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Canadian Lab Unravels SARS With A Beowulf Cluster

timothy posted more than 11 years ago | from the you-knew-they'd-come-in-handy dept.

Biotech 46

Amad writes "A Canadian Genetics Research Lab in BC, Canada has used a Linux Beowulf cluster to help sequence the genetic code of the virus linked to SARS. This lab is the first to crack it, and has posted the data to the public. You can read an article about the discovery, or check out the lab."

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In Soviet Russia, SARS unravels you! (0, Troll)

psicE (126646) | more than 11 years ago | (#5722537)

A Beowulf cluster of SARS... now that's a scary thought...

Re:In Soviet Russia, SARS unravels you! (0)

TaraByte (660047) | more than 11 years ago | (#5722571)

Is there enough room for all of them to fit in the SARS tower?

\/\/00t! (2, Insightful)

kingOFgEEEks (598145) | more than 11 years ago | (#5722542)

well now maybe they can get this disease under control and get back to finding cures for the diseases that are killing more people than SARS

(disclaimer: i understand that the fear is of SARS becoming a larger killer, but so far it seems to be under control.)

Re:\/\/00t! (2, Insightful)

Anonymous Coward | more than 11 years ago | (#5722566)

3,000 people (w/ disease, not killed) in 20+ countries in this short amount of time ain't nothing to sneeze at. Besides, they're probably sort of enjoying the diversion from the other diseases that are so much more difficult to knock down.

Re:\/\/00t! (2, Insightful)

Drakin (415182) | more than 11 years ago | (#5722607)

Well, considering acording to the story this machine is normally busy plunking away at a cure for cancer... I think it'll be going back to work fairly quickly.

SARS isn't under control though. The only thing that's containing it was the rapid responce to it's existance, and that dispite not knowing much about it, certain drugs have some effect against it, as well as the body does create antibodies, so a serum can be made.

But actually understanding what SARS is... that's beyond us at present.

Re:\/\/00t! (1)

jclendenan (530313) | more than 11 years ago | (#5729207)

Rapid responce? SARS was around and being documented in china since ~ December. By Febuary there were already health warnings going out to doctors in BC. The Toronto outbreaks were entirely preventable.. ohwell.

Re:\/\/00t! (3, Informative)

gl4ss (559668) | more than 11 years ago | (#5722646)

sars has higher mortality rate than the 'killer flu' that killed 20-40 million people in 1918, so keeping it under control is _very_ important, though, the chinese might have very hard time if gets to spread to rural areas where they can't even track it's progress well.

so it's definetely nothing to sneeze at, would f-* hate having to isolate at some cottage for it to pass(oh wait if it had internet i wouldnt notice any difference).

(yeah, sure, hiv has mortality rate of 100%, but to get it you at least have to have some sort of fun)

Re:\/\/00t! (0)

Anonymous Coward | more than 11 years ago | (#5722838)

I think you mean AIDS, not HIV, as there's some people,who have HIV, who will never develop AIDS due to the way certain cells are in thier bodies.

Re:\/\/00t! (1)

arthurs_sidekick (41708) | more than 11 years ago | (#5729365)

(yeah, sure, hiv has mortality rate of 100%, but to get it you at least have to have some sort of fun) Yeah, like all those people who got it from blood transfusions, or through being raped, or being paid to have humiliating sex with lots of people because there's no other way to feed your children. Please, do think about it.

Re:\/\/00t! (1)

jbridge21 (90597) | more than 11 years ago | (#5742280)

Just wait until HIV crosses with some cold virus in asia and then it can be passed through the air...

Is it the mortality-rate that's a worry? (1)

phorm (591458) | more than 11 years ago | (#5733479)

I think it's more the ability for the disease to spread so rapidly that is a concern than (currently) the possibility of death. For most people, SARS can now be dealt with and recovered from. But when your doctor won't even visit you because (s)he might contract the virus... not good.

SARS can kill, but the more immediate threat is the epidemic-like spreading, especially during the early period before it became widely known.

BEOWULF CLUSTER BEOWULF CLUSTER! (-1, Troll)

Anonymous Coward | more than 11 years ago | (#5722543)

Imagine a single node of one of those!

Ha! Beat you all to it! Second post!

Great... (5, Funny)

BoBathan (166436) | more than 11 years ago | (#5722559)

We just slashdotted information that could possibly (and probably) lead to a cure for SARS. Are we all terrorists now?

