Learning pathway

Using Jupyter Notebooks for biomolecular research

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Learning pathway written by:

  • Victoria Hill


competency [at] ebi.ac.uk

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How to use Jupyter Notebooks for your biomolecular research

Emma is starting a PhD to study the conformational dynamics of proteolytic enzymes using computational simulations. Following a master's project that introduced her to running simulations, Emma is now looking at how to use Jupyter Notebooks to facilitate her PhD work. Emma has a strong background in chemistry and biology, but a limited familiarity with coding and documentation, which will greatly enhance her learning.


Following this pathway, you can learn about Jupyter Notebooks, what they are, and how to use them effectively. The aim is to allow you to create your own notebooks ands give you an overview of what they can be used for.

General outcomes

After going through this learning pathway you should be able to:

  • Explain what Jupyter Notebooks are and the components of the Notebook
  • Create your own Notebook in any of the compatible programming languages
  • Use markdown to format the documentation
  • Convert the Notebook to any of the compatible formats
  • Follow good practice when creating your own notebook
  • Give examples of how Jupyter Notebooks can be useful in this field


There are no prerequisites for this learning pathway.

If you wish to follow the course on your local machine, a recent version of the Jupyter Notebook interface and its dependencies are required.