Date: Thu, 27 Jul 2000 11:53:13 -0400 (EDT) From: Siobhan Patricia Lynch <trish@bsdunix.net> To: Johann Visagie <wjv@cityip.co.za> Cc: chat@FreeBSD.ORG, advocacy@FreeBSD.ORG, janet@sanbi.ac.za Subject: Re: Bioinformatics Open Source Conference, 17-18 Aug, San Diego Message-ID: <Pine.BSO.4.21.0007271152180.3504-100000@superconductor.rush.net> In-Reply-To: <20000727122855.B414@fling.sanbi.ac.za>
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As the BSD columnist for Open the Magazine, I wouldn't mind some more information, maybe I can give a little more exposure to BSD in the bioinformatics field, drop me a line, we can set up a time to talk. -Trish __ Trish Lynch FreeBSD - The Power to Serve trish@bsdunix.net Rush Networking trish@rush.net On Thu, 27 Jul 2000, Johann Visagie wrote: > Damn, I should've posted this earlier! > > The Bioinformatics Open Source Conference (BOSC - previously BioPerl) takes > place in San Diego on 17-18 August. Unfortunately registration has already > closed - hence my lament that I forgot to post earlier! See: > http://ismb00.sdsc.edu/bosc2000/ > > I will be attending with others from my company and our associated academic > institute (http://www.sanbi.ac.za/). > > Some background as to why this is something FreeBSD users might want to take > note of (long - you may skip to summary at the end): > > You've probably all read the media reports about the completion of a first > draft sequence of the human genome last month: > http://www.sanger.ac.uk/HGP/draft2000/ > > Contrary to what the press hullabaloo might have suggested, this wasn't an > end - it was a beginning. We haven't found the "source code" for the human > species - we found the binary image in memory. Our task over the next few > years (decades?) will be to disassemble that binary and get back to fully > commented source code in a high level language. Calling this "difficult" may > be the understatement of the new millennium. > > <hype> > The science that is attempting this task is known as Bioinformatics. It is a > already the focus of dozens of elite academic establishments around the > world, and forms the backbone of a nascent multi-billion dollar industry. It > is where computer science meets the biosciences - in fact, bioinformatics > research requires massive amounts of processing power, and some of the bigger > supercomputers in the world are dedicated to it. In terms of human > scientific progress, this may well be "where it's at" for the next decade or > so. > </hype> > > Coming to this field from a commercial internet environment that would be > familiar to many of you, where I too constantly fought the good fight against > the hordes of Microsoft, I was amazed and not a little flabbergasted to find > that here, Unix is the _only_ game in town. Literally. A bioinformatics > application that runs on Windows? Never heard of one. You'd be ostracised > for even suggesting it. > > Most bioinformatics applications are huge, monolithic, archaic, incredibly > expensive and run on equally expensive commercial Unix boxes. SGI, Sun and > Compaq all play big roles on the hardware side of things. They support the > academic institutes with hardware, which means research crystallises into > software that runs on their operating systems, which means they can move > truckloads of boxes to big pharmaceuticals. > > As you might guess, a few insidious individuals down in the trenches have > been saying, "Hey, this sucks. Look at those internet blokes developing all > their software collaboratively and giving it away. We can do the same." And > so a number of open source initiatives in the field of bioinformatics have > been established, though most of them are still very young and immature. > > You can get some feel for the role of open source in bioinformatics by > reading Lincoln Stein's article about "How Perl saved the Human Genome > Project" here: > http://www.bioperl.org/GetStarted/tpj_ls_bio.html > > Or see Ewan Birney's plea to help "Hack the Genome" on advogato: > http://advogato.org/article/131.html > > Some of these projects - all of which will be the subjects of presentations at > BOSC2000 - are: > > The Bio* projects - Bioperl, BioPython, BioJava, BioXML, BioCorba - they all > have .org domains; you can guess the URLs. These tools all aim at providing > the basic building blocks for developing bioinformatics applications in their > respective environments. And there's a lot of cross-pollination going on > too. > > Ensembl is a fully open source gene annotation pipeline. That'll take too > long to explain, but you can find out a lot more on their site: > http://www.ensembl.org/ > > DAS, the distributed annotation system, may be one of the killer apps of the > field. You can find out more here... > http://www.genetics.wustl.edu/eddy/people/robin/das > > And read the interesting Wired article about how DAS means gene research > meets Napster, Gnutella and Freenet here: > http://www.wired.com/news/technology/0,1282,35404,00.html?tw=wn20000405 > > Oh, and Tim O'Reilly will provide a token presence from the open source side > of things by delivering one of the keynotes. > > Right, this is turning into an article, but let me continue. Where does > FreeBSD fit in? Unfortunately, nowhere yet. As more and more effort is put > into open source bioinformatics, the word on everybody's lips is, of course, > "Linux". Since this is an area where massive amounts of processing power is > the norm, another word that has been bandied about is "Beowulf". However, > the field is rooted in commercial Unix, and you can get a feel for some of > the Linux vs. Unix debate from these pages: > > http://www.portlandpress.com/biochemist/cyber/0006/default.htm > http://www2.mrc-lmb.cam.ac.uk/personal/rpg/CB/Linux.html > > They detail a specific lab's decision-making process. Eventually the lab > went for an Alphaserver over a couple of Linux boxes, _mostly_ because of > Linux's 2GB file size limit. Erk. > > As a FreeBSD user in bioinformatics, I see two obvious tasks ahead of me > (when I can find the time between the myriad other things on my plate): > - Educating the FreeBSD community about bioinformatics. > - Educating the bioinformatics community about FreeBSD. > > In summary: > > Bioinformatics is a 100% Unix-dominated field - one of the few remaining. It > is about to become a Very Big Thing indeed. Unless I (and others in my > position) do some advocacy of FreeBSD as a stable, secure, standard platform, > it is likely to be a Linux-dominated field a few years from now. > > I've started working on ports of some bioinformatics tools and will submit > them in due course. I'd also like to provide some feedback after BOSC if > anyone is interested. (Maybe I could get Daemon News interested?) > > -- Johann > > > To Unsubscribe: send mail to majordomo@FreeBSD.org > with "unsubscribe freebsd-chat" in the body of the message > To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-chat" in the body of the message
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