http://metabolizer.babelomics.org/doc/ 2026-04-18T18:10:57+00:00 http://metabolizer.babelomics.org/doc/ http://metabolizer.babelomics.org/doc/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2017-05-24T14:33:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=in-silico_knockout:design_data&rev=1495636427&do=diff Design data panel The experimental design file must include two columns: the first one with the names of the samples, the second one with the class to which each sample belongs. See how to upload files in Upload your data. The design data panel allows you: * Select sample for knockout text/html 2017-05-24T14:33:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=in-silico_knockout:logging_in&rev=1495636427&do=diff Logging in In order to use the Metabolizer you need to be logged in. If you do not have an account, you can either create a new user for you or log in as an anonymous user. * If you want to log in as an anonymous user, click on Start. * If you already have an account, log in by clicking on text/html 2017-05-24T14:33:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=in-silico_knockout:over_expression&rev=1495636427&do=diff In-silico knockout and over expression Metabolizer allows you to simulate effect of knockout (KO) and/or over-expression (OE) of one or several genes or the effect of drug(s) in the activity of metabolic modules. 2 different usage of Knockout tool exist: text/html 2017-05-24T14:33:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=in-silico_knockout:upload_your_data&rev=1495636427&do=diff Upload your data Follow the following steps to upload your data to Metabolizer. 1- Either select the My data button (1) in the upper bar of the Metabolizer web or the File browser (7) option of each pathway tool. 2- Your workspace folder (2) will appear. text/html 2017-05-24T14:33:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=in-silico_knockout:workflow_ko&rev=1495636427&do=diff Workflow For login, upload input and design data please visit Workflow. To use Knockout tool user can upload 1 sample or a dataset. Using 1 sample: 1) Upload Input data. id sample Gene1 10.02 Gene2 9.55 Gene2 2.34 2) Select Species. 3) Fill the Job information text/html 2017-05-24T14:33:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=in-silico_knockout:workflow&rev=1495636427&do=diff Workflow First step to use Metabolizer is to be logged in. Please visit Logging in to further information on this step. Metabolizer data is arranged in folders as in a personal computer. You can upload data to any folder and organize it as desired (1). To learn how to upload data to Metabolizer, please visit