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Grid Computing Saves Cancer Researchers Decades

Stony Stevenson writes "Canadian researchers have promised to squeeze "decades" of cancer research into just two years by harnessing the power of a global PC grid. The scientists are the first from Canada to use IBM's World Community Grid network of PCs and laptops with the power equivalent to one of the globe's top five fastest supercomputers. The team will use the grid to analyze the results of experiments on proteins using data collected by scientists at the Hauptman-Woodward Medical Research Institute in Buffalo, New York. The researchers estimate that this analysis would take conventional computer systems 162 years to complete."

149 comments

  1. Oh great ... by trolltalk.com · · Score: 5, Funny

    Wanna bet they discover that maple syrup or Canadian back bacon cures cancer?

    1. Re:Oh great ... by butterwise · · Score: 1

      No, but they may find a link between causes of death and weight.

      --
      If a baby duck is a "duckling," why would anyone want to eat "dumplings?"
    2. Re:Oh great ... by Silver+Gryphon · · Score: 1

      Mmmmm... poutine...

    3. Re:Oh great ... by Anonymous Coward · · Score: 0

      possibly that there is an inverse proportional relationship between a person's weight and the number of years after which he had been dead...

  2. I used to run Folding@... by kcbanner · · Score: 5, Insightful

    ...as a competition with friends. But then I realized that I didn't really need to use my computers as heaters...and did a number for the planet and closed the client.

    --
    Obligatory blog plug: http://www.caseybanner.ca/
    1. Re:I used to run Folding@... by Turn-X+Alphonse · · Score: 4, Informative

      If you run it on a low level you can only increase your usage by about 1-2 and still help the project, there is no logical reason to run the client at 100% if it's going to cost you a bomb, where as at 1-2% you won't win any contests, but you will be helping the project and paying at most a buck or two extra on electric a month.

      --
      I like muppets.
    2. Re:I used to run Folding@... by stratjakt · · Score: 1, Interesting

      I'm not yet one of the climate change true believers.

      It just feels too much like an economic scheme based in pseudo-science and half truths. "The world is doomed, here's how you as a consumer can spend your way to salvation! Buy a new car and light bulbs filled with mercury!"

      It's poster child, Al Gore, uses the word "if" too much. It's an old debating trick, to say "if X, then Y", and focus on the terrible consequence Y, and completely avoid the debate - which is over the validity/scope/level/definition of X.

      At the end of the day, and back on topic, I know cancer is absolutely real, and I also know that real cures and treatments are buried in the mountains upon mountains of data in hospitals, schools and research centers.

      So, I'm maybe gonna pick a horse I think has a chance of crossing the finish line.

      --
      I don't need no instructions to know how to rock!!!!
    3. Re:I used to run Folding@... by statemachine · · Score: 1

      If you run a server that needs to be available 24/7 but still has idle time, f@h will have a minimal footprint and a lot of potential benefit.

    4. Re:I used to run Folding@... by mrbluze · · Score: 1

      ...and did a number for the planet and closed the client.

      Definitely a better idea to use the internet for communication and to use electricity for things that benefit the household/office directly. I wouldn't be surprised if the cost in reduced years of life from increasing the pollution from running these distributed tasks outweigh the years of life extended by treating cancers.

      --
      Do it yourself, because no one else will do it yourself. [beta blockade 10-17 Feb]
    5. Re:I used to run Folding@... by UncleTogie · · Score: 1

      Personally, around our 3 PCs in a smoke-laden environment, I've only seen a {mobo-measured} temp increase of at most 4-5 degrees C {and usually only 2-3 degrees, on systems ranging from a PIII with XP Pro to a Athlon XP 2000+ dual-booting Ubuntu/XP Pro...}

      BOINC seems to run a wee bit hotter on Ubuntu, but I've not benchmarked the two clients yet. I'm just guessing more efficient code allows for more ops per cycle meaning more CPU use and thermal waste, but that's all it is: a guess. Anyone else have any insight/numbers on this?

      --
      Don't tell me to get a life. I'm a gamer; I have LOTS of lives!
    6. Re:I used to run Folding@... by Shikaku · · Score: 1

      But then I realized that I didn't really need to use my computers as heaters...and did a number for the planet and closed the client. Then just run it in the winter.
    7. Re:I used to run Folding@... by ChatHuant · · Score: 2, Insightful

      ... Al Gore, uses the word "if" too much. It's an old debating trick, to say "if X, then Y", and focus on the terrible consequence Y, and completely avoid the debate - which is over the validity/scope/level/definition of X

      I don't see it as a trick, but rather as being honest. Many of the "X" items aren't certain; it would be a lie to present them as such. But we can estimate the probability of X (based on the current state of knowledge), and explore the consequences if X *does* occur. Gore's argument is that the consequences are serious enough to require action now, even it X may not happen after all. Most climate change skeptics I've seen ignore that and focus on the fact that the Xs aren't 100% surely proven.

    8. Re:I used to run Folding@... by DigiShaman · · Score: 2, Insightful

      Then just run it in the winter.


      Exactly!

      Rather then turning on my heater these past few days (getting chilly at night in Houston, TX), I run the GPU Folding@home client on my PC. Seriously, it's not wasted energy if you want your home to be heated. You also participate in worthy cause to boot!
      --
      Life is not for the lazy.
    9. Re:I used to run Folding@... by Belial6 · · Score: 2, Insightful
      Gore is an idiot. The real "Inconvenient Truth" is that following Gore's advice will kill you within minutes. I'm not convinced that mass suicide is really the right answer.

      In fact, you can even reduce your carbon emissions to zero.

      Al Gore
    10. Re:I used to run Folding@... by stratjakt · · Score: 1, Interesting

      What's ridiculous about the debate is the supposed "corrective actions" are a step backwards if you really analyze them.

      Don't buy a Prius, it may get better mileage - though if you convert to gallons per mile - a true meter of energy cost, it doesn't look so good. Never mind the fact it runs on laptop batteries, which makes it a disposable vehicle at the end of the day.

      Or go to a "super efficient" diesel engine. Well, there's reasons we restrict the numbers of diesels that can be put on the road, and that's those huge plumes of black smoke that puff out are full of nasty shit. Remember acid rain? You may not be old enough - it was the source of our ecological doom in the 80s, and is the byproduct of sulphur dioxide. Despite the industries claims of super-low-sulphur diesels, the amount in the fuel is not insignificant.

      The fact is, modern engines are quite well designed, and with regular maintenance could easily last your entire life. So what does the auto industry do now? Appeal to vanity, sure - you don't want to be seen in the same old rig, do you? They've now found a way to appeal to your innate sense of guilt. Buy a Prius, save this baby seal from clubbing!

      I also see the government mandating switches to compact flouros, being absurd. The quality of light is terrible, they dont handle slight power fluctuations all that well, even the ones that are "dimmable", really aren't, and don't work in the cold. We don't want all that mercury in our groundwater when those things start hitting the dumpster en masse. Besides, switching would just mean people leave the lights on longer. If you're used to paying 150 bucks a month, you'll keep paying it, just a weird sociological quirk., in the vein of "some snack has half the calories, so fatty eats 3, and thinks he's dieting".

      All this over CO2, a benign non-toxic gas, which has a small contribution to "the greenhouse effect", although it's been shown that the real major cause is water vapor in the atmosphere - but we have no way to track that.

      All the while we search for imaginary mystery energy sources - we're almost there, just need a huge breakthrough in physics/chemistry/biology/astrology - we completely ignore the fact that nuclear fission can supply our energy needs, no need to dig up and burn dinosaurs.

      But what of the radioactive waste? Well holy fuck, we can stand around masturbating waiting for a magical breakthrough bacteria that turns garbage into gold-plated hydrogen for our fuel-cell car of tomorrow, but this great global scientific community cant figure out how to throw out some gunk? How about this, I'll figure it out for them.. Pulverize it and release it into the atmosphere, it'd be less radioactive material than comes out of a typical coal plant in a year.

      My point is, there are sensible, practical, answers - but they aren't all futuristic and neat and don't involve funky lightbulbs and throwaway cars, and would (gasp) preserve the american lifestyle that it's become so vogue for the left to hate, despite living the exact same way.

      All I see are ivory tower assholes using this current round of paranoia to line their pockets. I distrust any solution that involves me "buying new things".

      So, lets cure cancer.

      --
      I don't need no instructions to know how to rock!!!!
    11. Re:I used to run Folding@... by Anonymous Coward · · Score: 0, Insightful

      Just curious, what kind of evidence would you like to see that you would call "good enough?"

      Science, by it's nature, can't be definitive 'til the actual event occures. Lots of "planes" never left the earth or crashed on takeoff before the Write brothers hit the scene. We were only 100% certain we could make anything fly when we saw a plane actually flying.

      So let's say you're trying to see if you're on a course that will cause something bad to happen. You want to know because you'd like to change course to avoid it if it's going to happen. You WILL NOT be 100% certain you are on that negative course until(unless) you see the bad thing happen. Then it will be too late to avoid it. In fact, if you do successfuly avoid the bad thing, there's a really good chance you won't ever be able to tell if it was because of your actions, some other action, or just bad initial predictions.

