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Canadian Lab Unravels SARS With A Beowulf Cluster

Posted by timothy on 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."

33 of 46 comments (clear)

  1. \/\/00t! by kingOFgEEEks · · Score: 2, Insightful

    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.)

    --
    mechanicos ergo cogito
    1. Re:\/\/00t! by Anonymous Coward · · Score: 2, Insightful

      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.

    2. Re:\/\/00t! by Drakin · · Score: 2, Insightful

      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.

    3. Re:\/\/00t! by gl4ss · · Score: 3, Informative

      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)

      --
      world was created 5 seconds before this post as it is.
    4. Re:\/\/00t! by jclendenan · · Score: 1

      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.

    5. Re:\/\/00t! by arthurs_sidekick · · Score: 1

      (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.

      --
      "Oh, I hope he doesn't give us halyatchkies," said Heinrich.
    6. Re:\/\/00t! by jbridge21 · · Score: 1

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

  2. Great... by BoBathan · · Score: 5, Funny

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

    --
    EOF
  3. You'd think... by TaraByte · · Score: 1, Funny

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

    --
    Security is inversely proportional to the commitment of one desiring to circumvent it.
  4. Secure eh? by Alomex · · Score: 2, Funny


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

  5. Re:Uhh, are we sure this is such great idea? by AndyAMPohl · · Score: 4, Insightful

    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

  6. Posting genome on net... by sciwhiz007 · · Score: 1
    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!

    --
    Read my journal here.
    1. Re:Posting genome on net... by spotted_dolphin · · Score: 3, Interesting

      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.

    2. Re:Posting genome on net... by sciwhiz007 · · Score: 1
      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?

      --
      Read my journal here.
    3. Re:Posting genome on net... by spotted_dolphin · · Score: 2, Insightful

      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.

    4. Re:Posting genome on net... by sciwhiz007 · · Score: 1

      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...

      --
      Read my journal here.
    5. Re:Posting genome on net... by moncyb · · Score: 4, Insightful

      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!"

  7. This could save lives by Landaras · · Score: 3, Insightful

    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...

    --
    My legal education, in nifty podcast format
    1. Re:This could save lives by Ieshan · · Score: 1

      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.

    2. Re:This could save lives by KillerBob · · Score: 2, Informative

      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.

      --
      If you believe everything you read, you'd better not read. - Japanese proverb
    3. Re:This could save lives by Ieshan · · Score: 1

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

  8. What about the other virus? by spotted_dolphin · · Score: 3, Interesting

    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.

    1. Re:What about the other virus? by gene_tailor · · Score: 2, Informative

      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 . 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 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.

      --
      It also occurs to me that if one was drowning, yelling "Help! I'm drowning and I lost my bikini top" would probably be m
  9. Bush comments: by Anonymous Coward · · Score: 1, Funny

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

  10. SARS and Beowulf by bayankaran · · Score: 2, Interesting

    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?

    --
    Tat Tvam Asi
  11. Reverse Engineering by Corpus_Callosum · · Score: 2, Funny

    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?

    --
    The reason that it can be true that 1+1 > 2 is that very peculiar nonzero value of the + operator
    1. Re:Reverse Engineering by dunstan · · Score: 1

      Mod parent as insightful

      --
      The last scintilla of doubt just rode out of town
  12. Consider the audience by arthurs_sidekick · · Score: 1

    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.

    --
    "Oh, I hope he doesn't give us halyatchkies," said Heinrich.
    1. Re:Consider the audience by bayankaran · · Score: 1

      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.

      --
      Tat Tvam Asi
  13. Re:Uhh, are we sure this is such great idea? by kalidasa · · Score: 1

    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.

  14. Re:How about a beowulf cluster of these by The+Lynxpro · · Score: 1

    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...

    --
    "Right now, somewhere in this world, Scott Baio is plowing a woman he doesn't love," - Peter Griffin, *Family Guy*
  15. Is it the mortality-rate that's a worry? by phorm · · Score: 1

    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.

  16. wise for you to have a gun by knowledgepeacewi · · Score: 1

    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.