Michael Smith Genome Sciences Centre uses Linux to sequence SARS virus in 5 days !

Note: This article has been moved over from my previous blog for historical purposes

I have been tinkering about with linux for a long time now. It started with a local magazine (PCQuest) distributing free CDs (again a first in India) of linux then. A few months later i was to learn of and join PLUG (Pune Linux Users Group) - initially as a passive listener. It was during PLUGs online meeting (we used to meet on IRC then) that i learnt of a certain linuxjournal.com.
I have been hooked to the magazine ever since. Its been a long time since then. Today, i am a avid supporter and advocate of OSS. I not only actively use open source softwares, but have also put in some humble contributions of my own.

This particular article ("Sequencing the SARS Virus") in the Nov 2003 issue caught not only my attention, but also my fancy. The author writes about the B.C labs use of Linux to extract a sequence of the SARS virus in 5 days !! Here's the groups site (see: "Around the lab") that displays a annotated image of the lab with linux equipment that was used for the feat !
The article describes in detail how open source softwares such a Linux, Python, MySQL, LIMS, Perl, Sockeye 3D genome viewer and many more were used to sequence the genome of SARS Tor2 Coronavirus (see map) in 5 days. 

Reading that article was enough to convince me that not only was open source here to say, it has already made in-roads where commercial software were yet to even step-in. I also spent sometime scourging the net for more such examples, i wasnt surprised to find many more - though not so famous !

I have already known Perl to have been on the forefront of Bio-informatics. Today countless books, libraries have been written on and in perl on the subject. Several universities have been long using perl for this purpose. See this article "How Perl saved the human genome project" by Lincoln Stein (website)

I, personally believe, that open source by its very nature is realizing its potential that even the likes or Richard Stallman (of the famed GNU) had never imagined. I would even dare say that we have not even scratched the surface.

My hats off to the folks at Michael Smith Genome Sciences Centre for not only a job well done but also for how it was done. Way to go folks !! I am already passing on the linux of your work to a few of my friends working in the area of application. Most of them have already shown interest in using Linux. I am hoping that your example has put it into their "do-able" category of things.