Computational Biology – Spring 2016

Botany 4550/5550 and Computer Science 5010

Instructor: Alex Buerkle
Class meetings: Enzi STEM Building (north of Lewis Street) Room 155, 3:10–5:00 p.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 2016, pdf)

Required course materials:

  1. Jones, O., R. Maillardet, and A. Robinson. 2014. Introduction to Scientific Programming and Simulation Using R. Second Edition.
    This book will be available from the UW and online bookstores, possibly including some used copies. The full book is also available for free through the UW Library (click View Full Text on the following page and follow the link). Please find access to the Jones book (2nd edition) in the first week of classes, so that you can complete the reading assignments. I believe there is value in owning a paper copy of the book.
  2. Additional materials will be distributed in class or linked from the course website.

Supplementary books:

  1. Peng, R. 2015. R Programming for Data Science. Leanpub.
  2. Grolemund, G. and H. Wickham. 2016. R for Data Science. O'Reilly. This book will be pulished in 2016, but meanwhile it is online for free.
  3. 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.
  4. 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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