element;intro
#Welcome;Welcome to the interactive tour for <code>cbpManager</code>!<br><br>You will get to know the different components of the <code>cbpManager</code> user interface, and learn the basic usage mechanisms by doing.<br><br><code>cbpManger</code> can help you generating study files suitable for the import in cBioPortal for Cancer Genomics.<br><br>This introductory tour is best viewed if the app is full-screen. Click on the <code>'Next'</code> button to proceed with the interactive tour of the <b>Study</b> panel - If you click outside of the highlighted area, you will interrupt the tour, but you can resume it anytime by re-clicking on the <code>Tour</code> button.
#sidebarItemExpanded;On the left side of the app you'll see the sidebar, where you can access the different tabs of <code>cbpManager</code>, each with its dedicated functionality.
#StudyTab;In the <b>Study</b> tab, you can create a new study or select an existing one. In the next steps you will learn how to do this in detail.
#workflow_overview;But before we begin, you should know that <code>cbpManager</code> has a specific order of adding data to a study. The blue boxes symbolize the tabs of <code>cbpManager</code>.<br><br>Currently, we are in the <b>Study</b> tab, where we create or select an existing study. The next step would be to go to the <b>Patient</b> tab and add new patients. Only after adding patients, we should go to the <b>Sample</b> tab and add samples to already existing patients. After these three steps, we can optionally add mutation data, timeline data or resource data. Finally, we can validate the created files in the <b>Validation</b> tab.
#create_study;In this panel we can create a new study. Therefore, you should fill out the meta data fields of your new study.
#add_study_identifier;The only mandatory field is the cancer study ID field. But it is of course better to provide more information to your study.<br><br>You can also change the meta data of a study you created earlier by providing the same cancer study ID and filling out the remaining fields.
#ui_type_of_cancer;The cancer type is an important attribute. In the drop-down menu you can select from oncoTree codes. Alternatively, below is a table with the whole cancer type names, where you can select the type. (See the next tour step)
#cancer_type_table;In this table you can use the search to find cancer types. Select a cancer type by clicking on its row. The drop-down menu of the cancer type adapts to your selection.
#add_study; By clicking the <b>Add study</b> button, the study will be initialized. If successful you will see a small pop-up. In the background the appropriate study directory with the <code>meta_study.txt</code> file will be created.
#existing_study; In this box you can select from existing studies.
#ui_cancer_study_identifier;Select one of the existing studies or the study you created in the previous step.
#upload;Click on this button to load the study data of the selected study and modify it later on.
#studyTable;When the loading process was successful a table with the study meta data will appear below the <b>Load study</b> button as well as a small pop-up.<br><br>Now you can proceed with the Patient tab.
#tour_study;This is how you started the tour you are taking now. If you want to get shown around again through the study tab of <code>cbpManager</code>, you can click here.<br><br>All other tabs of <code>cbpManager</code> have a similar button in the same position of the page, with a dedicated tour for each section.
#Thanks;Thank you for taking the first tour of <code>cbpManager</code>!
