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Syllabus available

September 27, 2012 in Resources

Syllabus for the course is available as a Google Doc.  We will update if any of the order of lectures needs to change. The course will progress through Perl and then data driven problems.

The course will be organized with alternating 30 minute lectures and 30 minute workshops during the 2hr class period. The problem sets will be assigned in the middle of the week and are due the following week. Many of them you will have time to work during class and some will require out of class effort.

For the projects, you will be expected to work in teams of 3-4 people for the projects and the topics will be a blend of research topics you are interested in and the projects we have designed.

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Class begins Friday Sept 28

September 25, 2012 in Resources

We will kick of the class on Sept 28 with coverage of an introduction to UNIX. This will be possibly an intense course for some, learning a new language and the command line. There will be problem sets during class and for homework so you can practice and improve your skills.

Focus on learning how to make directories, move in and out of the directories. Running some simple programs to search for text (grep) and counting the number of lines in files (wc).

Check out a few of these tutorials in case that might help you get started

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by stajich

Reading Material

September 11, 2012 in Resources

There are several useful books and publications that can teach introduction to Perl and UNIX and programming.  I recommend the Unix and Perl to the Rescue! book recently published from Ian Korf and Keith Bradnam.  Also see their freely available primer on Unix and Perl For Biologists.

Also check out some other Perl tutorials.