Russell's Blog

New. Improved. Stays crunchy in milk.

Sneak Pique

Posted by Russell on July 13, 2011 at 3:41 a.m.
I'm about to release a new piece of Open Source software; it's a fast, fully automated and very accurate analysis package for doing ChIP-seq with bacteria and archaea. I'm doing my best to avoid the sundry annoyances of of bioinformatics software; it uses standard, widely used file formats, it generates error messages that might actually help the user figure out what's wrong, and I've designed the internals to be easily hackable.

I have two problems, though.

Most of the people who will be interested in using this software are microbiologists and systems biologists, not computer people. At the moment, the software is a python package that depends on scipy, numpy and pysam. I used setuptools, wrote tests with nose, and hosted it on github. If I were going to distribute it to experienced Linux users, it's basically done. However, installing these dependencies on Windows and MacOS is a showstopper for most people -- scipy in particular. So, how would you suggest distributing it to MacOS and Windows users?

The second problem is... it's kind of ugly. I wrote the GUI in Tk, which is not particularly great in the looks department. Should I bother creating native tooklkit GUIs? Would that make people significantly more comfortable? Or would it be a waste of time?

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