In this tutorial, you will learn how to create and run a notebook in JupyterLab on the platform, download data from the notebook, and upload results to the platform.
DXJupyterLab is accessible to all users of the UK Biobank Research Analysis Platform and the Our Future Health Trusted Research Environment.
Once your JupyterLab session is running, click on the
DNAnexustab on the left sidebar to see all the files and folders in the project.
To create a new empty notebook in the DNAnexus project, select
New Notebookfrom the top menu.
ipynbfile will be created and viewable in the DNAnexus project browser, which refreshes every few seconds.
You can rename your file by right-clicking on its name and selecting
You can open and edit the newly created notebook directly from the project (accessible from the
DNAnexustab in the left sidebar). To save your changes, simply hit
Ctrl/Command + Sor click on the
saveicon in the Toolbar (an area just below the tab bar at the top). A new notebook version will land in the project, and you should see in the "Last modified" column that the file was created recently.
Since DNAnexus files are immutable, whenever you save the notebook, the current version is uploaded to the project and replaces the previous version, i.e. the file of the same name. The previous version is moved to the
.Notebook_archivewith a timestamp suffix added to its name. Saving notebooks directly in the project as new files ensures that your analyses won't be lost when the DXJupyterLab session ends.
To process your data in the notebook, the data must be available in the execution environment (as is the case with any DNAnexus app).
dx download input_data/reads.fastq
If your notebook generates any data you'd like to keep, you should upload it to the project before the session ends, i.e. before the worker in which the JupyterLab runs is terminated. You can do it directly in the notebook by running
dx uploadfrom a notebook cell or from the terminal:
dx upload results.csv
If you create a notebook from the Launcher or from the top menu (
Notebook), the notebook will not be created in the project but in the local execution environment. In order to move it to the project, you will have to upload it to the project manually. Make sure you upload your local notebooks to the project before the session expires, or work on your notebooks directly from the project, so as not to lose your work.