{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T10:13:08Z","timestamp":1761559988931},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: An application has been developed to help with the creation and editing of Systems Biology Markup Language (SBML) format metabolic networks up to the organism scale. Networks are defined as a collection of Kyoto Encyclopedia of Genes and Genomes (KEGG) LIGAND reactions with an optional associated Enzyme Classification (EC) number for each reaction. Additional custom reactions can be defined by the user. Reactions within the network can be assigned flux constraints and compartmentalization is supported for each reaction in addition to the support for reactions that occur across compartment boundaries. Exported networks are fully SBML L2V4 compatible with an optional L2V1 export for compatibility with old versions of the COBRA toolbox.<\/jats:p>\n               <jats:p>Availability and implementation: The software runs in the free Microsoft Access 2007\u2122 Runtime (Microsoft Inc.), which is included with the installer and works on Windows XP SP2 or better. Full source code is viewable in the full version of Access 2007 or 2010. Users must have a license to use the KEGG LIGAND database (free academic licensing is available). Please go to www.bioinformatics.leeds.ac.uk\/\u223cpytf\/metnetmaker for software download, help and tutorials.<\/jats:p>\n               <jats:p>Contact: \u00a0pytf@leeds.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq425","type":"journal-article","created":{"date-parts":[[2010,7,30]],"date-time":"2010-07-30T02:42:33Z","timestamp":1280457753000},"page":"2352-2353","source":"Crossref","is-referenced-by-count":16,"title":["MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format"],"prefix":"10.1093","volume":"26","author":[{"given":"Thomas","family":"Forth","sequence":"first","affiliation":[{"name":"Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK"}]},{"given":"Glenn A.","family":"McConkey","sequence":"additional","affiliation":[{"name":"Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK"}]},{"given":"David R.","family":"Westhead","sequence":"additional","affiliation":[{"name":"Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK"}]}],"member":"286","published-online":{"date-parts":[[2010,7,29]]},"reference":[{"key":"2023012508234868900_B1","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. Protoc."},{"key":"2023012508234868900_B2","doi-asserted-by":"crossref","first-page":"D511","DOI":"10.1093\/nar\/gkj128","article-title":"MetaCyc: a multiorganism database of metabolic pathways and enzymes","volume":"34","author":"Caspi","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012508234868900_B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/msb.2008.15","article-title":"Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major","volume":"4","author":"Chavali","year":"2008","journal-title":"Mol. Syst. Biol."},{"key":"2023012508234868900_B4","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1093\/nar\/30.1.402","article-title":"LIGAND: database of chemical compounds and reactions in biological pathways","volume":"30","author":"Goto","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023012508234868900_B5","doi-asserted-by":"publisher","DOI":"10.1038\/npre.2008.2715.1","article-title":"Systems Biology Markup Language (SBML) Level2:Structures and Facilities for Model Definitions","author":"Hucka","year":"2008","journal-title":"Nature Precedings."},{"key":"2023012508234868900_B6","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1093\/bioinformatics\/18.suppl_1.S225","article-title":"The Pathway Tools software","volume":"18","author":"Karp","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012508234868900_B7","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/j.copbio.2003.08.001","article-title":"Advances in flux balance analysis","volume":"14","author":"Kauffman","year":"2003","journal-title":"Curr. Opin. Biotechnol."},{"key":"2023012508234868900_B8","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/nbt.1614","article-title":"What is flux balance analysis?","volume":"28","author":"Orth","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"2023012508234868900_B9","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/S0167-7799(03)00030-1","article-title":"Genome-scale microbial in silico models: the constraints-based approach","volume":"21","author":"Price","year":"2003","journal-title":"Trends Biotechnol."},{"key":"2023012508234868900_B10","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/1752-0509-3-38","article-title":"Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction","volume":"3","author":"Raghunathan","year":"2009","journal-title":"BMC Syst. Biol."},{"key":"2023012508234868900_B11","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1038\/nprot.2009.203","article-title":"A protocol for generating a high-quality genome-scale metabolic reconstruction","volume":"5","author":"Thiele","year":"2010","journal-title":"Nat. Protoc."},{"key":"2023012508234868900_B12","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1038\/nbt1094-994","article-title":"Metabolic flux balancing: basic concepts, scientific and practical use","volume":"12","author":"Varma","year":"1994","journal-title":"Nat. Biotechnol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/18\/2352\/48858440\/bioinformatics_26_18_2352.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/18\/2352\/48858440\/bioinformatics_26_18_2352.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:24:00Z","timestamp":1674635040000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/18\/2352\/209127"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,7,29]]},"references-count":12,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2010,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq425","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,9,15]]},"published":{"date-parts":[[2010,7,29]]}}}