{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T13:07:32Z","timestamp":1762866452157},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Several methods and computational tools have been developed to design novel metabolic pathways. A major challenge is evaluating the metabolic efficiency of the designed pathways in the host organism. Here we present FindPath, a unified system to predict and rank possible pathways according to their metabolic efficiency in the cellular system. This tool uses a chemical reaction database to generate possible metabolic pathways and exploits constraint-based models (CBMs) to identify the most efficient synthetic pathway to achieve the desired metabolic function in a given host microorganism. FindPath can be used with common tools for CBM manipulation and uses the standard SBML format for both input and output files.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0http:\/\/metasys.insa-toulouse.fr\/software\/findpath\/ .<\/jats:p>\n               <jats:p>Contact: \u00a0heux@insa-toulouse.fr<\/jats:p>\n               <jats:p>Supplementary information : Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu422","type":"journal-article","created":{"date-parts":[[2014,7,4]],"date-time":"2014-07-04T02:04:38Z","timestamp":1404439478000},"page":"2986-2988","source":"Crossref","is-referenced-by-count":17,"title":["FindPath: a Matlab solution for \n            <i>in silico<\/i>\n             design of synthetic metabolic pathways"],"prefix":"10.1093","volume":"30","author":[{"given":"Gilles","family":"Vieira","sequence":"first","affiliation":[{"name":"1 Universit\u00e9 de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France 2 INRA, UMR792, Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s, F-31400 Toulouse, France and 3 CNRS, UMR5504, F-31400 Toulouse, France"},{"name":"1 Universit\u00e9 de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France 2 INRA, UMR792, Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s, F-31400 Toulouse, France and 3 CNRS, UMR5504, F-31400 Toulouse, France"},{"name":"1 Universit\u00e9 de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France 2 INRA, UMR792, Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s, F-31400 Toulouse, France and 3 CNRS, UMR5504, F-31400 Toulouse, France"}]},{"given":"Marc","family":"Carnicer","sequence":"additional","affiliation":[{"name":"1 Universit\u00e9 de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France 2 INRA, UMR792, Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s, F-31400 Toulouse, France and 3 CNRS, UMR5504, F-31400 Toulouse, France"},{"name":"1 Universit\u00e9 de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France 2 INRA, UMR792, Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s, F-31400 Toulouse, France and 3 CNRS, UMR5504, F-31400 Toulouse, France"},{"name":"1 Universit\u00e9 de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France 2 INRA, UMR792, Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s, F-31400 Toulouse, France and 3 CNRS, UMR5504, F-31400 Toulouse, France"}]},{"given":"Jean-Charles","family":"Portais","sequence":"additional","affiliation":[{"name":"1 Universit\u00e9 de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France 2 INRA, UMR792, Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s, F-31400 Toulouse, France and 3 CNRS, UMR5504, F-31400 Toulouse, France"},{"name":"1 Universit\u00e9 de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France 2 INRA, UMR792, Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s, F-31400 Toulouse, France and 3 CNRS, UMR5504, F-31400 Toulouse, France"},{"name":"1 Universit\u00e9 de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France 2 INRA, UMR792, Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s, F-31400 Toulouse, France and 3 CNRS, UMR5504, F-31400 Toulouse, France"}]},{"given":"St\u00e9phanie","family":"Heux","sequence":"additional","affiliation":[{"name":"1 Universit\u00e9 de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France 2 INRA, UMR792, Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s, F-31400 Toulouse, France and 3 CNRS, UMR5504, F-31400 Toulouse, France"},{"name":"1 Universit\u00e9 de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France 2 INRA, UMR792, Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s, F-31400 Toulouse, France and 3 CNRS, UMR5504, F-31400 Toulouse, France"},{"name":"1 Universit\u00e9 de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France 2 INRA, UMR792, Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s, F-31400 Toulouse, France and 3 CNRS, UMR5504, F-31400 Toulouse, France"}]}],"member":"286","published-online":{"date-parts":[[2014,6,3]]},"reference":[{"key":"2023012711562494400_btu422-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. 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