element;intro
#Welcome;Welcome to the interactive tour for <code>cbpManager</code>!<br><br>In the <b>Sample</b> tab, you can add sample data to existing patients and edit already existing samples. In the following you will learn how to do this in detail.
#sample_description;This box contains an additional description of the <b>Sample</b> tab and how to use the buttons.
#sample_img;Here you can see an example image how the sample data will look later in cBioPortal.
#sample_col_description;This box contains additional informations on several mandatory and optional columns.
#sample_main;This is the main container of the <b>Sample</b> tab. Similarly to the <b>Patient</b> tab, you can see several buttons, which allow you to modify the table below. Whenever you manipulate the sample data with the buttons, this table changes on the fly.
#sampleTable;This table contains the current sample data of the selected study and is very flexible which means that you can add and delete columns and rows.<br>It has two visual sections:<br><br>(1) The first three blue rows represent some column meta data required by cBioPortal. The first blue row represents short names of the columns, the second blue row contains the long names of the columns. The third blue row describes the data type of the column.<br>(Most of the time you don't need to change these rows but you can edit them by clicking on the row and using the button <b>Edit patient</b>.)<br><br>(2) The remaining rows represent samples.<br><br>Further, the columns 'PATIENT_ID' and 'SAMPLE_ID' are mandatory.
#AddColumnSample;The button <b>Add column(s)</b> allows you to add new attributes to the table. When you click on this button a modal window opens where you can choose from two options:<br><br>You have the option to add pre-defined columns. Some of the pre-defined columns are entity specific, therefore do not be surprised.<br><br>The second option allows you to add a custom column. To create a custom column you need to provide a 'column name', a 'short name', a 'long name', and the 'data type'. The last three elements will be shown in the blue rows.
#DeleteColumnSample;This button allows you to delete columns. In the modal window select one ore more columns you want to delete and confirm your choice. You cannot delete the columns 'PATIENT_ID' and 'SAMPLE_ID'.
#NewSample;In the previous steps you probably added new columns to this table. Now, it's a good time to add new samples. By providing a 'PATIENT_ID' to a sample, cBioPortal will map the given sample to this patient. This enables one to associate multiple samples to one patient. For example, a single patient may have had multiple biopsies, each of which has been genomically profiled.<br><br>This button opens a dialog window with input fields correlating with the columns of the table. Some of the pre-defined columns generate pre-defined input fields like drop-down selections or numeric input.<br><br>You must provide a 'PATIENT_ID' and a 'SAMPLE_ID' for the new sample. The IDs allow only numbers, letters, points, underscores and hyphens.
#EditSample;By clicking on a row in the table and then using this button you can change the values of the row. A dialog window like the one of the 'Add sample' button appears where you can edit the values corresponding to the columns of the table.
#DeleteSample;Select a row by clicking on it and then click on the <b>Delete sample</b> button to delete the selected entry.
#SaveDataSample;The most important button is the <b>Save</b> button. By clicking on this button the study file containing the sample data will be overwritten. This makes the changes permanent. If you forgot to click on this button all changes in the table persist only for the current session. <br><b>Do not forget to use this button after you modified the data!</b>
#Thanks;Thank you for taking the <b>Sample</b> tab tour of <code>cbpManager</code>!
