The Oxford Computational Biochemistry Python Tutorial is a series of notebooks which aim to teach the basics of python to new users. It assumes no prior knowledge of python or any other programming languages.
The tutorial is broken down into 12 sections which progressively introduce various python concepts. We recommend that these be followed in order, however those already acquainted with python may wish to skip ahead to some of the later topics.
Please see the setup instructions to get started with the tutorial (installation, etc...). Note: the instructions included here are tailored for attendees of the Oxford Computational Biochemistry workshop.
If you are attending the Oxford Computational Biochemistry workshop, please follow the "getting started" instructions above. You will have been instructed to install the Anaconda python distribution in the main setup instructions.
This tutorial uses several libraries which are not provided in standard python installations. Whilst there are many means by which to install and manage python libraries, we recommend using the conda manager which is provided in the miniconda python distributions.
Python 3.6 or higher is required for this workshop. Note that Python 2.x reached End of Life (EOL) the 1st of January 2020. We advise that no new Python code be written in Python 2.x.
Default conda channel:
conda-forge channel:
The ideal way to participate in this tutorial is by setting up your own local conda environment (see the setup instructions). However, we appreciate that in some cases this may not be feasible.
Should this be the case, it is possible to follow most of this tutorial online via the use of binder.
Note: Binder is a free community-run service, load times can be slow. Patience may be required. Additionally some aspects of the tutorial, such as protein visualisation may not work as intended.
To use binder:
- Click on the following link.
- This will start you in the python tutorial folder.
- Click on the section you want to do and the relevant
.ipynbfile to start the notebook.
This tutorial was first created in 2017 as part of the Oxford Wellcome Trust course. It is the product of the work of several authors who have contributed to it over the years. Please see CONTRIBUTORS.md for a full list of acknowledgements. As the tutorial was not originally tracked on github, our apologies if any authors have been missed from this list.
If you happen to contribute to the python tutorial, please add yourself to this list.