Biology 720

This class will provide students with a brief introduction to three of the most important tools used in bioinformatics research. The class will consist of weekly meetings on Monday evenings for two hours 6-8pm. Classes will be held in MDCL 3017 and will begin with an organizational meeting Tues evening Sept 6 at 6pm in MDCL 3017.

Classes will be equally divided between introducing UNIX and command line interfaces; the R statistical environment; and the python programming language. Each week problem sets will be given to provide students with necessary practice on the class material. The problems will be related to common bioinformatics tasks where appropriate.

We recommend, but do not require, students buy “Practical Computing for Biologists”, by C. Dunn & S.Haddock, Sinauer Publ.

Contact Dr. Brian Golding (Golding@McMaster.CA, LSB 533) for more information.

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For the first class please ensure that you have R, R-studio, and Python installed on your laptops.
R - https://www.r-project.org/
R-studio - https://www.rstudio.com
Python - https://www.python.org

For windows users ensure you have installed mobaxterm,
http://mobaxterm.mobatek.net/

You can preview,
https://www.youtube.com/watch?v=id3DGvljhT4

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Week 1: Some commands
Week 2: Some utilities
Week 3: Some regexp
Week 3: Some shell stuffing
Week 8: Some Python #1
Week 9: Some Python #2
Week 10: Some Python #3
Week 11: Some Python #4


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Week 1: Some Exercises
Week 2: Some Exercises
Week 3: Some Exercises
Week 8: Some Python Exercises
Week 9: Some Python Exercises
Week 10: Some Python Exercises