Materials for the course run by the Graduate School of Life Sciences, University of Cambridge.

• Course website: http://mrccsc.github.io/training.html
• Booking website: http://www.training.cam.ac.uk/

If you wish to run the course on your personal computer, here are the steps to follow to get up and running.

git clone https://github.com/mrccsc/python-intro/python-intro.git
cd python-intro

Install Python 2 by downloading the latest version from https://www.python.org/.

Create first a virtual environment using the venv library. Update pip if needed, install jupyter and RISE to get a slideshow extension into jupyter.

Note A virtual environment is a Python environment such that the Python interpreter, libraries and scripts installed into it are isolated from those installed in other virtual environments.

python -m venv venv
# activate your virtual environment
source venv/bin/activate
# update pip if needed
pip install --upgrade pip
# install jupyter
pip install jupyter

# slideshow extension
pip install rise
jupyter-nbextension install rise --py --sys-prefix
jupyter nbextension enable rise --py --sys-prefix

# biopython
pip install biopython

On mac OSX you may need to run this command to accept the XCode license, before installing biopython:

sudo xcodebuild -license

Go to the directory where you've cloned this repository, activate your virtual environment and run jupyter.

Your web browser should automatically open with this url http://localhost:8888/tree where you see the directory tree of the course with all the jupyter notebooks.

cd python-intro
source venv/bin/activate
jupyter notebook

To shutdown jupyter, type ctrl-C into the terminal you've ran jupyter notebook, answer y and press enter.

You may wish to deactivate the virtual environment, by entering into the terminal:

deactivate

.