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5. Creating, editing and running Jupyter Notebooks

5.1. Creating Notebooks

After creating or deciding on a conda environment containing the Jupyter Kernel(s) you want to execute Notebook(s) with plus the packages want to import within Notebook(s) you can now create a Notebook or open an existing one.

To create a Notebook:

  1. Return to the Jupyter Home browser tab;

  2. Click the Files Jupyter tab;

  3. Browse to the directory where you want to create your new Notebook;

  4. Click New then (beneath Notebooks) the name of the Kernel/environment you wish to use (e.g. rdkit-sharc) - see Selecting a Jupyter Kernel for more information on selecting kernels.

    ../../_images/sharc-jh-new-nb-w-kernel.png
  5. A blank Notebook should appear in a new browser tab.

Your Notebook will have access to the packages installed in the selected environment.

5.2. Opening existing Notebooks

Alternatively you can click on an existing Notebook (.ipynb) file in Jupyter’s file browser to open it.

../../_images/sharc-jh-example-nb.png

5.3. Selecting a Jupyter Kernel

After opening a Notebook, you can change the Kernel used for executing code cells by clicking Kernel -> Select Kernel from the menu bar to bring up a list of availble Kernels.

Some of the Kernels in this list correspond to conda environments created by the system administrator; others were automatically found by a Jupyter plug-in that searches for valid Jupyter Kernels in all conda environments visible to you.

It is recommended that you create your own environments (typically one per project/workflow).

Do not use the jupyterhub or jupyterhub-dev environments. You are advised not to use the anaconda Kernels/environments either as these are read-only to most users and users have little control over if/when they are updated and what packages they contain.

5.4. Using Jupyter Notebooks

The basics of using Jupyter Notebooks to create self-describing, runable workflow documents are explained in the Jupyter Notebook official documentation.