Open writing projects/Sage and cython a brief introduction

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This is a quick introduction to [Sage], a powerful new computational platform that builds on the strengths of Python. This article was directly inspired by Julius B. Lucks' ["Python: All A Scientist Needs"]; I recommend reading it first as it explains some of the attractions of Python and biopython.

Sage () is a free and open-source project for computation of all sorts that uses Python as its primary language and "glue". One of the goals of Sage is to provide a viable free and open-source alternative to Matlab, Maple, and Mathematica. Sage unifies a great deal of open-source mathematical and statistical software; it includes biopython as an optional package and the statistics language R by default.

Sage notebook interface

(TODO: notebook interface screenshots, different computers, good 2-d graphics)


Sage initially used an alternative to SWIG (described in Julius's article) called Pyrex to compile Python code to C when performance concerns demanded it. Because they needed to extend Pyrex in various ways, they created a friendly fork of Pyrex called "Cython". I believe it is fair to say that Cython is the easiest way to create C code in Python.

(TODO: example of Cython usage)