I’ve recently become a big fan of IPython Notebook – I use it to keep track of command-line analyses and the thoughts/rationale/questions I have as I’m running them. But Greg Caporaso has another good use – an interactive textbook for teaching bioinformatics. In this blog post, he describes in detail how the textbook came about and how to get a copy for yourself.
Because the IPython Notebooks are interactive, students can (and actually do!) work with the notebooks in class and at home to experiment with the code, which drives active learning of the concepts. For example, one student this semester told us about his experiments with Smith-Waterman gap open penalties of 1000, and about what happens when you make the gap penalties negative (so they effectively become gap rewards; hint: you get a lot of gaps, but if want to see for yourself, install the notebook and try it out).