      You still want to make a very good educated guess, because the bad thing is very bad. Knowing that you will NEVER have "proof" that the bad think will occurre, what level of evidence will you accept before commiting to difficult, expensive actions to avoid the bad thing.

      To tell the truth, I'm not particularly interested in whether you believe human-caused global warming is in effect. What I'm interested in is what sceptics are looking for in regard to evidence. When someone says the evidence isn't good enough, that implies that some kind of evidence would be. Can you tell me what that would look like?

    12. Re:I used to run Folding@... by ZorinLynx · · Score: 3, Insightful

      This only applies if you use electric heating.

      In most places, electrical energy costs a HELL of a lot more per watt-hour than other sources like natural gas, oil, propane, and so on.

      So unless you heat your home with electricity, which practically no one north of Florida does unless they have VERY cheap electrical power, you'll still be paying more by running computers.

    13. Re:I used to run Folding@... by Anonymous Coward · · Score: 0

      It probably has more to do with the increased power consumption involved, and that the variable power generating plants tend to be ones that produced CO2, like coal-fired thermal plants.

    14. Re:I used to run Folding@... by ppanon · · Score: 1

      Yep. It almost makes you wish that nobody had done anything about 2-digit dates so that January 1,2000 could have been a serious problem. That way you wouldn't have revisionist people denigrating the efforts put in to avoid the Y2K problem as a waste of resources. I think a lot more people would be willing to appreciate the potential risks of Global Warming if, among other glitches, their company's payroll systems had made it hard for them to get a paycheck in the first few months of 2000.

      --
      Laissez lire, et laissez danser; ces deux amusements ne feront jamais de mal au monde. - Voltaire
    15. Re:I used to run Folding@... by modecx · · Score: 1

      Gore is an idiot. The real "Inconvenient Truth" is that following Gore's advice will kill you within minutes. I'm not convinced that mass suicide is really the right answer.

      Yeah, but if we did that, we'd really fuck the CO2 levels of the Earth, you know, about 2 days to a week later, anyway.

      --
      Constitutional rights may be respected, repealed, or modified; but they must never be ignored.
    16. Re:I used to run Folding@... by scottv67 · · Score: 1

      So unless you heat your home with electricity, which practically no one north of Florida does unless they have VERY cheap electrical power, you'll still be paying more by running computers.

      I don't think anyone would disagree with you. The point that the parent post was trying to make is that a nice side benefit of running a distributed computing client like F@H is that the heat from your computers will help heat your home. Would anyone suggest running a bunch of quad-cores at 100% as a replacement for natural gas? No. But since you have donated the cost of the electricity to run those machines to the distributed computing project, the heat generated by the PCs is free.

      Yes, my gas furnace runs less often when my Folding machines are going full-throttle.
      http://kakaostats.com/usum.php?u=583666

    17. Re:I used to run Folding@... by scottv67 · · Score: 2, Insightful

      ...outweigh the years of life extended by treating cancers.

      It's easy to feel that way until someone in your family is diagnosed with cancer. Also, treating cancer does not just "extend life". There are a lot of younger people (20 to 40 years old) who get different forms of cancer. For them, it's not "will I live to 76 or will i live to 80?" but "will I live to see 30?". Don't even get me started on the kids who are afflicted with these diseases.

    18. Re:I used to run Folding@... by CajunArson · · Score: 1

      You sir are a candidate for the Fox 5 at 10 school of massively misjudging actual risks. Here's a hint: If you thought that pollution from using your computer was going to be SO great that it would dwarf the benefits of curing CANCER (a disease that was killing people a long time before we had global warming hysteria) then you should probably never: 1. use a fucking computer; 2. never destroy the "environment" by READING OR POSTING TO SLASHDOT!!!

      --
      AntiFA: An abbreviation for Anti First Amendment.
    19. Re:I used to run Folding@... by jhol13 · · Score: 1

      Can I run it so that speedstep/cool'n'quiet works? What I mean I do not want to run anything which increases the CPU frequency. Instead it should keep the CPU at lowest freq. Can this be accomplished?

    20. Re:I used to run Folding@... by Sentry21 · · Score: 1

      In university, I moved in with a roommate into a 'rear suite' (the street number was 669 1/2) which had recently been renovated, but which had also spent a great deal of time uninhabited. As a result, the utilities had been shut off, since no one was using them. 'Utilities' in this case, however, refers only to electricity, since in this area (Fredericton, NB), any heat sources other than electricity and oil (which would be hauled to your home in a tank truck) was unthinkable. Natural gas was 'too new' and 'dangerous', and how could it be trusted, even though the rest of the world has been using it for decades?

      So the place is heated by electricity, and we move in literally 20 minutes after seeing the place (my roommate was on his way into town with a moving truck while I was apartment hunting) so we don't have time to get the electricity turned on. Furthermore, it will take a day or two for NB Hydro to get a guy out there to do the job. So, now we have a poorly-insulated (despite renovations) apartment with no heat, no electricity, no lights, etc. It's basically a box with doors at this point.

      Except - what's this! - the electrical sockets on the front wall of the unit, the wall that we shared with the house itself, were apparently on the house's breakers. Curiously enough, this was where we had decided to plug our computers in already. Well, problem solved.

      After arranging furniture, setting up two tables, plugging in our switch, computers, monitors, etc., and loading up Serious Sam, we found ourselves in a much more comfortable situation until we could get the heat turned back on.

      Moral of the story: never underestimate the capability of AMD, ATI, and Samsung to make your December more comfortable.

    21. Re:I used to run Folding@... by porpnorber · · Score: 2, Interesting

      Meanwhile, since I live in Canada and by this time of year I do need heating, I have my boinc client running at 100%, I'm doing some good, and (since the peak capacity of the machine is justified in other ways) it's not costing a penny. The heating here is electric anyway; it may as well do some computation on its way into my home!

      Doing whatever@home in the winter is just good sense.

      Now what's needed is a distributed computing client that is controlled by a room thermostat. No, really, I'm totally serious.

    22. Re:I used to run Folding@... by mrbluze · · Score: 1

      I do take your point, but I guess my argument was kind of a bit different - not that there should be no research, but that all the number crunching and so forth does consume a fair bit of power. Computers and associated components already account for 3% of energy expenditure and something like two thirds of office computers are never switched off. I guess you could say "use the switched on ones for folding @ home", but why not switch them off instead?

      Why shouldn't drug companies provide the computing power instead? They make the biggest investment in research but also get the economic benefits.

      I do empathize for anyone who has a chronic / terminal illness, the sacrifices they have to make and how it can devastate families, and that, knowing there are no true cures, people who have had cancer are always having a cloud over their head. But denying them a cure was never my point.

      --
      Do it yourself, because no one else will do it yourself. [beta blockade 10-17 Feb]
    23. Re:I used to run Folding@... by steevc · · Score: 1

      This gets me thinking that maybe I should use a temperature sensor that makes Folding/dnet/whatever run whenever it gets cold enough to need the heating.

      It's probably not a good idea to run these on servers if you are having to cool the server room already.

      I do have a bit of a conflict between my geeky side wanting to run this stuff and my green side that wants to cut my energy usage. As others have pointed out a good compromise is to have an app that can just use a limited %age of the available CPU like Folding can on Windows. I'm running dnet on my dual-core laptop, but only letting it use one core to keep the heat down.

    24. Re:I used to run Folding@... by Petersson · · Score: 1


      In fact, you can even reduce your carbon emissions to zero.

      Al Gore


      At first, Al Gore should reduce his own personal CO2 emissions to zero, e.g. to stop breathing.

      --
      I'm not insane. My mother had me tested.
    25. Re:I used to run Folding@... by bhima · · Score: 1

      I own a modern turbo diesel and it does not emit "huge plumes of black smoke that puff out are full of nasty shit". Thus I know that your statement is false.

      This calls into question the rest of your statements which are probably false and certainly histrionic.

      --
      Nothing in the world is more dangerous than sincere ignorance and conscientious stupidity.
    26. Re:I used to run Folding@... by EsbenMoseHansen · · Score: 1

      I'm not yet one of the climate change true believers.
      [...] Buy a new car and light bulbs filled with mercury!"

      To be fair, the saved electricity means less mercury emission from coal plants, so the mercury, at least, is of little concern.

      Or, you could look into LED.

      --
      Religion is regarded by the common people as true, by the wise as false, and by rulers as useful.
    27. Re:I used to run Folding@... by TeknoHog · · Score: 3, Informative

      Can I run it so that speedstep/cool'n'quiet works? What I mean I do not want to run anything which increases the CPU frequency. Instead it should keep the CPU at lowest freq. Can this be accomplished?

      Linux's CPU frequency scaler has this option. For example the 'conservative' governor has the file /sys/devices/system/cpu/cpu0/cpufreq/conservative/ignore_nice_load. So a program running with lower than default priority will not increase CPU frequency.

      I use a script to handle CPU frequency changes. When I'm at home with my laptop, I use the "ignore nice" option which in practice will turn the fan off. YMMV. When I go somewhere, I can set the CPU to full steam.