You'd think... (1, Funny)

TaraByte (660047) | more than 11 years ago | (#5722599)

that if they can set up a beowulf cluster, they could handle a little more web traffic ;)

Reverse Engineering (2, Funny)

Corpus_Callosum (617295) | more than 11 years ago | (#5726303)

No, not in trouble as terrorists.

However, should SARS turn out to be constructed (by terrorists, for instance) then this activity (decoding SARS with a beowolf cluster) may consider be considered reverse engineering of copyrighted material under the DMCA and therefore all of us, having participated in a conversation and a link to this "copyright violation" may be facing some jail time.

Who knew?

Re:Reverse Engineering (1)

dunstan (97493) | more than 11 years ago | (#5726783)

Mod parent as insightful

Dsicovered for what.. the tenth time now? (-1, Troll)

Anonymous Coward | more than 11 years ago | (#5722577)

Every couple of days there has been yet another news story that "We found what SARS is!", and every time it has turned out to be untrue. Why should I believe this?

Yet another lab trying to get exposure for itself in the news! I bet this was quickly followed up by grant applications.

Hopefully now that the invasion of iraq is nearly done, they'll find the records from where they created the biological weapon of mass destruction and maybe work out a real cure.

Uhh, are we sure this is such great idea? (0)

Anonymous Coward | more than 11 years ago | (#5722661)


and has posted the data to the public

The site has been /.'ed, so I'll have to take your word for it, but are you saying that they posted the entire genetic sequence for a highly contagious [and sometimes deadly] virus on the WWW for all to see?

What if someone like Mrs. Anthrax [google.com] gets her hands on this info? Yeah, Saddam's history, but don't think Kim-Jong Il doesn't have a small army of PhD's working on this sort of thing...

Re:Uhh, are we sure this is such great idea? (4, Insightful)

AndyAMPohl (573700) | more than 11 years ago | (#5722733)

Well there are plenty of nasty virii sequenced and deposited for all to see in genbank. For every 1 scientist using information for evil, there are 5,000 using the information for good. -Andy

Scientists and Evil (-1, Flamebait)

Anonymous Coward | more than 11 years ago | (#5722842)


For every 1 scientist using information for evil, there are 5,000 using the information for good.

Yeah, but the evil in this case is REALLY, REALLY evil. [Ever see a movie called The Andromeda Strain [imdb.com] , or one called or The Stand [imdb.com] ?]

PS: Not to pick nits, but the vast, overwhelming majority of scientists don't believe in quaint, archaic notions like "Good," or "Evil." They worship at the altar of a pagan religion they call "Science."

Re:Uhh, are we sure this is such great idea? (1)

kalidasa (577403) | more than 11 years ago | (#5731044)

Yes, the entire sequence is posted to the internet. It's not like someone else couldn't sequence the virus on his own...if you have the ability to reconstruct a virus from a published sequence (hell, CAN anyone reconstruct a virus from a published sequence yet?), you've got the ability to sequence it in the first place.

Secure eh? (2, Funny)

Alomex (148003) | more than 11 years ago | (#5722708)


i didn't read the article, but i knew it was just a matter of time before we saw the first beowulf linux virus....

Re:Secure eh? (0)

Anonymous Coward | more than 11 years ago | (#5725021)

That's just plain stupid. Slashdot is becomming less and less a place of news and information exchange and disscussion, and more and more a place to try to get that tired old joke in. Everypost lately has been a joke. pathetic

Yeah, but can you... (0)

jakub_sad (530314) | more than 11 years ago | (#5723027)

... make a Beowulf Cluster with it?

Damn, no wonder no one is responding to the article! What is there left to ask?

Posting genome on net... (1)

sciwhiz007 (665637) | more than 11 years ago | (#5723075)

As someone said before, I really don't think it's very wise for the lab to post its results online. The internet is a place where anyone can possible access anything at any time. If this information falls into the wrong hands, things can turn ugly...

P.S.: By the way, it's great that they used a Linux Beowulf cluster to achieve this. Another feather in Tux's hat!

Re:Posting genome on net... (3, Interesting)

spotted_dolphin (595858) | more than 11 years ago | (#5723549)

What is the harm in posting a string of letters online? The entire human genome sequence is already out there. Until someone figures out what all those letters mean, how they work and how they affect humans, I don't think we have too much to worry about.

