%0 Journal Article %1 Vieira2014FindPath %A Vieira, Gilles %A Carnicer, Marc %A Portais, Jean-Charles C. %A Heux, Stéphanie %D 2014 %I Oxford University Press %J Bioinformatics (Oxford, England) %K design design-principles metabolic-networks %N 20 %P 2986--2988 %R 10.1093/bioinformatics/btu422 %T FindPath: a Matlab solution for in silico design of synthetic metabolic pathways. %U http://dx.doi.org/10.1093/bioinformatics/btu422 %V 30 %X 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. http://metasys.insa-toulouse.fr/software/findpath/. heux@insa-toulouse.fr Supplementary data are available at Bioinformatics online. \copyright The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

@article{Vieira2014FindPath, abstract = {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. http://metasys.insa-toulouse.fr/software/findpath/. heux@insa-toulouse.fr Supplementary data are available at Bioinformatics online. {\copyright} The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.}, added-at = {2018-12-02T16:09:07.000+0100}, author = {Vieira, Gilles and Carnicer, Marc and Portais, Jean-Charles C. and Heux, St\'{e}phanie}, biburl = {https://www.bibsonomy.org/bibtex/24452383d4d860ce66ef1d729ffa9af8f/karthikraman}, citeulike-article-id = {13253034}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btu422}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/early/2014/07/03/bioinformatics.btu422.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/early/2014/07/03/bioinformatics.btu422.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/24994891}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=24994891}, day = 15, doi = {10.1093/bioinformatics/btu422}, interhash = {3d63f214839f6fa03434d487a3f3679f}, intrahash = {4452383d4d860ce66ef1d729ffa9af8f}, issn = {1367-4811}, journal = {Bioinformatics (Oxford, England)}, keywords = {design design-principles metabolic-networks}, month = oct, number = 20, pages = {2986--2988}, pmid = {24994891}, posted-at = {2014-12-22 03:14:01}, priority = {2}, publisher = {Oxford University Press}, timestamp = {2018-12-02T16:09:07.000+0100}, title = {{FindPath}: a Matlab solution for in silico design of synthetic metabolic pathways.}, url = {http://dx.doi.org/10.1093/bioinformatics/btu422}, volume = 30, year = 2014 }