Jupyter Notebooks
- Paul Whatmore (Deactivated)
What are Jupyter Notebooks?
Jupyter Notebooks are interactive notebook documents that can contain live code, equations, visualizations, media and other computational outputs.
An individual Jupyter Notebook runs on a specific ‘kernel’ - i.e. a programming language or environment. For example, the RNA-Seq differential expression analysis that we did in workshop session 3 can be converted to a Jupyter Notebook running an R kernel. In this way you can run the analysis from your web browser, using a server (such as the HPC) to do the computations.
As well as being able to run code (in code ‘cells’), Jupyter Notebooks can contain text, images, etc. Thus it can simultaneously allow the running of an analysis workflow and also containing the instructions and explanation for the code.
Jupyter Notebooks and the HPC
The eResearch team have set up a Jupyter Hub, which allows Jupyter Notebooks to be hosted and run on the HPC, all in your web browser. You only need a link to access and run a specific Notebook.
Click on the below link to open an RNA-Seq Notebook.
This link will download the Notebook from a repository to your HPC home directory, then open the Notebook in the HPC Jupyter Hub (make sure you are connected to the QUT network first, either by being on campus or connected remotely via VPN).
Once you’ve downloaded the Notebook by clicking the above link, you can access it again by again clicking on the above link, or going directly to the Jupyter hub here: https://jupyterhub.eres.qut.edu.au