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.
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.
Update: May 2012 - We have recently undertaken a big tidying up of the documentation, fixing many small typos but more importantly clarifying the text in many places and adding a few more examples (and jokes)! We've also tried to add more links to relevant pages at perldoc.perl.org and Wikipedia. The documentation has been primarily written in Markdown format.
last updated: October 2012
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.
We plan to make regular 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 the course:
Subscribe to Unix and Perl for Biologists
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
Mar 16, 2015: Danielle Lemay is interviewed by the UC Davis News team about the new publication by herself, Kristen Beck (lead author), Ian Korf and others that describes new milk proteomes for human and macaque.
Apr 22, 2013: The Assemblathon 2 paper has won the 2013 BioMed Central Open Data award
Dec 10, 2013: A short piece in the UC Davis Alumni Magazine that discusses the new Genomics undergraduate major that Ian Korf co-developed.
Nov 26, 2013: Ian Korf writes a News & Views piece for Nature Methods about two new comparisons of programs that work with RNA-seq data
Sep 24, 2013: An article on genome assembly by My Science Work includes an interview with Keith Bradnam about Assemblathon 2 & 3.
Aug 12, 2013: Biome Magazine includes a piece that features Ian Korf discussing a novel platform for bioinformatics education (with Daniel Barker)
For questions or comments about the website, please e-mail:
korflab AT ucdavis DOT edu
Contact information for specific members of our lab can be found on their personal pages.