{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,12]],"date-time":"2026-07-12T04:03:41Z","timestamp":1783829021651,"version":"3.55.0"},"reference-count":23,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2014,12,1]],"date-time":"2014-12-01T00:00:00Z","timestamp":1417392000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/s12859-014-0409-8","type":"journal-article","created":{"date-parts":[[2014,12,17]],"date-time":"2014-12-17T12:41:44Z","timestamp":1418820104000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":139,"title":["DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis"],"prefix":"10.1186","volume":"15","author":[{"given":"Jose A","family":"Gomez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"H\u00f6ffner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul I","family":"Barton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2014,12,18]]},"reference":[{"issue":"3","key":"409_CR1","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1038\/nbt.1614","volume":"28","author":"JD Orth","year":"2010","unstructured":"Orth JD, Thiele I, Palsson B\u00d8: What is flux balance analysis? . Nat Biotechnol. 2010, 28 (3): 245-248. 10.1038\/nbt.1614.","journal-title":"Nat Biotechnol"},{"key":"409_CR2","doi-asserted-by":"publisher","first-page":"1331","DOI":"10.1016\/S0006-3495(02)73903-9","volume":"83","author":"R Mahadevan","year":"2002","unstructured":"Mahadevan R, Edwards JS, Doyle FJ: Dynamic flux balance analysis of diauxic growth in Escherichia coli . Biophys J. 2002, 83: 1331-1340. 10.1016\/S0006-3495(02)73903-9.","journal-title":"Biophys J"},{"issue":"3","key":"409_CR3","doi-asserted-by":"publisher","first-page":"792","DOI":"10.1002\/bit.24748","volume":"110","author":"K H\u00f6ffner","year":"2013","unstructured":"H\u00f6ffner K, Harwood SM, Barton PI: A reliable simulator for dynamic flux balance analysis . Biotechnol Bioeng. 2013, 110 (3): 792-802. 10.1002\/bit.24748.","journal-title":"Biotechnol Bioeng"},{"key":"409_CR4","doi-asserted-by":"publisher","first-page":"1290","DOI":"10.1038\/nprot.2011.308","volume":"6","author":"J Schellenberger","year":"2011","unstructured":"Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson B\u00d8: Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 . Nat Protoc. 2011, 6: 1290-1307. 10.1038\/nprot.2011.308.","journal-title":"Nat Protoc"},{"issue":"2","key":"409_CR5","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1002\/bit.22954","volume":"108","author":"TJ Hanly","year":"2011","unstructured":"Hanly TJ, Henson MA: Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures . Biotechnol Bioeng. 2011, 108 (2): 376-385. 10.1002\/bit.22954.","journal-title":"Biotechnol Bioeng"},{"issue":"4","key":"409_CR6","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1093\/bioinformatics\/btt723","volume":"30","author":"L Mao","year":"2014","unstructured":"Mao L, Verwoerd WS: ORCA: a COBRA toolbox extension for model-driven discovery and analysis . Bioinformatics. 2014, 30 (4): 584-585. 10.1093\/bioinformatics\/btt723.","journal-title":"Bioinformatics"},{"key":"409_CR7","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1038\/ismej.2010.117","volume":"5","author":"K Zhuang","year":"2011","unstructured":"Zhuang K, Izallalen M, Mouser P, Richter H, Risso C, Mahadevan R, Lovley DR: Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments . ISME J. 2011, 5: 305-316. 10.1038\/ismej.2010.117.","journal-title":"ISME J"},{"key":"409_CR8","doi-asserted-by":"publisher","first-page":"2475","DOI":"10.1002\/bit.24528","volume":"109","author":"K Zhuang","year":"2012","unstructured":"Zhuang K, Ma E, Lovley DR, Mahadevan R: The design of long-term effective uranium bioremediation strategy using a community metabolic model . Biotechnol Bioeng. 2012, 109: 2475-2483. 10.1002\/bit.24528.","journal-title":"Biotechnol Bioeng"},{"key":"409_CR9","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1016\/j.ymben.2003.09.002","volume":"5","author":"R Mahadevan","year":"2003","unstructured":"Mahadevan R, Schilling C: The effects of alternate optimal solutions in constraint-based genome-scale metabolic models . Metab Eng. 2003, 5: 264-276. 10.1016\/j.ymben.2003.09.002.","journal-title":"Metab Eng"},{"key":"409_CR10","unstructured":"CPLEX Optimizer, IBM ILOG. http:\/\/www-01.ibm.com\/software\/commerce\/optimization\/cplex-optimizer\/."},{"key":"409_CR11","unstructured":"Gurobi Optimization I: Gurobi optimizer reference manual2014. [http:\/\/www.gurobi.com]"},{"key":"409_CR12","unstructured":"ApS M: The MOSEK optimization toolbox for MATLAB manual. Version 7.0 (Revision 128). [http:\/\/docs.mosek.com\/7.0\/toolbox\/]"},{"key":"409_CR13","volume-title":"Introduction to Linear Optimization","author":"D Bertsimas","year":"1997","unstructured":"Bertsimas D, Tsitsiklis JN: Introduction to Linear Optimization . 