setup.md

Setup instructions for the Oxford Computational Biochemistry Python workshop

Contents

This workshop is delivered through a series of Jupyter notebooks which allow for interactive Python programming.

To run these the following instructions should be followed:

1. Download the workshop materials

In a terminal, close the workshop repository:

git clone https://github.com/IAlibay/oxcompbio-python.git

2. Create the conda environment

First navigate within your shell to inside the repository

cd oxcompbio-python

Then create the conda environment

conda env create --file=environment.yml

Once it's finished, activate the environment

conda activate OxPython

3. Activate Jupyter extensions

The workshop leverages the extended utility of several Jupyter nbextensions.

To install these, the followed should be run once (after having activated the conda environment):

jupyter contrib nbextension install --user
jupyter nbextension enable splitcell/splitcell
jupyter nbextension enable rubberband/main
jupyter nbextension enable exercise2/main
jupyter nbextension enable autosavetime/main
jupyter nbextension enable collapsible_headings/main
jupyter nbextension enable codefolding/main
jupyter nbextension enable limit_output/main
jupyter nbextension enable toc2/main

4. Start a jupyter notebook seession

Finally start a jupyter notebook session by typing the following in your shell.

jupyter notebook