Videos

In this video we are going to: (i) edit the experimentTest.xml provided with the SNV quick-example and (ii) run RUbioSeq using the edited configuration XML file and monitor the progress. At the welcome screen we choose 'Run' to log in as user (the admin account is also valid). Once we are logged in, we go to the 'RUbioSeq home' and choose the 'Edit Experiment' option which allows us to select an existing configuration XML file (Page 12, Section 5.4.2 of the manual) to edit it. Here, we select the experimentTest.xml provided with the SNV quick-example which enables the 'Edit Experiment' button where we click to edit the parameters. The editing screen looks like the creation screen  (Page 11, Section 5.4.1.1 of the manual) with the only different that in the case of edition, the parameters stored in the XML file are already introcuded in the GUI. In this case, we have to add the sample provided in the quick-example so we click the 'Add sample' button which opens a dialog to add the sample information (name, files, suffix and type). Once we have added it, we execute the experiment by clicking in the 'Execute' button. Before executing it, a dialog asks us to save the configuration introcuded. After saving this configuration, we are redirected to the 'Execute experiment screen' (Page 12, Section 5.4.3 of the manual) where we select the configuration XML file of the experiment (in this case is the file that we have just saved) and the execution mode 'Complete', to run the entire pipeline. Then, by clicking the 'Run Experiment' button a new RUbioSeq execution of the SNV branch is started and we are redirected to the progress monitor screen, where we can see a progress bar indicating the percentage of experiment executed. When the experiment finishes, we are notified by a popup message indicating that the experiment is completed and we go to the user experiments section (Page 14, Section 5.4.4 of the manual) to see that the experiment exection has been saved.

In this video we are going to: (i) edit the experimentTest.xml provided with the CNV quick-example and (ii) run RUbioSeq using the edited configuration XML file and monitor the progress. At the welcome screen we choose 'Run' to log in as user. Once we are logged in, we go to the 'RUbioSeq home' and choose the 'Edit Experiment' option which allows us to select an existing configuration XML file (Page 12, Section 5.4.2 of the manual) to edit it. Here, we select the experimentTest.xml provided with the CNV quick-example which enables the 'Edit Experiment' button where we click to edit the parameters. In this case, we have to add the sample provided in the quick-example so we click the 'Add sample' button which opens a dialog to add the sample information (name, files, suffix and type). Once we have added it, we execute the experiment by clicking in the 'Execute' button. Before executing it, a dialog asks us to save the configuration introcuded. After saving this configuration, we are redirected to the 'Execute experiment screen' (Page 12, Section 5.4.3 of the manual) where we select the configuration XML file of the experiment (in this case is the file that we have just saved) and the execution mode 'Complete', to run the entire pipeline. Then, by clicking the 'Run Experiment' button a new RUbioSeq execution of the CNV branch is started and we are redirected to the progress monitor screen, where we can see a progress bar indicating the percentage of experiment executed. When the experiment finishes, we are notified by a popup message indicating that the experiment is completed and we go to the user experiments section (Page 14, Section 5.4.4 of the manual) to see that the experiment exection has been saved.

In this video we are going to: (i) edit the experimentTest.xml provided with the methylation quick-example and (ii) run RUbioSeq using the edited configuration XML file and monitor the progress. At the welcome screen we choose 'Run' to log in as user. Once we are logged in, we go to the 'RUbioSeq home' and choose the 'Edit Experiment' option which allows us to select an existing configuration XML file (Page 12, Section 5.4.2 of the manual) to edit it. Here, we select the experimentTest.xml provided with the CNV quick-example which enables the 'Edit Experiment' button where we click to edit the parameters. In this case, we have to add the two samples provided in the quick-example so we click the 'Add sample' button which opens a dialog to add the sample1 file. Then, we edit the sample2 field to select the other file. Once we have added the samples, we execute the experiment by clicking in the 'Execute' button. Before executing it, a dialog asks us to save the configuration introcuded. After saving this configuration, we are redirected to the 'Execute experiment screen' (Page 12, Section 5.4.3 of the manual) where we select the configuration XML file of the experiment (in this case is the file that we have just saved) and the execution mode 'Complete', to run the entire pipeline. Then, by clicking the 'Run Experiment' button a new RUbioSeq execution of the methylaation branch is started and we are redirected to the progress monitor screen, where we can see a progress bar indicating the percentage of experiment executed. When the experiment finishes, we are notified by a popup message indicating that the experiment is completed and we go to the user experiments section (Page 14, Section 5.4.4 of the manual) to see that the experiment exection has been saved.

In this video we are going to: (i) edit the experimentTest.xml provided with the ChipSeq quick-example and (ii) run RUbioSeq using the edited configuration XML file and monitor the progress. At the welcome screen we choose 'Run' to log in as user. Once we are logged in, we go to the 'RUbioSeq home' and choose the 'Edit Experiment' option which allows us to select an existing configuration XML file (Page 12, Section 5.4.2 of the manual) to edit it. Here, we select the experimentTest.xml provided with the CNV quick-example which enables the 'Edit Experiment' button where we click to edit the parameters. In this case, we have to define a new Experiment with one ChipSeq Unit with the samples provided in the quick-example. To do that, we: (i) click the 'Add experiment' button which adds a new experiment to the list; (ii) click the 'Add ChipSeq Unit' to add a new ChipSeq Unit to the experiment; (iii) edit the treatment and input samples by clicking the edit button which opens a dialog to add the sample information (name, files, suffix and type). Once we have added these information, we execute the experiment by clicking in the 'Execute' button. Before executing it, a dialog asks us to save the configuration introcuded. After saving this configuration, we are redirected to the 'Execute experiment screen' (Page 12, Section 5.4.3 of the manual) where we select the configuration XML file of the experiment (in this case is the file that we have just saved) and the execution mode 'Complete', to run the entire pipeline. Then, by clicking the 'Run Experiment' button a new RUbioSeq execution of the ChipSeq branch is started and we are redirected to the progress monitor screen, where we can see a progress bar indicating the percentage of experiment executed. When the experiment finishes, we are notified by a popup message indicating that the experiment is completed and we go to the user experiments section (Page 14, Section 5.4.4 of the manual) to see that the experiment exection has been saved.