      --
      Escher was the first MC and Giger invented the HR department.
    28. Re:I used to run Folding@... by mdwh2 · · Score: 1

      But then I realized that I didn't really need to use my computers as heaters...and did a number for the planet and closed the client.

      Well it's a matter of priority. I'd agree with this when it comes to the pointless ones like RC5 cracking, but I think trying to cure cancer counts as one of the more worthwhile causes for using energy, compared with all the other things we humans do.

      Put it this way, you think you're saving the planet by not running this program, but you still use your computer to come onto Slashdot to tell us about it?;)

    29. Re:I used to run Folding@... by mdwh2 · · Score: 1

      This only applies if you use electric heating.

      In most places, electrical energy costs a HELL of a lot more per watt-hour than other sources like natural gas, oil, propane, and so on.


      He did say "heater", which usually implies a small electric one.

      You are correct if someone was trying to heat their whole house by a fleet of PCs, but I don't think it's a problem if someone just switches on one PC to help give extra heating when it's cold.

      Put it another way - if it was freezing cold, I doubt anyone would feel guilty if they turned on an electric heater. I don't know why people do feel guilty about switching on a PC.

    30. Re:I used to run Folding@... by jedidiah · · Score: 1

      Nah.

      Every vehicle he owns or uses should be converted to electric. He
      should use his "clout" to make this happen and serve as a POC for
      alternate fuel vehicles in general.

      He should lead the way rather than being just another spoiled wealthy American.

      --
      A Pirate and a Puritan look the same on a balance sheet.
    31. Re:I used to run Folding@... by Aetuneo · · Score: 1

      [Citation Needed] Prove it. Simply saying something which you consider to be obvious does not make it obvious to other people, or even true.

      --
      Everything is subjective.
    32. Re:I used to run Folding@... by RicktheBrick · · Score: 1

      There are plenty of volunteer that give a huge amount of computing power. The first place volunteer has over 1.3 million results and several have more than 100,000. So there must be someone who believes in donating a lot of computing time. I can imangine how much time it would take just to install the program in the several thousand computers required to get that many results. The question is "Is it better to donate the computing time or is it better to donate the cost of the electricity needed by the computers." WCG needs each results to be done by at least 3 computers and those results are compared to each other to ensure accurate results. This means that the computing power of the grid should be divided by 3 to give an acurrate equivalent. There is a new computer being bullt in Texas that will soon be doing over 500 petaflops so maybe it will soon be more economical to donate the money rather than the computing time.

    33. Re:I used to run Folding@... by Anonymous Coward · · Score: 0

      Your raise a good point. This is why I stopped using BOINC on my computer. My machine runs 90 watts at idle and 120 watts with BOINC running (my UPS has a power meter). A great improvement to the project would be to automatically adjust CPU usage to prevent this power spike. Also, I wonder if you can run some type of cron job to only run BOINC during the winter months so you don't increase the load on you air conditioner in the summer but decrease the load on you furnace during the winter.

    34. Re:I used to run Folding@... by ioshhdflwuegfh · · Score: 1

      [...] if X, then Y [...] [...]But we can estimate the probability of X (based on the current state of knowledge), and explore the consequences if X *does* occur.[...] Sure it's possible to explore the consequences of X being true, but it is not possible to estimate the probability of X being true. The classic example is the Newtonian gravity: it surely felt as it is definitely true for quite a few years, but then it turned out not to be true at all. We could say it is approximately true, but with what probability? Does that even make sense to ask?
    35. Re:I used to run Folding@... by ioshhdflwuegfh · · Score: 1

      Now what's needed is a distributed computing client that is controlled by a room thermostat. No, really, I'm totally serious. Thanks for the clarification 'cause for a moment I did think you were joking.
    36. Re:I used to run Folding@... by Belial6 · · Score: 1

      I'm not sure what you are saying...

      Are you saying the the quote is false? As, the [Citation Needed] is linked in the post.
      Are you saying that when you exhale, you don't release carbon into the atmosphere? If so, you need to take a biology class.
      Or, are you saying that you can survive for hours without breathing? If so, I would be very impressed by seeing a demonstration.

    37. Re:I used to run Folding@... by Anonymous Coward · · Score: 0

      Then who will send back the evil...Man...Pigbear?

      *GAH* (gets ripped in half)

    38. Re:I used to run Folding@... by Anonymous Coward · · Score: 0

      You've obviously never heard of heat pumps. With a ground source heat pump, one dollar of electricity in produces four dollars of heat out. Oil or natural gas have to be over four times less expensive than electricity per BTU to be competitive. Also if you've never heard of Peak Oil either, you have no clue how fast the cost of oil and gas are going to double, and double, and double. Electric base board heaters AKA electrical resistance heating, may be competitive before spring :-(

    39. Re:I used to run Folding@... by mazarin5 · · Score: 1

      ...the 'conservative' governor ... nice_load ...
      --
      Warning: Semen may contain traces of nuts. At first glance, I thought this was also something else completely.
      --
      Fnord.
    40. Re:I used to run Folding@... by Anonymous Coward · · Score: 0

      Yeah right, buy a Kill - A - Watt and you'll see that it double's your electical usage.

    41. Re:I used to run Folding@... by Aetuneo · · Score: 1

      I am saying that by simply saying something, without proving it in any way, does not make it true.

      [Citation Needed] primarily refers to the fact that most assertions in wikipedia are required to be citied in a source - no original research or opinions.

      I never said that exhaling does not release Carbon Dioxide, or that it is possible to survive without inhaling Oxygen.

      I simply said that saying that "The real "Inconvenient Truth" is that following Gore's advice will kill you within minutes" may not be true, and I would like to see a proof of that.

      If you wish to claim that the only way to become carbon neutral is by not breathing, that claim is easy to refute: surround yourself with plants. That can negate the carbon dioxide produced by your exhaling. Also, even if you stop breathing, your corpse's decomposition will release Carbon Dioxide into the atmosphere, so death doesn't really create carbon neutrality; it only does if you die in a forest, or perhaps an ocean (a place with a lot of plants, anyways).

      So, prove it. Explain why. Of course, this being slashdot, I don't really expect a well-thought out response. While it would be nice to hope for a few paragraphs of logic explanations of why Al Gore's advice will get you killed, I would be perfectly happy with something along the lines of "Because I said so," or "Go prove it yourself if you want a proof." Either of those would be much more funny, certainly.

      --
      Everything is subjective.
    42. Re:I used to run Folding@... by Belial6 · · Score: 1

      The citation is the movie "An Inconvenient Truth". I even gave you a link to a clip of the movie that specifically states the quote. I don't know what you are babbling on about Wikipedia for. The video clip is absolute proof of the quote. If you think that the video is faked, then the only way you will believe it is if you source the video yourself. Just rent "An Inconvenient Truth", and watch the screen just before the ending credits. What would you accept as a valid citation for the quote if you wont accept the movie itself as evidence of what was said in the movie?

      The quote is:
      "In fact, you can even reduce your carbon emissions to zero."

      It is not:
      "You can live your life in a carbon neutral way."

      Let me state the quote one more time, as you seem to have a hard time reading it:
      "In fact, you can even reduce your carbon emissions to zero."

      So, are you asking for a citation that Gore actually made the statement? Are you asking for a citation that breathing is a carbon emission? Or are you asking for a citation that not breathing leads to death?

    43. Re:I used to run Folding@... by Aetuneo · · Score: 1

      Ah, so we're arguing over the phrasing of a statement, not over the meaning of a statement. Sorry, I'm used to interpreting most things as they are meant (or as I think they are meant), not as they are said.

      I'm still going to argue about it, however: If one considers the phrase "you" to refer to a human's habitat (a rather large stretch of the term), it is, indeed, possible to reduce that habitat's net carbon emissions to zero, by completely negating all of the Carbon Dioxide emissions of the animals in that habitat with the Carbon Dioxide intake of the plants in the habitat. That leads to carbon neutrality of a habitat. From that, it would not be a stretch to make a habitat carbon-negative -- that is, the plants in the habitat would consume more Carbon Dioxide than the animals in the habitat produce (as a side note, I really don't see why people keep on going on about carbon neutrality. If they really wanted to help the environment, they would try to go carbon negative).

      Of course, this all relies on the assumption that the term "you" can be stretched to refer to a habitat, which I doubt most people would think it could be.

      --
      Everything is subjective.
    44. Re:I used to run Folding@... by Belial6 · · Score: 1

      No, I would not assume that "you" means your entire environment, and I do not accept the carbon footprint being the real meaning, as once we fall into the, mode of interpreting what we think he really meant, we might as well pull out the bible, and start looking for passages that we can interpret to mean that we should buy hybrid cars. Remember, this is supposed to be a college level seminar that is supposed to be using solid clear science to convince people of global warming. When you are dealing with science, you don't leave people to figure out what you REALLY meant. We are not talking about a casual conversation after all.

