{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T13:05:26Z","timestamp":1762866326089},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Over past decades, constraint-based modelling has emerged as an important approach to obtain referential information about mechanisms behind biological phenotypes and identify physiological and perturbed metabolic states at genome-scale. However, application of this novel approach to systems biology in biotechnology is still hindered by the functionalities of the existing modelling software. To augment the usability of the constraint-based approach for various use scenarios, we present ORCA, a Matlab package, which extends the scope of established Constraint-Based Reconstruction and Analysis metabolic modelling and includes three unique functionalities: (i) a framework method integrating three analyses of multi-objective optimization, robustness analysis and fractional benefit analysis, (ii) metabolic pathways identification with futile loop elimination and (iii) a dynamic flux balance analysis framework incorporating kinetic constraints.<\/jats:p>\n               <jats:p>Availability and implementation: ORCA is freely available to academic users and is downloadable from https:\/\/sourceforge.net\/projects\/exorca\/; a mini-tutorial is supplied in the package for training purposes as well as a software manual.<\/jats:p>\n               <jats:p>Contact: \u00a0Longfei.mao@lincolnuni.ac.nz<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt723","type":"journal-article","created":{"date-parts":[[2013,12,15]],"date-time":"2013-12-15T01:09:42Z","timestamp":1387069782000},"page":"584-585","source":"Crossref","is-referenced-by-count":16,"title":["ORCA: a COBRA toolbox extension for model-driven discovery and analysis"],"prefix":"10.1093","volume":"30","author":[{"given":"Longfei","family":"Mao","sequence":"first","affiliation":[{"name":"Department of Molecular Biosciences, Centre for Advanced Computational Solutions, Lincoln University, Lincoln 7647, New Zealand"}]},{"given":"Wynand S.","family":"Verwoerd","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, Centre for Advanced Computational Solutions, Lincoln University, Lincoln 7647, New Zealand"}]}],"member":"286","published-online":{"date-parts":[[2013,12,13]]},"reference":[{"key":"2023012710424131800_btt723-B1","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.biosystems.2012.03.002","article-title":"Paint4Net: COBRA toolbox extension for visualization of stoichiometric models of metabolism","volume":"109","author":"Kostromins","year":"2012","journal-title":"Biosystems"},{"key":"2023012710424131800_btt723-B2","article-title":"Software applications for flux balance analysis","author":"Lakshmanan","year":"2012","journal-title":"Brief. 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