Computational Biology – Spring 2015

Botany 4550/5550 and Computer Science 5010

Instructor: Alex Buerkle
Class meetings: Visual Arts Building (22nd and Willett) Room 229, 10–11:50 a.m. on Monday and Wednesday

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

Course syllabus (spring 2015, pdf)

Required course materials:

  1. Jones, O., R. Maillardet, and A. Robinson. 2014. Introduction to Scientific Programming and Simulation Using R. Second Edition.
  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, possibly including some used copies. Of course, they are also available from bookstores online, potentially at a lower price. Please purchase these editions of the books and have the Jones book in the first week of classes, so that you can complete the reading assignment for the second class. I believe there is value in owning paper copies of these books.

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