%0 Generic %1 Raman2008PathwayAnalyser %A Raman, Karthik %A Chandra, Nagasuma %A Raman, Karthik %A Chandra, Nagasuma %D 2008 %I Nature Publishing Group %J Nature Precedings %K flux-analysis myown pathway\_analysis software systems\_biology %N 713 %R 10.1038/npre.2008.1868.1 %T PathwayAnalyser: A Systems Biology Tool for Flux Analysis of Metabolic Pathways %U http://dx.doi.org/10.1038/npre.2008.1868.1 %X Stoichiometric and constraint-based analyses of metabolic pathways have been gaining ground in the recent past with the increase in the quality and number of pathway databases available and the curation of genome-scale metabolic models. Genome-scale metabolic models of several organisms such as Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus have already been constructed. Flux Balance Analysis (FBA) and Minimisation of Metabolic Adjustment (MoMA) are two of the popular techniques for the constraint-based analysis of metabolic pathways.We have developed a computational tool, PathwayAnalyser, for the analysis of metabolic pathways, particularly by FBA and MoMA. PathwayAnalyser interfaces with the open-source GNU Linear Programming Toolkit (GLPK) for linear programming/FBA and Object Oriented Quadratic Programming (OOQP) for quadratic programming/MoMA. It gives a comprehensive report on gene deletions from the Systems Biology Markup Language (SBML) Model and objective function input for FBA. PathwayAnalyser is open-source and is available at http://sourceforge.net/projects/pathwayanalyser

@misc{Raman2008PathwayAnalyser, abstract = {Stoichiometric and constraint-based analyses of metabolic pathways have been gaining ground in the recent past with the increase in the quality and number of pathway databases available and the curation of genome-scale metabolic models. Genome-scale metabolic models of several organisms such as Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus have already been constructed. Flux Balance Analysis ({FBA}) and Minimisation of Metabolic Adjustment ({MoMA}) are two of the popular techniques for the constraint-based analysis of metabolic {pathways.We} have developed a computational tool, {PathwayAnalyser}, for the analysis of metabolic pathways, particularly by {FBA} and {MoMA}. {PathwayAnalyser} interfaces with the open-source {GNU} Linear Programming Toolkit ({GLPK}) for linear {programming/FBA} and Object Oriented Quadratic Programming ({OOQP}) for quadratic {programming/MoMA}. It gives a comprehensive report on gene deletions from the Systems Biology Markup Language ({SBML}) Model and objective function input for {FBA}. {PathwayAnalyser} is open-source and is available at http://sourceforge.net/projects/pathwayanalyser}, added-at = {2018-12-02T16:09:07.000+0100}, author = {Raman, Karthik and Chandra, Nagasuma and Raman, Karthik and Chandra, Nagasuma}, biburl = {https://www.bibsonomy.org/bibtex/2fd19a7161f946327fd0aa87c407a6ecd/karthikraman}, citeulike-article-id = {6781156}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/npre.2008.1868.1}, citeulike-linkout-1 = {http://precedings.nature.com/documents/1868/version/1}, day = 8, doi = {10.1038/npre.2008.1868.1}, interhash = {b8c151169b1a33540be7a37483117317}, intrahash = {fd19a7161f946327fd0aa87c407a6ecd}, issn = {1756-0357}, journal = {Nature Precedings}, keywords = {flux-analysis myown pathway\_analysis software systems\_biology}, month = may, number = 713, posted-at = {2010-03-09 15:03:49}, priority = {0}, publisher = {Nature Publishing Group}, timestamp = {2019-04-17T12:56:37.000+0200}, title = {{PathwayAnalyser}: A Systems Biology Tool for Flux Analysis of Metabolic Pathways}, url = {http://dx.doi.org/10.1038/npre.2008.1868.1}, year = 2008 }