donkang75/pdftk-brew
http://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/
Quantitative Insights Into Microbial Ecology (QIIME): Official repository for software and unit tests
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http://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/
Basic functions for clustering data: k-means, dp-means, etc.
IPython in-depth Tutorial, first presented at PyCon 2012
Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.