Besides, are you familiar with what's published in scientific journals? There's a *lot* of information in *all* sorts of fields which people can exploit.

Re:Posting genome on net... (1)

sciwhiz007 (665637) | more than 11 years ago | (#5723995)

Well of course I am aware that potentially *useful* information is printed in scientific journals. I am just not too sure if it's a wise idea to post the genome sequence of a possibly deadly pathogen. And by the way, how can one be so sure that other countries are not working on projects to understand genomes and use the information for potentially bad reasons.

One may say I am being paranoid... but is it really necessary to post the genetic sequence online?

Re:Posting genome on net... (2, Insightful)

spotted_dolphin (595858) | more than 11 years ago | (#5724244)

Seeing as you're a reader of Slashdot, you must agree that the Internet is an incredibly useful central location for sharing information. The international scientific community will only benefit from this information. Pharmaceuticals can be developed, futher mechanistic principles and models may be developed; it would be a much slower process otherwise. Which would you prefer if someone in your immediate family were affected with this? Would you like a solution now, or later? Besides, the influenza genome is out there too; why not fuss about that? It has a higher mortality rate.

In addition, scientific journal articles are just as accessible on the internet. Some are free to the everyday user, others require subscriptions. If you're out to do evil and happen to be working at an institution which have subscribed for access, we'd be screwed anyway!

But I ask again, what is someone going to do with a string of letters? Just because you can replicate a piece of genetic material (which is only an organic polymer) doesn't mean you have a fully functional organism.

Let's put this into perspective. What amount of explosive chemicals have been used since its development? Would we have trains going through mountains? How much coal and precious metals have been mined for? How often have we watched fireworks ignited to celebrate something? Obviously others have found less than nice ways to use the materials. It's the same with more advanced knowledge, but the bad stuff always gets to the media first and the way they present the material obviously can have a significant affect on society.

Re:Posting genome on net... (1)

sciwhiz007 (665637) | more than 11 years ago | (#5724518)

I have to agree with you on the fact that not everything has been misused, or will be misused. And yes, the internet is definitely a great place to facilitate the sharing of information to benefit the scientific community as a whole. Plus, I am not really being fussy about this. All I am doing is being a little wary and asking whether posting such information on the internet is the greatest thing to do..

Also, if we don't really understand the sequence of letters that make up the genome, why post it on the internet for the world to see? What good is it going to do? Isn't it better if we spend our time understanding what the letters mean rather than just putting the sequence up for viewing? Of course, this is an entirely different issue altogether.

You might say that this will help research facilities around the world in some way or the other, and I certainly agree with that.

Maybe posting the genome on the net is good, maybe it isn't. And as you said, if an evildoer wants to get something, he will get it anyway. All I'm saying is, why make his task easier?

I rest my case...

Re:Posting genome on net... (4, Insightful)

moncyb (456490) | more than 11 years ago | (#5725086)

You can't be serious. If "evildoers" were planning on using SARS as a biological weapon, they would not download the gene sequencing information from the internet. They would need lots of expensive equipment to manufacture the virus from that data. If they wanted SARS, they'd just get some real samples somehow--like kidnapping an infected person. Much cheaper. Much easier. Requires no scientific knowledge.

Also, if we don't really understand the sequence of letters that make up the genome, why post it on the internet for the world to see? What good is it going to do?

Hmm...could they be posting on the internet, so every scientist in the world can work on it if they want to, so a cure may be discovered more quickly? Naahh...they just want to give to terrorists!

Isn't it better if we spend our time understanding what the letters mean rather than just putting the sequence up for viewing?

What are you saying? That "we" should keep all the knowledge about this disease locked up in a single room, so only a handful of reasearchers can work on it?

Maybe posting the genome on the net is good, maybe it isn't. And as you said, if an evildoer wants to get something, he will get it anyway. All I'm saying is, why make his task easier?

You sound like the "zero tolerance" schools, homeland security, and the DRM cartel. "We have to act like jack-booted thugs and take everything away. Lest one single person may use a 'weapon of mass destruction' / 'tweety bird keychain' / P2P to wipe out the entire world!"

