Slightly related video presentations <i>Curing Cancer with Perl</i> by David Dooling of the Washington University Genome Center:<p>* part 1 - <a href="http://blip.tv/file/1997719/" rel="nofollow">http://blip.tv/file/1997719/</a><p>* part 2 - <a href="http://blip.tv/file/1998152" rel="nofollow">http://blip.tv/file/1998152</a><p>* part 3 - <a href="http://blip.tv/file/2000983/" rel="nofollow">http://blip.tv/file/2000983/</a>
Many moons ago, I worked on an FPGA-based platform that was among several research projects targeted at the Genome Project. The general idea was to offload BLAST-style sequence alignment to purpose-compiled FPGAs, such that sequencing across the entire dataset could be performed in order of magnitude less time. It really wasn't all that complex (I just implemented Smith-Waterman directly, as a demonstration), only intended to perform fuzzy matches at Gbps speeds to winnow the working dataset down to a size more palatable to a desktop workstation.<p>My understanding is that all these projects (mine included) were cast adrift when the funding for them evaporated in the post-9/11 climate. In the intervening years, I was aware that Perl was being picked rapidly at the Genomics labs in the nearby university hospital (i.e. since we never delivered them the FPGA platform), and I'm happy to read Perl has risen to fill this niche.
The part that made me smile was when he said "In all, between one and TERAbytes of data would generated!!!!" [exaggerated emphasis mine]<p>I've got 3-4 terabytes of storage within a dozen feet of me as I type this; it really drives home the pace of change in computing.
In the same vein, though sometimes with less detail:<p><a href="http://oreilly.com/pub/a/oreilly/perl/news/success_stories.html" rel="nofollow">http://oreilly.com/pub/a/oreilly/perl/news/success_stories.h...</a><p>O'Reilly also published some of these in at least two folded/stapled pamphlets that were handed out for free e.g. at conferences. I recall a finance-centered application where the Perl prototype far outperformed the subsequent implementation and ended up taking over the production role.<p>It looks like maintenance at that URL stopped in about 2004, but in googling "perl success stories" I saw a few more recent articles that might qualify.
Alternate title: How it happened to be Perl instead of any other just as capable language that saved the Human Genome Project (in the land of Dangling Participles and Allusion Errors).
In addition to Lincoln's thoughts I think one of the main reasons bioinformaticians are attracted to Perl is because it is forgiving. Biological data is often incomplete, fields can be missing, or a field that is expected to be present once occurs several times (because, for example, an experiment was run in duplicate), or the data was entered by hand and doesn't quite fit the expected format. Perl doesn't particularly mind if a value is empty or contains odd characters. Regular expressions can be written to pick up and correct a variety of common errors in data entry. Of course this flexibility can be also be a curse.