How Perl Saved the Human Genome Project
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How Perl Saved the Human Genome Project
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Re: How Perl Saved the Human Genome Project
#2In the same vein, though sometimes with less detail:
http://oreilly.com/pub/a/oreilly/perl/news/success_stories.h...
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.
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.
Re: How Perl Saved the Human Genome Project
#3Slightly related video presentations Curing Cancer with Perl by David Dooling of the Washington University Genome Center:
* part 1 - http://blip.tv/file/1997719/
* part 2 - http://blip.tv/file/1998152
* part 3 - http://blip.tv/file/2000983/
Re: How Perl Saved the Human Genome Project
#4In the same vein, though sometimes with less detail: http://oreilly.com/pub/a/oreilly/perl/news/success_stories.h... 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. It looks like m…
iirc: O'Reilly stopped maintaining perl.com content around that time and finally handed the domain over to the perl foundation a few weeks ago…
Re: How Perl Saved the Human Genome Project
#5Alternate 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).
Re: How Perl Saved the Human Genome Project
#6In 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.
Re: How Perl Saved the Human Genome Project
#7Alternate 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).
Python, perl and ruby are roughly the same language. The differences between them are primarily cultural, rather than technical.
I suspect the reason perl flourished here was a combination of luck and the cultural fit. Culture here includes the newbie-friendly online help (e.g. perlmonks), the ease of "publish and re-use components" (CPAN).
Re: How Perl Saved the Human Genome Project
#8Alternate 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).
Python, perl and ruby are roughly the same language. The differences between them are primarily cultural, rather than technical. I suspect the reason perl flourished here was a combination of luck and the cultural fit. Culture here includes the newbie-friendly online help (e.g. perlmonks), the ease of "publish and re-use components" (CPAN).
Also, remember that when the project started, Python and Ruby didn't exist yet. Perl still wasn't the only dynamic scripting language on the block, but it probably the most mature and best-suited to this problem domain.
I wonder if perl would still be used if the project was started today.
Re: How Perl Saved the Human Genome Project
#9Earlier quoted context omitted.
Python, perl and ruby are roughly the same language. The differences between them are primarily cultural, rather than technical. I suspect the reason perl flourished here was a combination of luck and the cultural fit. Culture here includes the newbie-friendly online help (e.g. perlmonks), the ease of "publish and re-use components" (CPAN).
Also, remember that when the project started, Python and Ruby didn't exist yet. Perl still wasn't the only dynamic scripting language on the block, but it probably the most mature and best-suited to this problem domain. I wonder if perl would still be used if the project was started today.
Perl was the only language on the block with strong built-in text-processing capabilities. For many a biologist the Camel book was the only programming book they read before moving on to solve real biological problems instead of fiddling with programs.
Re: How Perl Saved the Human Genome Project
#10Earlier quoted context omitted.
Also, remember that when the project started, Python and Ruby didn't exist yet. Perl still wasn't the only dynamic scripting language on the block, but it probably the most mature and best-suited to this problem domain. I wonder if perl would still be used if the project was started today.
Perl was the only language on the block with strong built-in text-processing capabilities. For many a biologist the Camel book was the only programming book they read before moving on to solve real biological problems instead of fiddling with programs.
It's also performant enough that it wasn't worth the time to learn a faster performing language.