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."

Comments

I used to run Folding@...

[kcbanner]

...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.

Re:I used to run Folding@...

[ChatHuant]

... 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.

Re:I used to run Folding@...

[DigiShaman]

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!

Re:I used to run Folding@...

[Belial6]

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

Re:I used to run Folding@...

[Anonymous Coward]

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?

Re:I used to run Folding@...

[ZorinLynx]

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.

Re:I used to run Folding@...

[scottv67]

...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.

How good are the programs

[gringer]

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.

162 years?

[sayfawa]

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 :(

Re:162 years?

[JK_the_Slacker]

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.

Re:162 years

[JK_the_Slacker]

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?

Re:This is great and all but...

[Anonymous Coward]

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.

Re:This is great and all but...

[FooAtWFU]

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.

Re:Desktops are not supercomputers

[deadline]

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.

Open Source Software Cures Cancer

[atwtftg]

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.

Re:I OBJECT!!

[defile39]

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.