{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T03:20:54Z","timestamp":1780111254194,"version":"3.54.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: In flux balance analysis of genome scale stoichiometric models of metabolism, the principal constraints are uptake or secretion rates, the steady state mass conservation assumption and reaction directionality. Here, we introduce an algorithmic pipeline for quantitative assignment of reaction directionality in multi-compartmental genome scale models based on an application of the second law of thermodynamics to each reaction. Given experimental or computationally estimated standard metabolite species Gibbs energy and metabolite concentrations, the algorithms bounds reaction Gibbs energy, which is transformed to in vivo pH, temperature, ionic strength and electrical potential.<\/jats:p>\n               <jats:p>Results: This cross-platform MATLAB extension to the COnstraint-Based Reconstruction and Analysis (COBRA) toolbox is computationally efficient, extensively documented and open source.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/opencobra.sourceforge.net<\/jats:p>\n               <jats:p>Contact: \u00a0ronan.mt.fleming@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq607","type":"journal-article","created":{"date-parts":[[2010,11,30]],"date-time":"2010-11-30T05:04:51Z","timestamp":1291093491000},"page":"142-143","source":"Crossref","is-referenced-by-count":40,"title":["von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models"],"prefix":"10.1093","volume":"27","author":[{"given":"Ronan M. T.","family":"Fleming","sequence":"first","affiliation":[{"name":"1 Science Institute and Center for Systems Biology and 2Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, Iceland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ines","family":"Thiele","sequence":"additional","affiliation":[{"name":"1 Science Institute and Center for Systems Biology and 2Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, Iceland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2010,11,28]]},"reference":[{"key":"2023012511154899100_B1","doi-asserted-by":"crossref","DOI":"10.1002\/0471332607","volume-title":"Thermodynamics of Biochemical Reactions.","author":"Alberty","year":"2003"},{"key":"2023012511154899100_B2","doi-asserted-by":"crossref","DOI":"10.1002\/047003646X","volume-title":"Biochemical Thermodynamics: Applications of Mathematica.","author":"Alberty","year":"2006"},{"key":"2023012511154899100_B3","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1038\/nprot.2007.99","article-title":"Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox","volume":"2","author":"Becker","year":"2007","journal-title":"Nat. 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