Introduction to Python for Bioinformatics

An introductory workshop to teach basic Python with a bioinformatics flavour.

This version was delivered at BioinfoSummer 2017.

Notebooks and associated data files are in notebooks, static HTML exported version are in docs.

There are currently two main modules:

• A basic introduction to the Python language (01_Intro).
• Running BLAST and parsing output, applied to a protein family (02_Evasins).

Running the notebooks

Zero installation method: run the notebooks is to use mybinder.org

Alternatively, install Jupyter, run jupyter notebook in the repository directory.

You can run also run a Dockerized version locally like:

pip install jupyter-repo2docker
jupyter-repo2docker https://github.com/MonashBioinformaticsPlatform/intro-to-python-for-bioinformatics

Building the static course notes

To export all notebooks to HTML:

./build.sh

License

Creative Commons Attribution 4.0 International (CC BY 4.0) License., expect for images and trademarks that are copyright of their respective owners.