Daily Life in an Ivory Basement

Course page at: http://ged.msu.edu/courses/2010-fall-cse-891/:

This course will introduce biologists to computational thinking, practical computational techniques, and research topics in computational evolution. The course will consist of three intensive hands-on 5-week modules: computational competence in UNIX; data mining and hypothesis generation using the Avida digital life platform and computational analysis of large-scale resequencing data from the Lenski Lab E. coli long-term evolution experiment.

This course is one of the two required entry courses for BEACON, an NSF-funded center for the study of Evolution in Action (see www.beacon.msu.edu).

The course will have 15-20 students from Michigan State (MSU), 2-3 from UW Seattle, 1-2 from U Idaho, and 2-3 from UT Austin (all partners in BEACON).

Briefly, we will be using EC2 and S3 to

1. demonstrate remote computer use and remote data analysis
2. compile, install, and run the Avida Digital Life system (see http://devolab.msu.edu and http://en.wikipedia.org/wiki/Avida)
3. do resequencing analysis of the Lenski Lab's E. coli long-term evolution experiment (http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment)

All of our materials will be made freely available under a Creative Commons license, as with my last EC2-using course (see: http://ivory.idyll.org/blog/jun-10/ngs-course-postmortem.html and http://ged.msu.edu/angus/).

We also hope to "export" this course outside of BEACON in the future.

--

I am open to a few people from outside the BEACON consortium attending the course via teleconf, although we may not grade your homework :). Let me know if this is of interest to you: ctb@msu.edu.

--titus

(Sigh, of 6 total semesters in which I've taught at MSU, I've taught 4 new courses. What am I thinking??)

My wife and I were talking with my USDA collaborator about some possible chicken research, and I asked about access to animals. His response? "Chickens are not a rate limiting factor."

Did you know that 1 million chickens are slaughtered per hour, on average, in the US? Wow.

--titus

So, I "organized" a Biology Birds of a Feather at SciPy 2007. This mainly consisted of posting about it and then trying to write stuff on a white board while keeping abreast of the conversation. About 15 people attended.

I didn't get everyone's name and in any case I don't want to pin good/bad opinion labels on people ;). So this will be anonymous reporting!

Notes from the meeting were posted by two different people, and they are available from the biology-in-Python archives.

First things first: People who are interested in discussion their work in Python and biology should subscribe to the biology-in-Python mailing list. (After a number of negative comments from people about the first two discussions on the list, I will endeavor to be a bit of a moderator, so don't take past discussion as indicative of future ;)

Second, the biggest decision to come out of the BoF was to make an effort to build up a community presence with a bit of a Web site as well as things like tutorials, code links, discussion, etc. Brandon King has very kindly agreed to provide a basic Web site, and we'll probably start off by hosting everything at scipy.org. More on that when it happens.

Third, and I feel like this is a big enough issue that it's worth saying loudly and clearly, only one person in the room was positive about BioPython. Everyone else either had a bad opinion of it ("ugly", "non-Pythonic") or had been warned off by people with bad opinions of it -- and surprisingly it was dominated by the former and not the latter. To me this indicates that these feelings about BioPython are widely shared. I don't know that it's worth going into detail on why -- and we didn't cover it in depth at the BoF -- but it needs to be mentioned.

The general consensus was that we needed to get the BioPython guys involved in the biology-in-python mailing list, though, whether or not we wanted to use "their" code!

Fourth, there was general agreement that Python could solve a lot of problems for biology (big surprise there!) and that it could do so by providing next-generation solutions rather than simply providing a slightly nicer BioPerl-style interface. What this precisely means will have to be left to the imagination, but one experienced BioPerl user said that the type of stuff being done with pygr represented a real break with what he'd seen from bioinformatics previously.

At the same time, we all still need to parse, we still need to talk to big databases, and we still need to break down large problems. This suggests that there's room for at least common interfaces, if not necessarily One True Package. I hope to push on this area myself.

One person made a push for One True Package, but I argued that we had no Linus/Guido/Larry in the community. Perhaps we could go with a ring system like PostgreSQL, which seems to have no BDFL but instead a small group of sensible people who contribute? This might be an option for pushing "BioPython 3k" ;).

We will be setting up facilities to pimp other people's code, as well as places to discuss it, refine it, and help people build and test it. Even more interestingly, there was common agreement that doing something like hosting published results (+ code/source data) was a great idea. This is a second area where I hope to really push.

Not sure what else there is to say. Overall it was a good, albeit occasionally heated, discussion, and it was really good to meet everyone. Hopefully we can follow up with a PyCon BoF/Sprint where we can get more the people together in one room!

--titus

To get people talking, I've created a "biology-in-python" mailing list. You can subscribe here: http://lists.idyll.org/listinfo/biology-in-python, and you can post to it at bip@lists.idyll.org once you're a member.

This list is a tool/package/library-agnostic list, for people who use Python to work in the biological sciences. Join us!

--titus

http://www.youtube.com/watch?v=u9dhO0iCLww

(Things start to heat up in the 4th minute.)