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Grid Computing Saves Cancer Researchers Decades
Posted by
samzenpus
on Wed Nov 07, 2007 08:41 PM
from the begin-the-beowulf-cluster-comments dept.
from the begin-the-beowulf-cluster-comments dept.
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."
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Oh great ... (Score:5, Funny)
Wanna bet they discover that maple syrup or Canadian back bacon cures cancer?
I used to run Folding@... (Score:5, Insightful)
Re:I used to run Folding@... (Score:5, Informative)
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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...}
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Re:I used to run Folding@... (Score:4, Informative)
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 [iki.fi] 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.
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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 di
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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
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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
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I don't see it as a trick, but
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Al Gore
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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
Re:I used to run Folding@... (Score:4, Insightful)
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.
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I don't think anyone would disagree with you. The point that the
Storm Botnet (Score:5, Funny)
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I think you are thinking of the Folding@home project at Stanford:
http://folding.stanford.edu/English/FAQ [stanford.edu]
How good are the programs (Score:5, Insightful)
(1) although from their point of view, it's just slow code.
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harnessing the power.... (Score:2)
162 years? (Score:5, Insightful)
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
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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
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This is great and all but... (Score:5, Interesting)
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Re:This is great and all but... (Score:4, Informative)
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.
Desktops are not supercomputers (Score:4, 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 [clustermonkey.net] article to clear up the mis-conceptions that abound. I also did a piece [linux-mag.com] on the Linux Magazine site as well that debunks much of the spam-bot supercomputer legend (need to register for that one)
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Re:Desktops are not supercomputers (Score:4, 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.
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If you know so much about the topic, why aren't you a
PS3 Supercomputer (Score:4, Informative)
I run their PC sw on my systems I keep on. They are getting results, and publishing papers based on the research.
Patents? (Score:3, Interesting)
Because that would make me feel a little less charitable with my computing power. (Only a little, though.)
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The alternative is "don't help the distributed computing project" and those drugs will never be 'discovered'. Then, inste
I don't get it... (Score:4, Informative)
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.
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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-c
Open Source Software Cures Cancer (Score:3, Insightful)
World Community Grid [worldcommunitygrid.org] 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 [boincstats.com] shows you who is contributing to World Community Grid projects. Check it out...and ask yourself why you aren't contributing.
How could this be? (Score:2, Funny)
I can see it now (Score:3, Interesting)
I OBJECT!! (Score:5, Interesting)
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.
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Or, as a lo
Me next! (Score:2)
Oh wait.
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cluster of animated Angelina Jolie-lizards?
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The Folding@home project at Stanford has been around that long as well.
http://folding.stanford.edu/ [stanford.edu]