During the Biology birds of a feather meeting at
SciPy 2007, which was organized by Titus Brown, we meet to discuss were those of us using Python for biology/bioinformatics should work together as a community. Two interesting thoughts came up:
- Need to establish python/biology community, via website, biology-in-python mailing list, rss, blogs, etc.
- Having a core set of "interfaces" for handling basic bioinformatics objects would allow independent projects to share these basic objects. I am sure others will describe this better and in more detail in the near future.
I personally believe that even if we only accomplish the first item, it would significantly help the bioinformatics community. I do hope the 2nd is accomplished as well.
What I see is that most people who are new to the python bioinformatics community end up finding
BioPython. The only problem is that many people doing bioinformatics with Python who choose not to use BioPython end up doing there own thing an not communicating with the community. The idea here is to make a new python/biology community site were we can communicate, share code, share ideas, etc. In other words support the community as a whole rather than just having communities for individual projects.
I agreed to setup this initial site and seed it information, bioinformatics python packages by category, a place holder for cookbooks, advice for testing and software engineering (referencing
Greg Wilsion's Software Carpentry material, etc.). I would like to thank
Enthought as they have agreed to host the website. I will add the more information on the community site as it is being setup. We'll see how it goes.
Also, check out
Titus Brown's Birds of a Feather post.
Labels: bioinformatics, biology, python, scipy
