“Programming for Evolutionary Biology” course – suggestions for the applicants that have not been accepted

The selection phase for the participants to the “Programming for Evolutionary Biology” course in Leipzig has finished. Congratulations to all the applicants accepted!

I am very sorry for the people who have not been accepted, but we have received a lot more applications than the places available, and the selection process has had to be very strict. As Katja Nowick, the organizer of the course, said, this is a sign of how much introductory courses to programming for researchers are needed. Hopefully we will be able to repeat the course or other people will organize similar courses in the future.

In case you have not been selected, I would like to give you a few suggestions on how to start to learn Unix/R/Perl skills.

– Are there any other courses for learn Programming oriented to biologists?

I think that the “Unix and Perl Primer for Biologists” course is a very good resource for researchers wishing to learn the basics of the Bash shell and Perl. Their material is easy to read, and explains everything step by step. The authors also wrote a book (which I didn’t read yet), and released some good material on this website.

Another good course that should not be missed is “Software Carpentry for Biologists“. This course covers a wider range of topics than the other, and, more important, dedicates a good effort on explaining what should be the “good practices” for a bioinformatician. Maybe the contents are a bit more advanced than the “Unix and Perl Primer”, although there are classes on the shell. In any case, once you feel a bit confident on your programming skills, you should definitely read all the materials on Software Carpentry, and make sure you have understood everything before starting a research project. There is also an “Advanced Software Carpentry for Bioinformaticians“, by Titus Brown, focused on Python programming.

– Are there other courses on Programming for Evolutionary Biologists, or on Next Generation Sequencing?

Thanks to reddit/bioinformatics, I have found two other courses similar to ours: a “Workshop on Molecular Evolution” from the University of Texas, and a “Computational molecular evolution” Course from EMBO in Greece. Both these courses seem very valid, although I don’t have any direct experience with them.

A good course on Next Generation Sequence is the Angus course, by Titus Brown. Titus Brown is a skilled bioinformatician and programmer, who developed, among other things, libraries such as Pygr and parts of nosetests. The website of the course is full of good documentation and examples, it should be a good place to start.

– where can I get help?

Internet is a good place where to ask for help on programming related questions. The StackOverflow network is the most active community for anything related to Programming and Unix in general. For next generation sequencing analysis, a good place is SeqAnswers. And, for the general bioinformatics question, biostar is of course a nice resource 🙂


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