MEDC0106: Python Workshop

This repository contains material for the Bioinformatics in Applied Biomedical Science (MEDC0106) Python workshop.

Getting Started

To get started with the workshop please click here: .

Alternatively, if you prefer not to use Colab, click the following link: . Binder may take ~10 minutes to load, although there is nothing you will need to install on your local computer.

Workshop format

This workshop takes place over three sessions, consisting of a set of introductory notebooks and exercises to complete. You should complete the introductory notebooks in the current session before attempting the excersises, unless you are already comfortable with the material. The exercises contain a mix of easy to challenging tasks. Do not worry if you struggle to complete some exercises, we will go over them at the begining of the next session.

• Session 1 (Introduction to Python)

  1. (01) Introduction to Python
  2. (02) Functions
  3. (03) Modules and packages
  4. (04) Exercises

• Session 2 (Bioinformatics with BioPython)

  1. (05) Handling sequences with Biopython
  2. (06) Exercises
  3. (07) Handling protein data with Biopython (supplementary material)
  4. (08) Supplementary exercises

• Session 3 (Introduction to Data Analysis)

  1. (09) Pandas
  2. (10) Exercises
  3. (11) NumPy (supplementary material)
  4. (12) Predictive modelling (supplementary material)
  5. (13) Supplementary exercises

By the end of these sessions you should feel more confident about programming with Python and understand the application of programming and Python to specific domains. Hopefully you will feel encouraged to learn more and use Python in your research or future career.

All the material in these sessions is freely available if you wish to come back to it at a later date to refresh your knowledge.

Contact

Please contact us if you have questions or suggestions:

• Students please use the UCL Moodle module discussion forum.
• Questions regarding bugs or incorrect information please open an issue or pull request

License

This work is licensed under the Attribution 4.0 International (CC BY 4.0). To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

Acknowledgments

External resources

Python packages

• Bioinformatics:

  • biopython

• Data science:

  • pandas, scikit-learn, scipy, numpy,

• Data visualisation:

  • matplotlib, seaborn

If we are using your resource and forgot to add it here, please contact us so that we can rectify this, thank you!

Authors

• Oliver Scott
• Mateusz Kaczyński