Re:Posting genome on net... (0)

Anonymous Coward | more than 11 years ago | (#5731208)

Times like this I wish I could mod you -1:Ignorant. If you don't understand something, become informed - don't spout fear, uncertainty and doubt. We already know people are dying of SARS. You merely suggest there's a chance somebody could use this information for evil deeds. Given a choice between trying to save lives and sticking heads in the sand to hide from a non-existent threat, I'll take the science thanks. Your style of censorship is going to kill those people faster. Get a clue.

Re:Posting genome on net... (0)

Anonymous Coward | more than 11 years ago | (#5732900)

I was just wondering, how do you say it is a non-existent threat? How are you so sure that the threat of biological warfare (not just using the SARS genome) doesn't exist? Just because we haven't seen any yet doesn't mean there isn't a chance for it to show its face at all...

wise for you to have a gun (1)

knowledgepeacewi (523787) | more than 11 years ago | (#5734159)

And I don't think its very wise for you to be allowed to buy a gun.

Does it mean that because you can use your power for evil, that you will?
No. That doesn't mean that I like it.

If information didn't fall into our hands we wouldn't be able to protect ourselves from _1984_.

I agree this is a great achievement for all of the people working on Linux. Kudos.

*BSD is dying of SARS (-1, Troll)

Anonymous Coward | more than 11 years ago | (#5723347)

It is official; Netcraft now confirms: *BSD is dying

One more crippling bombshell hit the already beleaguered *BSD community when IDC confirmed that *BSD market share has dropped yet again, now down to less than a fraction of 1 percent of all servers. Coming on the heels of a recent Netcraft survey which plainly states that *BSD has lost more market share, this news serves to reinforce what we've known all along. *BSD is collapsing in complete disarray, as fittingly exemplified by failing dead last [samag.com] in the recent Sys Admin comprehensive networking test.

You don't need to be a Kreskin [amazingkreskin.com] to predict *BSD's future. The hand writing is on the wall: *BSD faces a bleak future. In fact there won't be any future at all for *BSD because *BSD is dying. Things are looking very bad for *BSD. As many of us are already aware, *BSD continues to lose market share. Red ink flows like a river of blood.

FreeBSD is the most endangered of them all, having lost 93% of its core developers. The sudden and unpleasant departures of long time FreeBSD developers Jordan Hubbard and Mike Smith only serve to underscore the point more clearly. There can no longer be any doubt: FreeBSD is dying.

Let's keep to the facts and look at the numbers.

OpenBSD leader Theo states that there are 7000 users of OpenBSD. How many users of NetBSD are there? Let's see. The number of OpenBSD versus NetBSD posts on Usenet is roughly in ratio of 5 to 1. Therefore there are about 7000/5 = 1400 NetBSD users. BSD/OS posts on Usenet are about half of the volume of NetBSD posts. Therefore there are about 700 users of BSD/OS. A recent article put FreeBSD at about 80 percent of the *BSD market. Therefore there are (7000+1400+700)*4 = 36400 FreeBSD users. This is consistent with the number of FreeBSD Usenet posts.

Due to the troubles of Walnut Creek, abysmal sales and so on, FreeBSD went out of business and was taken over by BSDI who sell another troubled OS. Now BSDI is also dead, its corpse turned over to yet another charnel house.

All major surveys show that *BSD has steadily declined in market share. *BSD is very sick and its long term survival prospects are very dim. If *BSD is to survive at all it will be among OS dilettante dabblers. *BSD continues to decay. Nothing short of a miracle could save it at this point in time. For all practical purposes, *BSD is dead.

Fact: *BSD is dying

How about a beowulf cluster of these (0, Offtopic)

Tuxinatorium (463682) | more than 11 years ago | (#5723520)

$50 Athlon XP 1700+ Thoroughbred Revision B [newegg.com] : Easily overclocked to 2.4ghz (3000+) stably on air, and they can be modded into Athlon MPs [cluboverclocker.com] by just closing the last L5 bridge with a conductive pen. That way you can build a 30 gigaflop dual processor rig for around $500.

Re:How about a beowulf cluster of these (1)

The Lynxpro (657990) | more than 11 years ago | (#5731828)

Wouldn't overclocking ruin the data? Supposedly SETI@home's crunched data packets are ruined by volunteers who use overclocked machines to process the data chunks...

This could save lives (3, Insightful)

Landaras (159892) | more than 11 years ago | (#5723554)

I'm glad that they appear to be giving the information out freely. I applaud that.