1997, Athena Scientific, Belmont, MA"},{"issue":"9","key":"409_CR14","doi-asserted-by":"publisher","first-page":"R54","DOI":"10.1186\/gb-2003-4-9-r54","volume":"4","author":"JL Reed","year":"2003","unstructured":"Reed JL, Vo TD, Schilling CH, Palsson B\u00d8: An expanded genome-scale model of Escherichia coli K-12 ( i JR904 GSM\/GPR) . Genome Biol. 2003, 4 (9): R54-10.1186\/gb-2003-4-9-r54.","journal-title":"Genome Biol"},{"key":"409_CR15","volume-title":"Proceedings of the Eight International Conference on Foundations of Computer-Aided Process Design","author":"K H\u00f6ffner","year":"2014","unstructured":"H\u00f6ffner K, Barton PI: Design of microbial consortia for industrial biotechnology . Proceedings of the Eight International Conference on Foundations of Computer-Aided Process Design . Edited by: Eden M, Siirola JD, Towler GP. 2014, Elsevier, Cle Elum, Washington, USA,"},{"key":"409_CR16","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1038\/msb.2011.52","volume":"7","author":"RL Chang","year":"2011","unstructured":"Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson B\u00d8, Salehi-Ashtiani K, Papin JA: Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism . Mol Syst Biol. 2011, 7: 518-10.1038\/msb.2011.52.","journal-title":"Mol Syst Biol"},{"issue":"7","key":"409_CR17","doi-asserted-by":"publisher","first-page":"1298","DOI":"10.1101\/gr.2250904","volume":"14","author":"NC Duarte","year":"2004","unstructured":"Duarte NC, Herrg\u00e5rd MJ, Palsson B\u00d8: Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model . Genome Res. 2004, 14 (7): 1298-1309. 10.1101\/gr.2250904.","journal-title":"Genome Res"},{"key":"409_CR18","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1016\/0043-1354(83)90283-X","volume":"17","author":"HO Buhr","year":"1983","unstructured":"Buhr HO, Miller SB: A dynamic model of the high-rate algal-bacterial wastewater treatment pond . Water Res. 1983, 17: 29-37. 10.1016\/0043-1354(83)90283-X.","journal-title":"Water Res"},{"key":"409_CR19","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1016\/S0032-9592(99)00082-5","volume":"35","author":"XW Zhang","year":"1999","unstructured":"Zhang XW, Chen F, Johns MR: Kinetic models for heterotrophic growth of Chlamydomonas reinhardtii in batch and fed-batch cultures . Process Biochem. 1999, 35: 385-389. 10.1016\/S0032-9592(99)00082-5.","journal-title":"Process Biochem"},{"key":"409_CR20","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1111\/j.1365-3040.2007.001662.x","volume":"30","author":"KD Balkos","year":"2007","unstructured":"Balkos KD, Colman B: Mechanism of CO 2acquisition in an acid-tolerant Chlamydomonas . Plant Cell Environ. 2007, 30: 745-752. 10.1111\/j.1365-3040.2007.001662.x.","journal-title":"Plant Cell Environ"},{"key":"409_CR21","doi-asserted-by":"publisher","first-page":"11181","DOI":"10.1021\/ie200723w","volume":"50","author":"A Yang","year":"2011","unstructured":"Yang A: Modeling and evaluation of CO 2supply and utilization in algal ponds . Ind Eng Chem Res. 2011, 50: 11181-11192. 10.1021\/ie200723w.","journal-title":"Ind Eng Chem Res"},{"issue":"Suppl 4","key":"409_CR22","doi-asserted-by":"publisher","first-page":"S5","DOI":"10.1186\/1471-2164-12-S4-S5","volume":"12","author":"C Gomes de Oliveira Dal\u2019Molin","year":"2011","unstructured":"Gomes de Oliveira Dal\u2019Molin C, Quek LE, Palfreyman RW, Nielsen LK: AlgaGEM - a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome . BMC Genomics. 2011, 12 (Suppl 4): S5-10.1186\/1471-2164-12-S4-S5.","journal-title":"BMC Genomics"},{"key":"409_CR23","unstructured":"Charles River Watershed Association: Total Maximum Daily Load for Nutrients in the Upper\/Middle Charles River, Massachusetts. http:\/\/www.mass.gov\/eea\/docs\/dep\/water\/resources\/n-thru-y\/ucharles.pdf. 190 Park Rd, Weston, MA 02453 2011."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-014-0409-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0409-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0409-8","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0409-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T06:56:53Z","timestamp":1630565813000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-014-0409-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,12]]},"references-count":23,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["409"],"URL":"https:\/\/doi.org\/10.1186\/s12859-014-0409-8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,12]]},"assertion":[{"value":"8 July 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 December 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 December 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"409"}}