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README.md

An introduction to solving biological problems with Python - course materials

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

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

Clone this github project

git clone https://github.com/pycam/python-basic.git
cd python-basic

Dependencies

Install Python 3 by downloading the latest version from https://www.python.org/.

Python 2.x is legacy, Python 3.x is the present and future of the language.

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.

python3 -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

Usage

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-basic
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

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Python3 teaching materials for basic introduction to Python (2 days)

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