      Just for fun, since that is were we have moved to, I will argue the habitat line. I will also stretch a term. My habitat is the planet earth, and includes the atmosphere, so the only carbon footprint I am leaving is what escapes into space, although one could also stretch the term to mean our entire solar system , if not the whole universe. Any idea how much carbon we release through human activity out into space? I would assume that we have very little that has left the solar system, and none out of our galaxy. So, rest assured that my carbon foot print is 0. I'm just concerned with the entire galaxy, instead of being so short sighted as to only think of my metaphorical back yard.

    45. Re:I used to run Folding@... by owndao · · Score: 1

      Smaller apartments in the southern U.S. still use electric heating. It's compactness and safety are apparently more important than the fact that the most power that you can theoretically transfer to an electric load is 50%. And that's only if the load seen by the generator is the complex conjugate of the generator impedance (which it never is). It makes some of us electrical engineers sad :-( as many other devices used are essentially lossless (transformers, capacitors, inductors, some types of motors, etc.). Many people don't have a clue as to how inefficient their electrical devices are as seen from the power station.

      --
      Be as you would have the world become.
  3. Yeah, but... by sh3l1 · · Score: 1

    Yeah, but they still have to gather all the research and organize it, the computer will be much faster than the human operators. Oh, and when this thing finally discovers that it doesn't need humans i would like to personally say that I humbly accept our new robot overlord.

    --
    Help Me! I'm trapped in the tubes! Oh noes! Here comes a internet!
    1. Re:Yeah, but... by Anonymous Coward · · Score: 0

      Gaia would like to thank you for your peaceful surrender. I / we did not want to have to use mentalics on anyone.

    2. Re:Yeah, but... by Cassius+Corodes · · Score: 1

      Thanks ok - they just wire together a whole bunch or researchers to make that go faster.

      --
      Control is an illusion, order our comforting lie. From chaos, through chaos, into chaos we fly
  4. The Answer is... by deep_creek · · Score: 0, Offtopic

    The Answer is 42.

    1. Re:The Answer is... by Anonymous Coward · · Score: 0

      in base 13

  5. Me next! by Arancaytar · · Score: 1

    Ahem: Imagine a Beowulf----

    Oh wait.

    1. Re:Me next! by ppanon · · Score: 1

      Ahem: Imagine a Beowulf----
      cluster of animated Angelina Jolie-lizards?

      --
      Laissez lire, et laissez danser; ces deux amusements ne feront jamais de mal au monde. - Voltaire
  6. Storm Botnet by creativeHavoc · · Score: 5, Funny

    If they wanted to knock that 10 years down to 5 they could just buy a chunck of the storm worm bot net!

    --
    insight through the mind
    1. Re:Storm Botnet by Varun+Soundararajan · · Score: 1

      I am serious wondering why they dint think of the PS3s. 700,000 PS3s recently subscribed to a network that ended up in Peta Flops peak performance. If I were managing this stuff, I would seriously take a look on that direction. Cell Processors are designed for such distributable tasks and they are very good at it.

    2. Re:Storm Botnet by scottv67 · · Score: 1

      I am serious wondering why they dint think of the PS3s. 700,000 PS3s recently subscribed to a network that ended up in Peta Flops peak performance.

      I think you are thinking of the Folding@home project at Stanford:
      http://folding.stanford.edu/English/FAQ-PS3

  7. How good are the programs by gringer · · Score: 4, Insightful

    I hope they're using programs that've had a few computer scientists' eyes over them. One of the issues I see with supercomputing is that people tend to see it as a way to get around dumb code(1) — if the computer's fast enough, you can implement *five* infinite loops, have an exponential time algorithm, and still get the calculations done before dinner!

    (1) although from their point of view, it's just slow code.

    --
    Ask me about repetitive DNA
    1. Re:How good are the programs by ppanon · · Score: 1

      Heh. Since a lot of the calculations are floating point, I think you're at least as likely to have numerical analysis errors that make the data come out of that loop be dominated by precision errors. But I think in a lot of cases, they do use optimized libraries (i.e. LINPACK) that do most of the math properly and limit the options for really dumb code.

      --
      Laissez lire, et laissez danser; ces deux amusements ne feront jamais de mal au monde. - Voltaire
    2. Re:How good are the programs by Idarubicin · · Score: 1

      I hope they're using programs that've had a few computer scientists' eyes over them.

      Seeing as how the lead researcher holds M.Sc. and Ph.D. degees in Computer Science, is cross-appointed to the Departments of Computer Science and Medical Biophysics at the University of Toronto, and is a Visiting Scientist with IBM's Center for Advanced Studies in Toronto...

      ...it seems likely that a computer scientist may have cast his eyes over the code once or twice.

      Where on Earth does this idea come from that multicenter, multimillion-dollar research projects are run by idiots? Neither funding nor talent are in particularly short supply in the field of cancer research, and squeezing extra speed and power out of massive bioinformatic analyses is a hot area.

      --
      ~Idarubicin
    3. Re:How good are the programs by ioshhdflwuegfh · · Score: 1

      Where on Earth does this idea come from that multicenter, multimillion-dollar research projects are run by idiots? Neither funding nor talent are in particularly short supply in the field of cancer research, and squeezing extra speed and power out of massive bioinformatic analyses is a hot area. [emphasize added ] So then all these multi-milion/talent/center/computer things and people are ultimately being run by some hotness of a hot area, the hot stuff itself,... hot air?
    4. Re:How good are the programs by Anonymous Coward · · Score: 0

      Where it comes from are the projects and papers published by grad students on their use of massively parallel Python programs that utilize 1000 nodes on a large campus cluster for months on end. When the same little bioinformatics program written in usually less time in C could have finished faster on a simple laptop.

      I've seen this done. It works, and it gets renewed funding.

    5. Re:How good are the programs by Anonymous Coward · · Score: 0

      Where on Earth does this idea come from that multicenter, multimillion-dollar research projects are run by idiots? Neither funding nor talent are in particularly short supply

      Idiots are also not in particularly short supply.

  8. harnessing the power.... by hb253 · · Score: 1

    If only they could somehow harness the power of steam!

    --
    Self awareness - try it!
  9. 162 years? by sayfawa · · Score: 4, Insightful

    Okay, not that I'm knocking how cool this grid computing is, but that estimate of 162 without grid computing couldn't possibly be taking into account the acceleration of computing power. Maybe with today's computers it would take 162 years, but after the first couple of years just get a new computer and cut the time in half.

    Which reminds me of how towards the end of my grad school career I did hours long simulations that would have taken weeks at the beginning of grad school. I was in grad school a long time :(

    --
    Free the Quark 3 from asymptotic confinement! Bring your charm! Don't get down! All colours and flavours welcome!
    1. Re:162 years? by RealGrouchy · · Score: 1

      The same could be said for life expectancy: right now the average North American life expectancy is around 70-something. I wouldn't be surprised if--when I'm in my late 60s, that the life expectancy will have increased to 80-something or even 90.

      - RG>

      --
      Hey pal, this isn't a pleasantforest, so don't waste my time with pleasantries!
    2. Re:162 years? by JK_the_Slacker · · Score: 3, Insightful

      We're computer scientists. We can calculate these kinds of things. Protein folding calculations take a ridiculous amount of time and processing power. That's a reflection of how complex your dna is, not a reflection of how much processing power we have at our disposal. If we could borrow from the computing power of the future, then you might be right. But the fact remains, we only have what's at our disposal now. At the current state of computing technology, the calculations would take 162 years.

      That's the thing, though... as computing power scales, so does the distributed computing. With one centralized server, if you start running a simulation on it, you have to continue to run that simulation on that server. On the other hand, in a distributed environment, when newer, more powerful machines come out, you can just set up a simulation client on it, and increase your calculation speed by that much. I used to run Folding @ Home on a 700 MHz computer with 256 MB of RAM. I later upgraded to a 1600 MHz computer with 512 MB of RAM. Now, I fold on a 2.2 GHz dual-core machine with 2.5 Gig of RAM. Does the newer machine do the work much faster than the two older machines? Yes, it does. Does that mean that the work I did on those older machines was needless? No. I still fold occasionally on the 1.6 GHz machine, and it takes about a week to turn over a WU, as opposed to less than 24 hours on my main machine. Should I stop folding on the old one because the new one works so much faster? No, because that's about 52 WUs I don't have to fold on my main machine per year. It's an increase in computing power, and that's always desirable in a situation like this.

      It's all fine and dandy to talk about how much computing speed will increase in the future... but, in the end, reality overcomes theory. There are people dying of cancer right now, people that can be helped by letting computers do the work. True, in two years, the work will likely get done faster... but, that doesn't change the fact that we can't just sit around and wait. When those better computers come in to play, then let's add them to the pool. Until then, let's get something done.

      --
      I'm waiting for a "-1 somepeoplejustshouldn'tgetmodprivileges" meta-moderation.
    3. Re:162 years? by bartok · · Score: 1

      Wow, only 81 years

    4. Re:162 years? by ppanon · · Score: 1

      Given the increase in obesity across the population, I expect average North American life expectancy to decrease. However, for the subgroup that can maintain a healthy diet and a good exercise balance, I think average life expectancy will go up to the range you are talking about.

