Bioinformatics

Restructured Text to S5 Presentation (lots of caffeine today so 2 posts in one day) The stub example presentation I'll be talking about is viewable as a presentation here (click on that page to advance the demo slides). There's a nice browser-based tool for presentations called S5 . In recent python docutils , there's a tool called rst2s5.py which converts restructured-text to an s5 presentation. However, it's not obvious how to get syntax highlighting for code blocks to work. So pygments , a python library that will highlight syntax for many programming languages comes with this file which they recommend you use as a starting point. That's what I did, and I've created a stub example project accessible via subversion: $ svn export http://bpgeo.googlecode.com/svn/trunk/rst2s5_template/ with a build script and a couple of example slides (and a nice theme). It's possible to change the theme by editing rst-directive.py (included in the source) and changing th...

I've been working with and on the Rtree python module. It's some cool work done by Howard Butler (hobu) (originally with Sean Gillies ) to make python bindings for the Spatial Index C++ library by Marios Hadjieleftheriou which provides various tree structures for efficient spatial searches in n-dimensions. Hobu has written a C API for that along with a new ctypes wrapper to that API which appears in Rtree 0.5 and greater. There is some cool ctypes stuff in there which I'm starting to understand. From the website: ctypes is a foreign function library for Python. It provides C compatible data types, and allows calling functions in DLLs or shared libraries. It can be used to wrap these libraries in pure Python. as a simple example of how ctypes works we can pretend there's no atan() in python's math module and access the one from libm in c like this: import ctypes libm = ctypes.CDLL('libm.so.6') # the following 2 lines correspond to the c signature: double...