Web application for genetic modification flux with database to estimate metabolic fluxes of genetic mutants
Section snippets
Systems overview
Fig. 1 shows a workflow of the web application of GMF. Metabolic reaction network files written in the Microsoft Excel format are registered in the database attached to the GMF web application. These files can be freely downloaded. Users either select a registered or uploaded user's own data file. The application reads the selected or uploaded file and generates its associated stoichiometric matrix with the format available for the efmtool (13). Users can select one algorithm out of the three:
GMF web application
Fig. 2 shows the main page of the GMF web application. Users can (i) upload their own file or (ii) select a file out of the registered files. (iii) Users select an algorithm to estimate a flux distribution and an objective function out of the four functions (MEP, QP, LP, or MeanLP). When ECF is used, they can select a ratio type of gene expression and enzyme activity profiles. (iv) Once an input file is selected, details in the metabolic network are displayed. One hundred and twelve metabolic
Acknowledgments
This work was supported by Grant-in-Aid for Scientific Research (B) (25280107) from Japan Society for the Promotion of Science and by Manufacturing Technology Association of Biologics. We thank Dr. Akira Ishii (AISoftware Inc.), who helped developing the web application.
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