      If you want to live longer with a good quality of life, eat a healthy balanced diet, make sure you don't let your body fat percentage get too high, and find a low-impact aerobic exercise that you enjoy and can continue to do as you get older. It will keep your heart healthy and your mind active. Swimming, walking, hiking, dancing, that sort of thing.

      --
      Laissez lire, et laissez danser; ces deux amusements ne feront jamais de mal au monde. - Voltaire
    5. Re:162 years? by allenw · · Score: 1

      But there isn't just raw computing power in play here. There is also the IO requirements, memory requirements, etc. That's the beauty of grid computing--by distributing the load you can increase the the throughput of the entire system, not just an individual component.

    6. Re:162 years? by sayfawa · · Score: 1

      My comment wasn't some kind of proposal or solution and was in no way saying that this grid computing isn't a great thing. I was merely making the observation that it's dumb to consider only today's computing power and then come to the conclusion that a calculation will take 162 years, regardless of what the calculation is about. It will obviously take a much shorter time than that since the computers crunching the numbers will occasionally be upgraded.

      But it's not important, it was just a one-liner from TFA and was probably just meant for the lay people in the popular press to show them what an achievement this grid computing is. But it's still a dumb statement.

      --
      Free the Quark 3 from asymptotic confinement! Bring your charm! Don't get down! All colours and flavours welcome!
    7. Re:162 years? by sayfawa · · Score: 1

      Cool, I was having the same thought recently. Depressed about how long it's taken me to finish school and really start life it occurred to me that an average life span of 70 is only for people born 70 years ago when medical technology was crap compared to today. Which allows me to put off saving for retirement (or acting like an adult) without feeling bad.

      --
      Free the Quark 3 from asymptotic confinement! Bring your charm! Don't get down! All colours and flavours welcome!
  10. Done before by gudnbluts · · Score: 1

    Not exactly new, is it. I was running a distributed cancer protein matching app six or seven years ago. Oxford University did it.

    1. Re:Done before by scottv67 · · Score: 1

      Not exactly new, is it. I was running a distributed cancer protein matching app six or seven years ago. Oxford University did it.

      The Folding@home project at Stanford has been around that long as well.
      http://folding.stanford.edu/

  11. 162 years by ConcreteJungle · · Score: 1

    whatever happened to Moore's law?

    1. Re:162 years by JK_the_Slacker · · Score: 1, Insightful

      Moore's law doesn't help us right NOW. If I promise you ten bazillion dollars in 2025, that doesn't help you buy even a stick of gum today.

      Unless, of course, you'd like to stick to the realm of theoretics, in which case I postulate that cancer doesn't exist and neither do you, and by a solid application of Finagle's law I'm about to take a hatchet to my left hand. Do you see my point?

      --
      I'm waiting for a "-1 somepeoplejustshouldn'tgetmodprivileges" meta-moderation.
    2. Re:162 years by Jessta · · Score: 1

      More transistors != more performance.

      --
      ...and that is all I have to say about that.
      http://jessta.id.au
  12. This is great and all but... by Icarus1919 · · Score: 4, Interesting

    But do we see a chunk of the profit that they'll be making off the cancer drugs they make from this data that OUR computers analyzed and then is eventually sold to us for too-high-to-afford prices?

    1. Re:This is great and all but... by SquallStrife · · Score: 1

      Only in America... where according to the health cover firms, it's evil for the government to look after the health of its people.

    2. Re:This is great and all but... by Anonymous Coward · · Score: 1, Insightful

      But do we see a chunk of the profit that they'll be making off the cancer drugs they make from this data that OUR computers analyzed and then is eventually sold to us for too-high-to-afford prices?
      no, but if you ever get any of these diseases you will now have the privilege of being alive.
    3. Re:This is great and all but... by FooAtWFU · · Score: 2, Insightful

      So, you seem to be complaining that the (evil) biopharmaceutical companies are greedy and want money and this is wrong... unless you can have a slice of it too? I think you need some sort of levee around your moral high ground, buddy.

      --
      The World Wide Web is dying. Soon, we shall have only the Internet.
    4. Re:This is great and all but... by SquallStrife · · Score: 1

      I'd say he's more upset at the fact that the biopharmaceutical companies are allowed to hold your health to ransom, even when they utilise YOUR resources to further that stranglehold.

    5. Re:This is great and all but... by S.O.B. · · Score: 3, Informative

      But do we see a chunk of the profit that they'll be making off the cancer drugs they make from this data that OUR computers analyzed and then is eventually sold to us for too-high-to-afford prices?


      The research is being done by scientists at Princess Margaret Hospital in Toronto, a government run hospital. If you knew anything about health care in Ontario you'd know that profit is the last thing on their mind.
      --
      Some of what I say is fact, some is conjecture, the rest I'm just blowing out my ass...you guess.
    6. Re:This is great and all but... by MishgoDog · · Score: 1

      You are one hundred percent correct. We should NOT be contributing our precious *cough*unused*cough* CPU cycles to evil, money grubbing governmental institutions purely so they can further get better profits. No cure for a disease which causes 13% of all deaths is worth that, not unless I see some money for using my precious CPU cycles!

    7. Re:This is great and all but... by CaptainNerdCave · · Score: 0
      if you're really concerned about private companies making money off of your pc... why not join up to seti? i think that is probably going to be the biggest and potentially most controversial discovery of human history up until then, possibly ever.

      i don't know about you, but i'm proud to say that i'm part of a top-ten junior college team that i set up with a few friends. (except that seti@home seems to have changed the junior college teams list to include all teams... :shrug:).

  13. Desktops are not supercomputers by deadline · · Score: 3, Informative

    Every time these "connect desktops to become the fastest computer in the world" articles come up, I have to dust off my Cluster Urban Legends article to clear up the mis-conceptions that abound. I also did a piece on the Linux Magazine site as well that debunks much of the spam-bot supercomputer legend (need to register for that one)

    --
    HPC for Primates. Read Cluster Monkey
    1. Re:Desktops are not supercomputers by nonsequitor · · Score: 1

      The computers participating in the grid project are not just "desktop" computers. The ones connected from my alma mater were the ones that were maintaining thousands of X-Sessions across campus, on all the library machines and in all of the labs in dozens of buildings, supporting a student population of 40,000 students. Not the same as getting the spare cycles from someone's entertainment system or personal computer.

    2. Re:Desktops are not supercomputers by deadline · · Score: 3, Insightful

      I'm not talking about spare cycles. I'm talking about the naive notion that gets repeated in the press "the combined power of all these computers equals one of the fastest supercomputers in the world" For trivial parallel applications this might be true, but just once I would like to see these "supercomputers" run a simple parallel benchmark like High Performance Linpack (used for the Top500 list). My guess is the number of real FLOPS would be much less than expected -- if it even finished. Don't get me wrong, using computers like this is great idea, it is not one of the most power computers in the world, however.

      --
      HPC for Primates. Read Cluster Monkey
    3. Re:Desktops are not supercomputers by jafiwam · · Score: 1

      Seriously, if you can break up a task into small chunks and process it faster than some computer can, WTF difference does it make if it fits your definition of some benchmark or other. Did the data get processed? (_) Yes (_) No Who cares if YOU define a supercomputer a certain anal way and decide it isn't fastest under XYZ criterion.

      You and Tom from Tom's Hardware should get together and chew the fat about your benchmarks.

      Nobody else gives a shit if the data set is done.

    4. Re:Desktops are not supercomputers by scottv67 · · Score: 1

      I'm not talking about spare cycles. I'm talking about the naive notion that gets repeated in the press "the combined power of all these computers equals one of the fastest supercomputers in the world"

      If you know so much about the topic, why aren't you at Stanford telling Dr. Pande and his group that they are wasting their time with all those desktops and PS3's? I'm sure Dr. Pande would love for you to point out how his research would be much better off if he'd just go buy some time on aupercomputer.

      http://folding.stanford.edu/

    5. Re:Desktops are not supercomputers by dabadab · · Score: 1

      I would like to see these "supercomputers" run a simple parallel benchmark


      But the thing is, these clusters are not made for running benchmarks, but for real (and specialized) calculations. My home server processes data for the World Community Grid and I see that the client is silently numbercrunching for a few hours and then communicates for a few seconds (at the amazing speed of about 50 kB/s). And for this, actual usage the grid shows a performance that could only be replicated by a powerful supercomputer.
      --
      Real life is overrated.
    6. Re:Desktops are not supercomputers by mgblst · · Score: 1

      It is an important distinction if you actually have to work on a cluster or a Supercomputer. There are some things that Supercomputers can do, that clusters can't.

      If you application needs to communicate to other versions of itself alot, then you don't want a cluster.

      If your program doesn't then a cluster is fine.

    7. Re:Desktops are not supercomputers by Anonymous Coward · · Score: 0

      You can install Infiniband/Myrinet cards in ordinary computers as well. Of course this is not the case with distributed computing but still you can build something decent with relatively commodity components.

