Category: Useful Links

Useful tools and resources submitted by Bio-IT community members

Python Koans

An interactive tutorial for learning Python by making tests pass. A port of Edgecase’s “Ruby Koans”. Apart from learning Python, it is a good way to get a taste of Test-Driven Development.

display git branch and status in shell prompt

When coming back to a project after a bit of time away, I used to always lose track of which branch I was working on. Now I have the branch name displayed automatically in my shell PS1, as well as a colour-coded indication of the current repo status, to prevent me from making a bunch of changes and then realising I’m working on the wrong branch!

Brandon Rhodes – Pandas from the Ground Up

A great video tutorial introducing pandas – the data analysis library for Python, not the endangered Asian bear species. Brandon is an outstanding instructor, and the session starts with the basics of data handling, building up to the more complex and powerful applications of the library to data handling, exploration, analysis, and visualisation.


A collection of EMBL utility scripts. Includes scripts to simplify cluster interaction, job submission, file-sharing and local use of docker.


A convenient script to automatically generate iTol tree annotation files from spreadsheets.