Bioinformatics, biocomputing and Perl - an introduction to bioinformatics computing skills and practice

Bioinformatics is a tool biologists need to make sense of new types of methods involving large quantities of data. The thrust to develop bioinformatics comes from biologists, not from computer scientists. Take away bioinformatics and computer scientists will start looking elsewhere for ways of applying and developing string or graph theory, or whatever they are working on at the time. The biologists, on the other hand, would be in deep trouble. It is therefore surprising that so few biologist are fluent in bioinformatics. Bioinformatics ought to be taught as part of the curriculum to all biologists exactly in the same way as statistics, biochemistry, anatomy or population genetics. There will be some who will hate it and do their utmost to find a branch of biology to hide from it (it will be hard), but a large majority will decide to make the effort and will find it useful. Then, of course, there are those who cannot have enough of it – and they will be joining the ranks of us bioinformaticians. The new book by Michael Moorhouse and Paul Barry is one of the better answers to this common problem of what to teach to biologists about bioinformatics. The premise of the book is that to do bioinformatics you have to learn to program. In that, it differs from – and builds on – the hugely successful book by Jean-Michael Claverie and Cedric Notredam ‘Bioinformatics for Dummies’, which uses existing programs and web sites to do all the work. This is of course a useful approach in the beginning as makes it easier to start learning the methods and concepts of bioinformatics, but nevertheless, if you want to start using bioinformatics to something new, you will just have to start programming. The programming in this context does not have to be anything exceedingly complicated. A dabbling student of bioinformatics needs mostly to automate the management of textual data, which includes storing and displaying it without graphical user interfaces. In ‘Bioinformatics, Biocomputing and Perl’ the tool is perl, the programming language most closely resembling natural ones in its messiness and unabashed use of shortcuts. Although no one uses perl to teach programming to computer scientists, perl is the most commonly used language in bioinformatics. This must have something to do with the historical nature of biological sciences, which leads to proliferation of exceptions at the expense of rules. Moorhouse and Barry teach the basics of perl before moving to more biologically oriented topics. In that they differ from older books by James Tisdall (‘Beginning Perl for Bioinformatics’ and ‘Mastering Perl for Bioinformatics’), who gives a very thorough coverage of perl programming language using bioinformatics examples. The Moorhouse and Barry book is less exhaustive, but no less educational. The authors do not cover advanced topics of perl programming, such as objects, or the intricacies of biological sequence data management, nor do they try to give all the details of every topic discussed in the book. The subtitle of the book is ‘An Introduction to Bioinformatics Computing Skills and