Note: Last week, I submitted my review of Stephen R. Piccolo, Adam B. Lee, and Michael B. Frampton's paper, Tools and techniques for computational reproducibility. Soon after, Dan Katz wrote a blog post about notebooks, and in a comment I mentioned Piccolo's paper; and, after dropping a note to Dr …
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The IPython Notebook (or 'ipynb' for short) is one of the most exciting technologies for teaching and research that I've seen in recent years. It is a completely open source, well architected, and fairly stable system for scientific computing and data exploration.
I've now been using it for teaching for …
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As part of the 2012 Analyzing Next-Generation Sequencing Data course, I've been trying out ipython notebook for the tutorials.
In previous years, our tutorials all looked like this: Short read assembly with Velvet -- basically, reStructuredText files integrated with Sphinx. This had a lot of advantages, including Googleability and simplicity; but …
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