Unix & Perl Primer for Biologists

We have written a basic introductory course for biologists to learn the essential aspects of the Perl programming language. This started as a course for grad students at UC Davis, and we then ran it as a one week intensive course for anyone on campus who was interested (sponsored by the UC Davis Genome Center). The feedback from these courses was very positive and so we have decided that we should make it available to anyone who is interested.

The course is very much aimed at people with no prior experience in either programming or Unix. It is increasingly common that biologists have to deal with vast amounts of in silico data as part of their research, often in the form of many large text files that are the output from research equipment or computer programs. If you complete this course you will hopefully learn enough to be able to write programs to interrogate, refine, and process such data.

Although this course was initially developed for biologists, we feel that it is suitable for anyone in the life sciences...you don't need to have experience with bioinformatics to use this material. In fact, the biological examples are relatively simple and so we also feel that this course would be useful for anyone who wants to learn the basics of Unix and Perl, no matter what your background.

Update: 2015-06-24.The Unix material in the Primer was originaly written for people to learn on a Mac (the teaching workshops we used had Macs). Because so much of modern bioiformatics work happens on Linux, we have also made a smaller version of just the command-line material that is suitable for people to use if they are using Ubuntu Linux.

To start the course, you first need to download the course material (a set of test files and directories that relates to the documentation). You can either download the entire course (files + documentation, 38 MB compressed) or just the documentation.

Unix and Perl Primer for Biologists - v3.1.2

last updated: October 2016

If you download the entire course and uncompress the resulting zip file, then this should create a directory called 'Unix_and_Perl_course'. Inside this directory will be a 'Documentation' folder which has all three versions of the documentation (text, HTML, and PDF). The documentation is mostly aimed to be read from start to finish, though if you are comfortable with Unix you can jump to the sections on Perl.

Command-line Linux Bootcamp - v1.01

last updated: 2015-06-24

We plan to make occasional updates to the course (to fix typos, make clarifications, and occasionally add/remove sections based on user feedback). The latest version of the course will always be available on this page. Our course is also supported by dedicated Google Group where you should go to if you have any questions or comments about any of the above resources:

Subscribe to Rescued by Code Email: Visit this group

We hope you enjoy this course and find it useful for your work. It would be great to get feedback from people in order to keep on making this course better. Overall, we hope that more biologists will try their hand at programming, and maybe even discover that they actually like it!

Keith Bradnam & Ian Korf