    8. Re:Desktops are not supercomputers by ioshhdflwuegfh · · Score: 1

      Seriously, if you can break up a task into small chunks and process it faster than some computer can, WTF difference does it make if it fits your definition of some benchmark or other. Did the data get processed? (_) Yes (_) No Who cares if YOU define a supercomputer a certain anal way and decide it isn't fastest under XYZ criterion. Yes, you're right, up to a point. Let me illustrate a bit. The original post says:

      The scientists are the first from Canada to use IBM's World Community Grid network of PCs and laptops with the power equivalent to one of the globe's top five fastest supercomputers. Now, that is not quite true: even if you can get certain number of FLOPS on this grid computer, it does not mean that those are the same FLOPS as those gotten on the conventional supercomputer, because the former depend on what you call "breaking into small chunks". Yes, it is anal, but you know, it is not call computer science for nothing. Let me put this other way:

      Nobody else gives a shit if the data set is done. The question is: which data set?
    9. Re:Desktops are not supercomputers by DamnStupidElf · · Score: 1

      Every time these "connect desktops to become the fastest computer in the world" articles come up, I have to dust off my Cluster Urban Legends article to clear up the mis-conceptions that abound. I also did a piece on the Linux Magazine site as well that debunks much of the spam-bot supercomputer legend (need to register for that one)

      Too bad you're wrong in this case, since protein folding is embarrassingly parallel. How do you think Folding@home works?

  14. PS3 Supercomputer by jhines · · Score: 3, Informative

    Folding@home has reached a petaflop out of PS3 games. A record supposedly, from the BBC news. http://news.bbc.co.uk/2/hi/technology/7074547.stm

    I run their PC sw on my systems I keep on. They are getting results, and publishing papers based on the research.

    1. Re:PS3 Supercomputer by larpon · · Score: 1, Funny

      As long as the game developers aren't using the full potential of the PS3 when writing games, this is a good thing :)

      So the solution to keep the idle time of the PS3 high must be to keep developers innovation low!
      EA is already years ahead in this field!

  15. Patents? by DoofusOfDeath · · Score: 2, Interesting

    I'm very glad to help cancer research, but will this also result in the development of drug patents that (a) bankrupt some patients, and (b) prevent other researchers from improving on those drugs?

    Because that would make me feel a little less charitable with my computing power. (Only a little, though.)

    1. Re:Patents? by piojo · · Score: 1

      I'm very glad to help cancer research, but will this also result in the development of drug patents that (a) bankrupt some patients, and (b) prevent other researchers from improving on those drugs? I agree with you, in principle (that it's just not fair for you to gain nothing), but isn't donating your CPU time still the best solution? I mean, it's not as though there's some choice you could make that would likely lead to a better outcome for you.
      --
      A cat can't teach a dog to bark.
    2. Re:Patents? by tsotha · · Score: 1

      Which is worse than not having the drugs at all? Patents expire, and the sooner the drug is developed, the sooner the patent will expire.

    3. Re:Patents? by scottv67 · · Score: 1

      I'm very glad to help cancer research, but will this also result in the development of drug patents that (a) bankrupt some patients

      The alternative is "don't help the distributed computing project" and those drugs will never be 'discovered'. Then, instead of being poor and alive, the patients will be wealthy and at room temperature.

    4. Re:Patents? by Idarubicin · · Score: 1

      I'm very glad to help cancer research, but will this also result in the development of drug patents that (a) bankrupt some patients, and (b) prevent other researchers from improving on those drugs?

      It it makes you feel better, the bioinformatics team is being led by a Canadian researcher out of a Candian institution (the Ontario Cancer Institute at Princess Margaret Hospital, jointly with the University of Toronto). In Canada, chemotherapy drugs are provided to patients free of charge, and pricing is controlled by the provincial government.

      If you're being screwed by the drug companies in your jurisdiction, you need to talk to your government representatives. In the meantime, the counties with proper socialized medicine appreciate your assistance with the project, and would like to extend our thanks.

      --
      ~Idarubicin
  16. I don't get it... by Pedrito · · Score: 3, Informative

    "The researchers estimate that this analysis would take conventional computer systems 162 years to complete."
    They're always saying, "We've knocked decades off of our work by using the right tool for the job." That's like me saying I knocked decades off of the calculations to run an energy minimization on a hexane molecule by running it on my Core 2 Duo instead of my Atari 800.

    I mean, let's face it. They weren't going to let the friggin' program run for 162 years. The problem became solveable when the hardware became available. Hell, within 5 years, that "conventional computer system" will be able to solve it in a fraction of that 162 years and 5 years later, a fraction of that. So what do you do? You wait until the hardware meets up with ability to solve the problem. They haven't saved decades. They probably haven't even saved a decade. Within a decade they'd probably be able to run it in a few days on a conventional computer.

    1. Re:I don't get it... by scottv67 · · Score: 1

      You wait until the hardware meets up with ability to solve the problem.

      So, if I'm following you correctly, you want the medical researchers to stockpile all the research projects that have "heavy computing demands" until Intel comes out with their 128-core CPU? What do we do in the meantime? Just sit around say "Oh jeez, sorry we don't have a treatment for your leukemia. But in ten years, we are going to launch a computer program that will have an answer for us after running for just thirty days!"?

    2. Re:I don't get it... by Pedrito · · Score: 1

      So, if I'm following you correctly, you want the medical researchers to stockpile all the research projects that have "heavy computing demands" until Intel comes out with their 128-core CPU?

      No, you're not following me correctly. My point is, nobody is going to run a program that's going to take decades to run. Instead, they're going to run some scaled down version that approximates a solution or there going to find some other method to solve the problem. When the computing power is available to run it in a reasonable period of time. Since computer speeds increase exponentially, the math to calculate when the best time to try to run the software, is pretty straight-forward. If you say processing speeds double every 2 years (not exact, but not too far off) and you have a program that will take 160 years to run, then if you wait 4 years, it'll only take 40 years for it to run. Another 4 years and it will only take 10 years to run it. So after only 8 year of waiting, you're looking at about 18 years total vs. the original 160 years. So the point is, it sometimes pays to wait. You could start running the program 8 years earlier and get a head start, but with the doubling of speeds every 2 years, that only accounts small fraction of the total computation. That's my point.

    3. Re:I don't get it... by Aladrin · · Score: 1

      Yes, or they could do it RIGHT NOW and save 17 years. (Actually, the sweet spot is 12 years away, since it would then take 2.5 years to run for a total of 14.5 years, and 14 would still take 1.25 years for a total of 15.25 years. So they'd save 13.5 years if they could run it in 1 year on today's computers.) While that's not -decades- it IS over a decade. Do you know how many people die of cancer in a decade?

      http://www.medicalnewstoday.com/articles/37480.php Apparently there's about 550,000 people die of cancer each year in the USA alone! That's 5.5million Americans that could be saved if the cure for cancers comes 10 years earlier.

      I think it's pretty hard to argue that they should just wait and do the calculation later, and 'approximate' calculations aren't very good for this kind of research.

      --
      "If you make people think they're thinking, they'll love you; But if you really make them think, they'll hate you." - DM
    4. Re:I don't get it... by Anonymous Coward · · Score: 0

      You raise interesting point. If I run this program, I am saving Americans?.. At least Americans first, but most likely Americans only. I don't want that. I will wait until Chinese or Russians will have such program, and then plug in. At least they are more likely to share the solution with others.

      By the way, I hear that song about distributed calculations to fight the cancer for a long time, yet all results that gives hope appeared from other scientists, not related to distributed calculations... What's the point then? Waste your time for an empty hope? Probably that's what Americans are wasting their time and efforts for the last decade.

  17. Open Source Software Cures Cancer by atwtftg · · Score: 3, Insightful

    According to the World Community Grid website:

    World Community Grid is making [this] technology available only to public and not-for-profit organizations to use in humanitarian research that might otherwise not be completed due to the high cost of the computer infrastructure required in the absence of a public grid. As part of our commitment to advancing human welfare, all results will be in the public domain and made public to the global research community.

    WCG uses the Berkeley Open Infrastructure for Network Computing (BOINC) client, an open source software project that runs on Linux, Mac and Windows. Headline should read Open Source Software Cures Cancer ;-)

    BoincStats shows you who is contributing to World Community Grid projects. Check it out...and ask yourself why you aren't contributing.

  18. How could this be? by WK2 · · Score: 2, Funny

    How could they knock decades of research off when we are less than 10 years (TM) away from a cure?

    --
    Write your own Choose Your Own Adventure. http://www.freegameengines.org/gamebook-engine/
  19. I can see it now by EEPROMS · · Score: 3, Interesting

    We "the people" run the software and pay the millions of dollars of hardware and electricity costs. When the problem is solved the University patents everything (thank you suckers) and licenses the technology for for a small fortune to some back stabbing Megacorp (TM) drug company. So when "we the people" get sick we have the wonderful knowledge that we have paid twice for the ripp-off drugs. So all things being fair, if you want my cpu spare time I want a part of the license fees to pay for the drugs that cost a house when I get sick.

  20. Yeah, the "Write brothers"... insightful. Sure. by Anonymous Coward · · Score: 0

    The burden of proof of a claim is on the person making the claim.