Now imagine that they went and {patented | copyrighted | appropriate IP protection} the information first so they could commercially leverage it. Wouldn't there be a worldwide public outcry?

Then why isn't there one when other genetic information, that could possibly save even more lives, is locked down? Just my thoughts...

Re:This could save lives (1)

Ieshan (409693) | more than 11 years ago | (#5723946)

Just for your own info-
It's very hard to patent DNA sequences. It's a very difficult case to argue. Sure, you could point out many exceptions, but on the whole, it's a difficult thing to do.

However, I think that you ought to step back and realize what you're saying. Medicine is a commerical endeavor, just like everything else. The guys who made this discovery need to eat tomorrow night, just like the guys who have SARS need medical attention. If we didn't pay them for it, we'd never have people doing new things, because no one would live a comfortable lifestyle for a large achievement.

I'm not saying I agree with the patenting of the research, especially in the fields of biotechnology. But, there are some serious implications you're talking about - if we start trying to make it impossible to patent techniques, etc, then we're essentially destroying a very profitable and very rewarding industry - both for community health and for the people who do the work.

Re:This could save lives (2, Informative)

KillerBob (217953) | more than 11 years ago | (#5724767)

It's very hard to patent DNA sequences. It's a very difficult case to argue. Sure, you could point out many exceptions, but on the whole, it's a difficult thing to do.


Just for your own info-
It's not legal to patent a DNA or RNA sequence in Canada. That information is considered "public domain". At best, you can patent the method you use to derive the DNA sequence, or to implant it if you're talking about genetic engineering/cloning.

Remember the stories a few months ago about Canada refusing to honour the patents on lab mice that had been engineered in Boston? The logic was that you can patent the method used to engineer the mice, but the mice that were being resold in Canada weren't violating the copyright, because they were the results of breeding, not cloning.

Re:This could save lives (1)

Ieshan (409693) | more than 11 years ago | (#5725769)

Yes, but it's legal to patent lots of other things, which can be claimed derived from the DNA sequence.

What about the other virus? (3, Interesting)

spotted_dolphin (595858) | more than 11 years ago | (#5723567)

They've only sequenced the coronavirus which has been implicated in SARS. What about the paramyxovirus which some labs have also been finding in affected patients? In any case, both of these viruses are RNA based and are highly susceptible to mutagenesis and recombination. If a new, slightly modified virus appears, we could be in for another epidemic. We go through this yearly with influenza.

Re:What about the other virus? (2, Informative)

gene_tailor (601527) | more than 11 years ago | (#5725928)

It is impressive that this lab quickly cranked out the complete sequence of this coronavirus, and it's alot more informative than the story that made headlines a few days ago here [slashdot.org] . But, spotted dolphin rightly points out that this is only the coronavirus. As far as I'm aware no on has fulfilled Koch's postulates [wsu.edu] to prove THIS virus is the causative agent of "SARS". It's possible this sequence will be very useful, but it's too early to tell.

Bush comments: (1, Funny)

Anonymous Coward | more than 11 years ago | (#5723706)

http://www.whitehouse.org/news/2003/040903.asp

SARS and Beowulf (2, Interesting)

bayankaran (446245) | more than 11 years ago | (#5723963)

What is more important...finding the genetic info of SARS virus or the fact some cluster was used to find it...I would be more happy if the editors can include some info about the type of software or techniques used rather than hardware.

Does it really matter if it was Beowulf or mainframes?

Consider the audience (1)

arthurs_sidekick (41708) | more than 11 years ago | (#5729432)

Given that "regular" media isn't likely to focus on the Beowulf cluster, and that this is a geeky tech site where there are a lot of fans of open source, I think that it clearly does matter that open source technology was heavily implicated in the matter. If you wanted to know that a lab had sequenced the virus, all you had to do was turn on your TV, read a newspaper, or listen to the radio.

Re:Consider the audience (1)

bayankaran (446245) | more than 11 years ago | (#5732687)

Well, my point was that if they could find some info on the software or techniques used for cracking the gene code it would be more interesting. If the editors contacted the Canadian lab which did the cracking, I am sure they would have given some interesting info on how it was done.

This would be more interesting since cracking the SARS gene code was a race against time.

It does not really matter whether a Beowulf cluster or mainframes were used.
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