Bioinformatics Open Source Conference 2010 (and a poll)

The 11th Annual Bioinformatics Open Source Conference (BOSC) 2010 is coming up in Boston, July 9-10 2010. The BOSC meetings are a great get-together of a community of programmers who are like-minded in their advocacy of open source code for science, and specifically for bioinformatics. The whole thing is run by volunteers who take a lot of time and effort to bring a top-notch meeting every year, so a big thanks to this year’s organizing committee!

If you are reading this, and you are in Boston on those dates, consider showing up, it is a great experience. There will also be a codefest on the two days before the meeting. This year’s topic is cloud computing for bioinformatics. If you like using AWS for bioinformatics or if you want to learn more, this is your chance. Amazon have provided a grant towards this codefest. (Thanks!) Biopython, Bioperl, Biojava and Bioruby developers will all be there, tailoring code to the cloud.

Which brings me to the latest poll: if you are a bioinformatics programmer, which of the Bio* packages  are you using in your programming, if any? If more than one, check the one you use most frequently. Poll answers on the right. As with all Internet polls, you must be crazy if you take it at all seriously.

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3 Responses to “Bioinformatics Open Source Conference 2010 (and a poll)”

  1. Kevin says:

    The survey question in the text and in the poll are different. One asks which you use, the other asks which is your favorite.

    I do a lot of boinformatics programming, but I don’t use any of the “Bio*” projects, as they never seem to have much that is of use to me, and what little is useful to me is easier for me to code myself than to install any Bio* project and deal with its idiosyncracies.

  2. gsgs says:

    everything self written, Basic or C
    mainly influenza

  3. Iddo says:

    Yes, you’re right that the questions differ, in an ideal world we could all use what we like, but we usually can’t. I actually meant “use”, but I cannot change the poll header now for technical reasons.

    As in all community developments, the Bio* projects have idiosyncrasies, since contributers usually put in code that they have pre-written for their own use, and then tweak & polish to fit the project they are working with. That being said, I used quite a few Biopython modules (I am not referring to those I have contributed) and some Bioperl and Biojava modules too. I must say I would not like to code a FASTQ or a BLASTXML parser myself, and I am grateful for those who did this work. Full disclosure: I am a semi-retired Biopython developer.