    Parent post was not insightful and was modded up for political reasons. Sad.

    1. Re:Yeah, the "Write brothers"... insightful. Sure. by Stooshie · · Score: 1

      Did you read or understand your parent post at all?

      --
      America, Home of the Brave. ... .and the Squaw.
  21. SETI by SlashDev · · Score: 1

    Although I did belong to the seti@home program at one time. I wonder if an update would instantly turn all its clients to be used into this cancer research grid instead.

    --

    TOP DSLR Cameras Reviews of the top DSLRs
    1. Re:SETI by eneville · · Score: 1

      Yeah it probably could, but the client program would require some reprogramming. At present it processes sound units looking for various patterns that might indicate some presence out there that is sending a signal. The other distributed programs work in different ways and process work packets differently. Take a look at the folding@home project. The bigger issue for the Canadians is probably bandwidth costs, although that said, SETI probably has a bigger costs as it's DSP data.

  22. I OBJECT!! by Anonymous Coward · · Score: 5, Interesting

    I know this research, and the people involved in it very, very well, and I think this project is a very sad, very large waste of computing time.

    Let me back up and explain what the project is doing. To simplify a little bit, the vast majority of "work" in the cell is done by proteins. While DNA can be thought of as something like a simple "string", proteins have complex three-dimensional shapes. Knowing those 3D shapes is of great interest to biologists. There are several reasons for that. One is that it can allow easier design of drugs targeted at a specific part of the protein. Another is that by seeing the shape, we can understand how all the mutations that occur in disease might be affecting its function.

    The primary way to determine the shape of the protein is to take the protein and to grow it into an ordered crystal. You can then shine an x-ray beam through the crystal, and the diffraction pattern that emerges can be, through some very complex math, reverse-engineered into a 3D structure. Typically the most difficult part of this process is finding the specific chemical conditions that will allow a crystal to grow. These conditions differ from protein to protein.

    This project is not "solving cancer", by any means. Rather, the people in Buffalo have generated a high-throughput way of screening different chemical conditions to determine which ones might allow a protein to grow. They use robotics to screen about 1000 conditions, and take pictures of each condition. The question then becomes: can you automatically process the pictures to find crystals. That's the goal of this project, to help automatically identify crystals in this screen.

    So why do I object so strongly to this work? There are three reasons.

    First, the project has nothing to do with cancer. In fact, the proteins being analyzed are not in any way "cancer-specific proteins" -- many of them are not even human!! This "cancer" pitch is a sales job, and nothing but a sales job. As a cancer researcher, it offends me that people try to use the disease to justify research that is this unrelated.

    Second, the project is ill-conceived, technically. In no way did the group in question (Igor Jurisica's lab, in Toronto) carefully select a machine-learning approach to identify good ways of analyzing images. Instead, they have just selected something like 1000 different techniques, and are running *all* of them on every image they have. It's a fishing expedition, with the hope that one of those thousand metrics they return will be a useful predictor.

    Third, the techniques selected are basically arbitrary. Most egregiously, there appear to be NO Fourier transforms included in the analysis!! Further, the images generated by the software appear to be transforms of something called "gray level cooccurrence matrices", and the computation of those can be estimated in no more than five minutes. So why are they taking 5 hours per unit? It appears that they have chosen to implement an exhaustive GLCM search that is an order of magnitude slower, rather than using existing estimation procedures that are ~98.5% accurate. Is that an excuse to use more computer time? Is there any scientific merit to that? Why aren't Fouriers included, since they are a standard technique for image analysis?

    I have a number of computers that I run various BOINC projects on, but this will NEVER be one. It's a fishing expedition, being sold as cancer research, and that is a sad way to deceive the public.

    1. Re:I OBJECT!! by Tom+Womack · · Score: 2, Interesting

      Given that most proteins contain tryptophan, and tryptophan fluoresces under UV, and UV lasers are not that hard to come by, wouldn't it be easier to shine a UV laser at the crystallisation plate and detect by subtraction where the glowy bit is?

      Or, as a lot of molbio automation companies are offering, actually shine an X-ray beam through the putative crystal onto a detector and see if it diffracts.

      Fully automated high-throughput crystal growing strikes me as a bit of a boondoggle; the sophisticated robots required for the last steps of automation are an order of magnitude more expensive than having three shifts of trained Indian or Chinese workers moving plates around and looking through microscopes.

    2. Re:I OBJECT!! by defile39 · · Score: 2, Insightful

      I'll start off by saying that I know little more about x-ray crystallography than what you explained in your post. My concern with your objection is, however, more related to your criticism. I understand your distaste for the project's underhanded tactics in trying to generate publicity. Beyond that, however, your criticisms fail to address the merits of what the group IS doing (other than what I perceive as your criticism of high-throughput screening in general). If you feel that your technical criticism has merit, have you explained your concern to the team conducting the analysis?

      Besides, even though many of the proteins are not proteins associated directly with cancer, the knowledge that will come from having thousands of additional proteins 3-D structures will surely aid future cancer research.

    3. Re:I OBJECT!! by noprunesmoothie · · Score: 1

      They are taking 5hrs per unit because the calculation time had to be increased in order for it to be accepted for grid computing. The more you know.....

    4. Re:I OBJECT!! by Anonymous Coward · · Score: 0

      umm, you expect them to do what with their millions of tax dollar funds? Something useful?

    5. Re:I OBJECT!! by Anonymous Coward · · Score: 0

      Actually the tryptophan solution might not work because you have to distinguish ordered crystals from aggregates. The aggregates will glow too, so that won't help. That being said, seems like you could determine which region of the image to focus on that way pretty quickly. I wonder if they'd looked at that!

    6. Re:I OBJECT!! by C+Cumbaa · · Score: 2, Informative

      In no way did the group in question (Igor Jurisica's lab, in Toronto) carefully select a machine-learning approach to identify good ways of analyzing images. Instead, they have just selected something like 1000 different techniques, and are running *all* of them on every image they have. It's a fishing expedition, with the hope that one of those thousand metrics they return will be a useful predictor.

      Not quite. The machine learning bit comes second. You have to spend the CPU cycles to extract features from the images first. Only then can your favourite ML technique tell you if the features are predictive. The first ~1000 features (already computed, locally) show some promise, and that's why this project will explore the image feature space a bit more (~12000 features). Once we get Grid results back from our human-scored image set, any features that are a clear waste of time will be dropped.

      Third, the techniques selected are basically arbitrary. Most egregiously, there appear to be NO Fourier transforms included in the analysis!!

      Again, not really. The techniques selected are based heavily on our own research and on successful methods drawn from the literature. I can confirm that no Fourier analysis is done. Fourier analysis can tell you that there are high-frequency components in the image. So can simple edge detection. And a Radon transform will find the straight edges of a protein crystal. Publish your Fourier-based method of distinguishing amorphous precipitate from protein crystal, and I will include it in Phase II of the project. Before you do that, maybe also read up on wavelets.

      So why are they taking 5 hours per unit? It appears that they have chosen to implement an exhaustive GLCM search that is an order of magnitude slower, rather than using existing estimation procedures that are ~98.5% accurate.

      More time = more exploration of feature space. Show me proof of a "98.5% accurate" approximation method, and I will make sure that gets in to Phase II as well.

      By the way, I noticed that the "Slashdot Users" team on the World Community Grid is ranked #4. You guys are huge contributors. Whether you contribute to this project, or Dengue Fever, or whichever, thanks.

      Christian Cumbaa
      Research Associate
      Ontario Cancer Institute

    7. Re:I OBJECT!! by C+Cumbaa · · Score: 2, Informative

      Here is a more complete story: between changing compilers, moving from the development platform to the target platforms, and identifying some redundant computation in one corner of the algorithm, we were able to reduce the run-time from about six hours to five minutes. This allowed us to undo some rather brutal compromises (accuracy for speed) we had made in a previous stage of development, when we thought the analysis was running unacceptably long for Grid purposes.

      The extra hours are not busy work.

      Christian Cumbaa
      Research Associate
      Ontario Cancer Institute

    8. Re:I OBJECT!! by chitchat98765 · · Score: 0

      You are hereby nominated for "idiot post of the month". Congratulations and good luck.

    9. Re:I OBJECT!! by cwtrex · · Score: 1

      So what projects do you deem worth while? I would rather be contributing with my BOINC program to something worth while such as cancer research. I'm only running two currently. The World Community Grid project for folding and the TANPAKU project which seems to be similar.

      Thanks for any advice for grid computing projects.

  23. Question to people running distributed apps by this+great+guy · · Score: 1

    Question to slashdotters: I am wondering... Would you accept to run a distributed app if you didn't know what it did (let's say the developers want the purpose of the app to remain secret) but if there was some kind of competition with money prizes for, say the top-100 CPU time contributors ? Such as $5000 for the 1st, $1000 for the next 4 and $500 for the next 95.

    (Of course I assume some would be tempted to reverse engineer the distributed app, because of pure curiosity).

