Please note: this page is currently a stub with minimal information!!

This is the page for Bio720 (2016), a practical introduction to fundamental computational skills for biologists.

Weekly, on Mondays 6 - 8 PM, MDCL 3017

For this class we are not assuming students have background in programming/scripting, nor in bioinformatics. We do assume that students have a working knowledge of basic molecular biology and genetics and have basic familiarity with using computers.

A laptop with internet access and the ability to install several programs (in particular, R, Python and a shell emulator in not using a Mac (OS X) or linux.

The primary goal of this course it to provide graduate students an opportunity to develop the basic, fundamental computational skills necessary to go on and (in the future) develop the appropriate (and more advanced) skills for bioinformatics, genomics, etc.

1. Introduction to UNIX and the command line. (Brian)

2. Introduction to basic shell commands, logging onto remote systems

3. Fundamentals of programming using R(Ian). Link to R portal for class

4. Fundamentals of programming in R.

5. How to avoid repetive strain injury while programming. Control flow in R. Using the apply family of functions in R. Simple simulations.

6. Working with data in R. Getting data in. Data munging (subsetting, merging, cleaning). Working with strings in R.

7. Basics of plotting in R. Other topics TBD.

8. Fundamentals of program using python. (Brian).

Dr. Brian Golding

Dr. Ian Dworkin

You are responsible for ordering your own copies of these books. Both are excellent, but we are only highly recommending the first book (PCfB) for this class.

Practical Computing for Biologists. This book provides a nice, gentle introduction to the basic computational skills all biologists should have. In particular, with introduction to using the UNIX command line, shell scripting, basic python programming, regular expressions, working on remote machines and a few other topics. The book is written to be agnostic with respect to discipline (i.e. it is not a bioinformatics book per se), but does a great job of being both very accessible and immediately useful. It seems a bit pricy on Amazon.ca, but look around for used copies (it is 4 years old). If you plan to continue in computational research, this is a fantastic resource.

Bioinformatics Data Skills. HIGHLY RECOMMENDED This is a new book, but which fills an important gap in that is oriented towards the day to day skills for anyone working in the fields of genomics and bioinformatics. In addition to covering the basic UNIX skills (and why we use UNIX in bioinformatics and genomics), it also covers subjects like overviews of the essential file types (.fasta, .fastq, .gff, etc) that are ubiquitous in the field. There is also a nice, but brief introduction to the essentials of R, using bioconductor and in particular range data, and two important chapters on how to organizing (and maximize reproducibility) of computational projects. Currently this is ~52$ on Amazon. It is available as an e-book as well from the publisher.

For Brian's section. This will have pertinent links to Brian's section of the course.

R tutorial screencasts. A link to the playlist for screencasts I have put together for the R tutorials. I will be adding more as the semester progresses.