CSE 891, Computational Science for Evolutionary Biologists

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.


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

Legacy Comments

Posted by Grig Gheorghiu on 2010-08-24 at 13:22.

Awesome, Titus! Let me know if you need an expensive consultant who
knows how to scale your systems in the cloud and how to keep them up
and running 24x7 ;-)

Posted by Titus Brown on 2010-08-24 at 18:09.

Sorry, Grig, that appears to be ... me.  Except for the 24x7.  And
"expensive".  Alas.

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