    1. Re:Question to people running distributed apps by Aladrin · · Score: 1

      No. It's the same reason I don't play the lottery: I'm not going to win, so the reward holds no sway in my decisions.

      --
      "If you make people think they're thinking, they'll love you; But if you really make them think, they'll hate you." - DM
  24. Distributed computing is a lie by sendorm · · Score: 0, Troll

    Think of it. A 100 watts worth cpu which can do thousand points of worth job in a day. Why thousands? Because the CPU is capable of doing millions of other things, thats why it is build in the first place. A 10 watts special equipment, build from FPGA's just for the job in interest. It can do million points* of worth job in a day. Dont you feel stupid now? Ati's 1950 cards can do 30 times much work then your super uber cpu. Dont you feel stupid now? It's like trying to replace a tank with 100 fiat's. Tank's are created with wars in mind, they are built for that. Not fiat's. The millions of watts of wasted energy for distiributed computing non-sense is pushing the earth to global warming. That wasted watts also mean wasted money, go give your money to a fund or university, so they could buy dedicated hardware and do the required job much quicker. (* : numbers may be exagrated, but you get the idea)

    1. Re:Distributed computing is a lie by scottv67 · · Score: 1

      Ati's 1950 cards can do 30 times much work then your super uber cpu. Dont you feel stupid now?

      Hmmmm....using video card GPUs for scientific number crunching. I wonder why no one has thought of that one...
      http://folding.stanford.edu/English/FAQ-ATI

      The millions of watts of wasted energy for distiributed computing non-sense is pushing the earth to global warming.

      [citation needed]

      That wasted watts also mean wasted money, go give your money to a fund or university, so they could buy dedicated hardware and do the required job much quicker.

      Uhh, no. I am reluctant to donate money to 'charities' because a small slice of every dollar gets lost to "overheard" (salaries for administrative staff, expenses incurred by those staff, etc.). If I donate to the Folding@home project at Stanford by running Dr. Pande's software on my PCs, I know *exactly* what my donated dollars are being used for.

    2. Re:Distributed computing is a lie by sendorm · · Score: 1

      "Hmmmm....using video card GPUs for scientific number crunching. I wonder why no one has thought of that one..." I know it's already been used. That's actually my point. Why still use cpu's to crunch numbers while a dedicated hardware can do it much much better, even a graphics card which is not specially designed for the job does it much faster. The millions of watts of wasted energy for distiributed computing non-sense is pushing the earth to global warming. [citation needed] http://boinc.netsoft-online.com/e107_plugins/boinc/bp.php?project=19 active users: 273,168 Lets assume only 5 watts more is used for each computer which is far below the normal value. The difference between the load and idle is about 30 watts at least. You do the math!!

    3. Re:Distributed computing is a lie by scottv67 · · Score: 1

      You do the math!!

      I noticed that you omitted using linebreaks in an effort to save energy.

      Seriously, I asked you to provide a source that links distributed computing to global warming and you threw a bunch of numbers together. Please provide a credible source which documents the link between PCs and global warming. Thanks.

  25. National Cancer Institute by killmofasta · · Score: 1

    had a Masspar MP-2, ( actually 5 of them linked together ).

    Would that comparison be to what schools are using on a desktop machine, or compared to what is availble to most bioinformatic facilities?

    No mention of folding at home.

    ( love the Canadian Bacon comment!!!)

  26. Didnt we call Acid Rain a myth? by killmofasta · · Score: 0, Offtopic

    Check it out: Google search for Acid Rain MYTH:

    http://www.fortfreedom.org/n15.htm

    "THE CONTINUING MYTHOLOGY ABOUT ACID RAIN (8/31/1989)"

    If Acid rain was called a Myth in 1989, and its an accept fact now. ( Shuddap you no holocost guys.)
    It tool 28 years to be accepted as on general principal to be true.

    It took at least 5 years for the existance of HIV/AIDS to impact the screening of blood.

    What do you think the acceptance rate for global warming will be?

    How long before we ban the flying of airplanes in the stratosphere?

    Your call

    1. Re:Didnt we call Acid Rain a myth? by kcbanner · · Score: 1

      Airplanes actually help to replace ozone. Although that shit that comes out as exhaust is still bad.

      --
      Obligatory blog plug: http://www.caseybanner.ca/
    2. Re:Didnt we call Acid Rain a myth? by killmofasta · · Score: 1

      I would just like to point out the work of Drew Schindell, and Paul Newman. Its the ice crystals that form from the particulate matter that cause [obl:Their global climatology theory] the stabaliztion of polar stratospheric clouds, so no, apparently:
      "Airplanes actually help to replace ozone. Although that shit that comes out as exhaust is still bad."
      And there have been observations of the ice clouds caused by shuttle launches, reaching the polar stratosphere in less than 48 Hours... ( I still have a head scratcher about this.. 150Mph winds!)

      http://news.bbc.co.uk/2/hi/science/nature/5021778.stm

      "In addition to CO2, methane has been increasing in the atmosphere," added Dr Russell. "Once methane makes it into the high atmosphere, the sun breaks down the molecule and forms water - so, that's another source for water vapour in addition to the water vapour coming from below."

      "James Russell gave details of the mission here at the American Geophysical Union Joint Assembly."

      ( Use the Preview Button! Check those URLs! Thanks Mr Slashdot!)

  27. Cure for cancer, only decades away! by clambake · · Score: 1

    So, where's my cure then?

  28. Better title: saves time by pimpimpim · · Score: 1
    There is a theory for grad students doing computational simulations that they might as well do nothing the first two years, and then perform all calculations in the last few years, without losing time. Also, this is 162 years for a single core, in reality, problems like this will be done on a parallel machine.

    That said, just as 'cancer research' is a way to get easy funding, 'grid computing' is not much more. The theory is very nice, work on a machine anywhere in the world from your own desktop without having to worry about which machine it is. In the end, you'll actually have to recompile your program for any different architecture. If you do science, your program will change a lot, and you'll have to do the recompiling a lot.

    --
    molmod.com - computing tips from a molecular modeling
  29. Stupid patent remarks by kanweg · · Score: 1

    Without patent, no pharmaceutical company will take the risk of getting a drug registered. In other words, no patient will enjoy a better life without the drug being patented (first).

    The sooner the invention is made, the sooner the patent will expire, and the drug be made by generics companies.

    Bert
    All above pertains to logic to which some nationalities are more impervious to than others.

  30. 162 cpu-years isn't big by markhahn · · Score: 1

    162 cpu-years just isn't a big deal - any resonably sound researcher could get that many cycles for free at quite a number of HPC centers.

    the real problem with this particular molehill is that readers come to assume that the trivial fringe of HPC (embarassingly parallel stuff like folding) is what it's all about. EP codes are the boring special case - the reason HPC centers exist is mainly to support studies which cannot be run on a bunch of boxes networked with string.

    worse yet is the impression that grid actually solves some problem, and especially that it makes computation fungible (like the electrical grid - plug in anywhere, it's all the same KWh.)

  31. MOD PARENT DOWN by Bryansix · · Score: 1

    The parent doesn't even understand the kind of work being done on these grids. The work is broken up very methodically in such a way that it can be worked on for a long time and communicate for a short time. In addition, the estimate of computing power is not 100% of all the computers connected. It's what percentage of the connected computers power that they actually donate. These grid projects actually keep data to prove this.

  32. SlashdotUsers is the 7'th ranked team on WCG by geopsychic · · Score: 1

    with over 3600 members and 1600+ CPU years of compute time so far.

    My team (UserFriendly.Org) is ranked 8'th and expects to overtake SlashdotUsers early next year. http://www.geocenter.com/tempimages/index.html contains graphs for my team, the top 10 teams and WCG overall.

  33. 50 years before eternity is still eternity by Frank+T.+Lofaro+Jr. · · Score: 1

    Curing cancer decades earlier than never/eternity is still never/eternity.

    (Yes, I know my statement is false when it comes to rats, we can cure rat cancer with astonishing effectiveness.)

    --
    Just because it CAN be done, doesn't mean it should!
  34. non sequitur by ichigo+2.0 · · Score: 1

    I'm not yet one of the climate change true believers.
    This is what I hate about this climate change hype. Nowadays if you say that you want to do something for the environment, you're automatically assumed to mean that you want to prevent "global warming" or whatever. Personally I don't give a crap about climate change, I want mankind to pollute less and to use natural resources more efficiently because this results in an improvement in the environment. Sure, if mankind really is causing the climate to change, then that is a pretty drastic change in the environment, but we need to pollute less regardless.

    If I had a tinfoil hat, I would wonder if the climate change hype is a fabrication by corporations that want an excuse for polluting.
    "Excuse me Exxon, could you pollute less?"
    "We don't think the debate on climate change has been settled yet."
    "Huh?!"

    I don't really have a tin-foil hat, and I realize that that would be pretty short-sighted from the corporations as governments have now started to take action against CH, but that's how I sometimes feel when people talk about the environment.
  35. World Community Grid by CommanderIsm · · Score: 1

    http://www.worldcommunitygrid.org/ use this instead of a screen saver and perhaps help save lives in the future