               <jats:p>Contact: \u00a0neel@eng.buffalo.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn061","type":"journal-article","created":{"date-parts":[[2008,3,1]],"date-time":"2008-03-01T01:13:23Z","timestamp":1204334003000},"page":"1109-1111","source":"Crossref","is-referenced-by-count":8,"title":["<i>In silico<\/i> Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks"],"prefix":"10.1093","volume":"24","author":[{"given":"Gang","family":"Liu","sequence":"first","affiliation":[{"name":"1 Department of Chemical and Biological Engineering, and 2NY State Center for Excellence in Life Science and Bioinformatics, State University of New York, Buffalo, NY 14260, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sriram","family":"Neelamegham","sequence":"additional","affiliation":[{"name":"1 Department of Chemical and Biological Engineering, and 2NY State Center for Excellence in Life Science and Bioinformatics, State University of New York, Buffalo, NY 14260, USA"},{"name":"1 Department of Chemical and Biological Engineering, and 2NY State Center for Excellence in Life Science and Bioinformatics, State University of New York, Buffalo, NY 14260, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,2,28]]},"reference":[{"key":"2023020210001782100_B1","doi-asserted-by":"crossref","first-page":"10101","DOI":"10.1073\/pnas.97.18.10101","article-title":"Singular value decomposition for genome-wide expression data processing and modeling","volume":"97","author":"Alter","year":"2000","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020210001782100_B2","doi-asserted-by":"crossref","first-page":"3289","DOI":"10.1093\/bioinformatics\/bth378","article-title":"BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains","volume":"20","author":"Blinov","year":"2004","journal-title":"Bioinformatics"},{"key":"2023020210001782100_B3","doi-asserted-by":"crossref","first-page":"1076","DOI":"10.1137\/S1064827501380630","article-title":"Adjoint sensitivity analysis or differential-algebraic equations: the adjoint DAE system and its numerical solution","volume":"24","author":"Cao","year":"2003","journal-title":"Siam Journal on Scientific Computing"},{"key":"2023020210001782100_B4","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1145\/1089014.1089020","article-title":"SUNDIALS: Suite of nonlinear and differential\/algebraic equation solvers","volume":"31","author":"Hindmarsh","year":"2005","journal-title":"Acm Transactions on Mathematical Software"},{"key":"2023020210001782100_B5","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1089\/cmb.2004.11.544","article-title":"Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data","volume":"11","author":"Janes","year":"2004","journal-title":"J. Computat. Biol."},{"key":"2023020210001782100_B6","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1093\/bioinformatics\/bti118","article-title":"Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signaling","volume":"21","author":"Liu","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020210001782100_B7","first-page":"563","article-title":"Gepasi - a software package for modeling the dynamics, steady-states and control of biochemical and other systems","volume":"9","author":"Mendes","year":"1993","journal-title":"Comput. Appl. Biosci."},{"key":"2023020210001782100_B8","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1093\/bioinformatics\/15.1.72","article-title":"E-CELL: software environment for whole-cell simulation","volume":"15","author":"Tomita","year":"1999","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/8\/1109\/49045993\/bioinformatics_24_8_1109.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/8\/1109\/49045993\/bioinformatics_24_8_1109.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T10:01:13Z","timestamp":1675332073000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/8\/1109\/212624"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,2,28]]},"references-count":8,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2008,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn061","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,4,15]]},"published":{"date-parts":[[2008,2,28]]}}}