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Biotech Science

Canadian Lab Unravels SARS With A Beowulf Cluster 46

Posted by timothy from the you-knew-they'd-come-in-handy dept.
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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Canadian Lab Unravels SARS With A Beowulf Cluster More

Canadian Lab Unravels SARS With A Beowulf Cluster

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  • \/\/00t! (Score:2, Insightful)

    by kingOFgEEEks ( 598145 )
    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! (Score:2, Insightful)

      by Anonymous Coward
      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! (Score:2, Insightful)

      by Drakin ( 415182 )
      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.
      • 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! (Score:4, Informative)

      by gl4ss ( 559668 ) on Sunday April 13, 2003 @02:48PM (#5722646) Homepage Journal
      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)
      • (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.
      • Just wait until HIV crosses with some cold virus in asia and then it can be passed through the air...
    • 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.

  • Great... (Score:5, Funny)

    by BoBathan ( 166436 ) <.bobathan. .at. .softhome.net.> on Sunday April 13, 2003 @02:32PM (#5722559) Homepage Journal
    We just slashdotted information that could possibly (and probably) lead to a cure for SARS. Are we all terrorists now?
    • that if they can set up a beowulf cluster, they could handle a little more web traffic ;)
    • 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?

  • Secure eh? (Score:3, Funny)

    by Alomex ( 148003 ) on Sunday April 13, 2003 @03:02PM (#5722708) Homepage

    i didn't read the article, but i knew it was just a matter of time before we saw the first beowulf linux virus....
  • 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... (Score:4, Interesting)

      by spotted_dolphin ( 595858 ) on Sunday April 13, 2003 @05:54PM (#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.
      • 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?

        • 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 gen

          • 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

            • Re:Posting genome on net... (Score:5, Insightful)

              by moncyb ( 456490 ) on Sunday April 13, 2003 @10:23PM (#5725086) Journal

              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!"

    • 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.

  • This could save lives (Score:4, Insightful)

    by Landaras ( 159892 ) <neil@wehnem[ ]com ['an.' in gap]> on Sunday April 13, 2003 @05:55PM (#5723554) Homepage
    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...
    • 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 t
      • 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 th

  • What about the other virus? (Score:4, Interesting)

    by spotted_dolphin ( 595858 ) on Sunday April 13, 2003 @05:57PM (#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.
    • 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: (Score:1, Funny)

    by Anonymous Coward
    http://www.whitehouse.org/news/2003/040903.asp

  • SARS and Beowulf (Score:2, Interesting)

    by bayankaran ( 446245 )
    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?

    • 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.

      • 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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