Featured Posts

SciPy 2008 - Software & Tools STATUS: Day 1 - Thursday: Concluded. Day 2 - Friday: In progress. Astronomy: Enzo [ home ] yt (related to Enzo) [ home | scipy ] Books: Computational Modeling and Complexity Science...


An example of checking out a git tag using Qt 4.6.0... Clone the Qt repository: $ git clone git://gitorious.org/qt/qt.git Show available tags: $ git tag -l output: v4.5.1 v4.5.2 v4.5.3 v4.6.0 v4.6.0-beta1 v4.6.0-rc1 v4.6.0-tp1 Checkout v4.6.0: $...


Building 64-bit/32-bit Debug&Release Universal Build... See my directions on checking out Qt 4.6.0 from the git repository if you do not already have the source code. Launch a Terminal and cd to the source directory. Run configure w/ 64-bit & 32-bit...


  • Prev
  • Next


Posted on : 18-09-2007 | By : Brandon W. King | In : Bioinformatics, Python, Science, Software Development/Engineering

Tags: , , ,


As I said I would do, I am now in the progress of setting up and seeding the biology in python community site, which can be found at bio.scipy.org. Part of the goal, as set at the SciPy 2007 Biology Birds of a Feather (BoF) meeting (organized by Titus Brown), is to establish a community site where anyone using Python in the field of Biology can come together, communicate, share ideas, and share code.

As part of the programming guide, I posted my “Preparing to learn python guide“, in which, I mention the things about Python I wish I had known when I started learning Python. I am guessing it will be most useful to those who have programmed before in another language and are trying to learn Python.

Also, I posted a link to Software Carpentry in the programming guide. Thanks Greg for starting that project!

SciPy 2007 – Biology Birds of a Feather meeting

Posted on : 17-08-2007 | By : Brandon W. King | In : Bioinformatics, Python, Science, Software Development/Engineering

Tags: , , ,


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:

  1. Need to establish python/biology community, via website, biology-in-python mailing list, rss, blogs, etc.
  2. 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.