Rosalind - a platform for studying bioinformatics

Widely known sites for solving Olympiad programming problems, such as, for example, TopCoder and Codeforces , as well as collections of mathematical puzzle problems, for example, Project Euler . Over the past year, there has been a boom in online education: Coursera and Udacity startups have emerged, offering online courses from top US universities ... but for those who want to study bioinformatics, there is nothing yet.

Rosalind - a project being developed in St. Petersburg and the University of California, San Diego since May 2012, just fills this niche. It is a platform for learning bioinformatics through problem solving , free and open.
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All training is built around the tasks that make up the main content of the site:



Each task contains a biological justification and a rigorous formulation sufficient for a formal solution. For example, in the twelfth task, it is necessary to assemble the genome from small DNA fragments. It also tells what sequencing is and why it is needed:



The user can solve problems in any programming language and even on a piece of paper, but after downloading a test dataset from the site, he will have only five minutes to process it. If the answer is incorrect, nothing terrible, you can try an unlimited number of times, but at the same time it will be generated every time.

Not all tasks can be solved immediately, or rather, immediately only the first can be solved. Tasks are lined up in a dependency graph, so that the learning process is more meaningful and the material is mastered in order. But if you are more interested in, for example, only the assembly of genomes (genome assembly), or alignment (sequence alignment), or computational proteomics (computational proteomics), then you can delve in a certain direction in the dependency graph and not solve other problems. Thus, the knowledge gained will be deeper in the chosen topic.



And, of course, the site has profiles, as well as the beginnings of game mechanics: levels and badges.





I hope Rosalind will be useful to anyone who wants to plunge into this most interesting world of bioinformatics or just learn something new.

The project is actively developing, so we are happy to hear any criticism. In particular, on August 26 in St. Petersburg an international conference RECOMB Bioinformatics Education will be held, one of the main topics of which will be Rosalind.

The system already supports the re-use of tasks in its courses, the so-called “professorial accounts”, so we will introduce Rosalind into the UCSD and Harvey Mudd educational process in spring 2013. For Russia, this is not so much needed because there are no special programs on bioinformatics. But with Rosalind it becomes easier - maybe it will appear?

We are constantly adding new tasks: now there are 42 of them and about the same are in the drafts. Recently, it became possible to accept and control user ideas for tasks, so that the bioinformatics community can participate in the content creation process.

The plans are videotape of lectures on bioinformatics in UCSD and the creation of several online courses based on this material.

PS The project is named after Rosalind Franklin , whose research led Watson and Crick to the discovery of the spiral structure of DNA. Rosalind died of cancer four years before being awarded the Nobel Prize for this discovery, at 37, because she had a hereditary predisposition and worked a lot with radiation.