Computational Biology – Spring 2014

Botany 4550/5550 and Computer Science 5010

Instructor: Alex Buerkle
Class meetings: Earth Sciences Building 1004, 10-11:50 a.m. on Tuesday and Thursday

During the semester, dynamic content for the course will be available on the Course wiki (restricted to class participants).

Course syllabus (spring 2014, pdf)

Required course materials:

  1. W. J. Braun and D. Murdoch. 2007. A First Course in Statistical Programming with R. Cambridge University Press. (FCSPR)
  2. R. L. Schwartz and T. Christiansen. 2011. Learning Perl. 6th edition. O'Reilly and Associates. (LP)
  3. Additional materials will be distributed in class or linked from the course website.

Both books will be available from the bookstore, including some used copies. Of course, they are also available online, potentially at a lower price. Please purchase these editions of the books and have the Braun and Murdoch book in the first week of classes, so that you can complete the reading assignment for Thursday.

Supplementary books:

  1. Bolker, B. 2008. Ecological Models and Data in R. Princeton University Press. I will provide copies of sections of this book in class, but you might want to have a copy of the book for yourself. It is generally useful for analysis, not just for ecological models and data.
  2. Haddock, S. and C. Dunn. 2010. Practical Computing for Biologists. Sinauer Associates. This book has substantial material on UNIX and general computing, as well as an introduction to Python. If it described Perl instead, I would probably use it for this course, as it would be a good one-stop reference for a lot of things.

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UC-Berkeley Stat Labs links:

Statistics and probability