IBM Sponsors Humanitarian Grid Computing Project 181
BrianWCarver writes "Reuters reports that IBM and top scientific research organizations are joining forces in a humanitarian effort to tap the unused power of millions of computers and help solve complex social problems. Following the example of SETI@home, the project, dubbed The World Community Grid, will seek to tap the vast underutilized power of computers belonging to individuals and businesses worldwide and channel it into selected medical and environmental research programs. The first project to benefit will be Human Proteome Folding, an effort to identify the genetic structure of proteins that can cause diseases. The client is currently available for Windows XP, 2000, ME, and 98."
Curious.... (Score:2, Funny)
Forgive my ignorance... (Score:5, Insightful)
Re:Forgive my ignorance... (Score:5, Informative)
For those of you who don't know Stanford's project, called Folding@Home [berkeley.edu], uses computer cycles to observe and find out more about how proteins fold.
Now how is this really different from IBM's project?
From IBM's World Community Grid website [worldcommunitygrid.org]:
"However, scientists still do not know the functions of a large fraction of human proteins. With an understanding of how each protein affects human health, scientists can develop new cures for human disease.
Huge amounts of data exist that can identify the role of individual proteins, but it must be analyzed to be useful. This analysis could take years to complete on super computers. World Community Grid hopes to shrink this time to months. Human Proteome Proteins are long and disordered chains folded into globs. The number of shapes that proteins can fold into is enormous. Searching through all of the possible shapes to identify the correct function of an individual protein is a tremendous challenge.
The Human Proteome Folding project will provide scientists with data that predicts the shape of a very large number of human proteins. These predictions will give scientists the clues they need to identify the biological functions of individual proteins within the human body. With an understanding of how each protein affects human health, scientists can develop new cures for human diseases such as cancer, HIV/AIDS, SARS, and malaria."
From Stanford's Folding@Home website:
"What are proteins and why do they "fold"? Proteins are biology's workhorses -- its "nanomachines." Before proteins can carry out their biochemical function, they remarkably assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, remains a mystery. Moreover, perhaps not surprisingly, when proteins do not fold correctly (i.e. "misfold"), there can be serious effects, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, and Parkinson's disease."
"What does Folding@Home do? Folding@Home is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases. We use novel computational methods and large scale distributed computing, to simulate timescales thousands to millions of times longer than previously achieved. This has allowed us to simulate folding for the first time, and to now direct our approach to examine folding related disease."
They both sound like they're out to accomplish the same exact thing. I could not spot any real differences, anyone care to enlighten us?
Re:Forgive my ignorance... (Score:3, Interesting)
Seriously, I don't think there is a difference in goal. The only difference there might be is in method. Differences in how to share data and process it should be negligable, but Folding@Home is hardly speedy. But, then, it's not a simple task.
It would be good if IBM and Stanford worked out a way to link their databases, so they could split the problem-space up. They could then customize their clients to focus on that specific subset of folding probl
Re:Forgive my ignorance... (Score:2)
Re:Forgive my ignorance... (Score:2)
There are then two ways they could share - by splitting the problem space statically or dynamically. Databases can be merged at the end or real-time.
Statically: It should be easy for them to either define some kind of scope - by protein or by some sub-class of folding problem. IBM then solves one set of problems, Stanford solves the oth
Re:Forgive my ignorance... (Score:2)
Re:Forgive my ignorance... (Score:4, Informative)
This Human Proteome Protein project is looking at primary human proteins and how they could affect human function.
My opinion is both are important since each can affect each other for example the SARS which usually start in fowl and then transmit to human to cause SARS.
Because IBM are control freaks? (Score:5, Insightful)
Now how is this really different from IBM's project?
A skeptic might think that IBM simply want to have a foot in the door of these big anarchic distributed projects.
Despite the stunning power available to this kind of distributed computing, it is less useful than it appears. In my research area (computational biology) [berkeley.edu], the effort of parallelizing an algorithm and collating the results is seldom worth the dividend in speedup. Supercomputers generally run idle at most universities, for this very reason.
Folding@home was a nice success story, and there are further applications of those models, e.g. simulations of prion aggregation [dailycal.org] (mad cow disease, Alzheimer's, etc). But (IMO) this is the exception, rather than the rule. Anyone who thinks that parallelization is a quick & easy panacea to difficult computational problems in general is living in a dream world (and I say that as a proud owner of several Macs with parallelized RISC CPUs *and* go-faster stripes).
I've lost count of the number of times I've heard these cheap parallelization ideas floated (another example is building cheap clusters out of console hardware [uiuc.edu] which I reckon I first heard in 1996!). And every other month someone offers me supercomputer time... the problem is in redesigning the algorithm to work in parallel. Certain algorithms, such as MCMC [umn.edu], are better suited to this treatment than others.
Of course, then you have to persuade a bunch of other scientists that Your Algorithm is the most deserving, which is a political issue (but hey, if it saves those CPUs from being used for the eminently futile task of looking for bug-eyed aliens, maybe it's a good thing...)
Re:Because IBM are control freaks? (Score:2)
Damn. I thought that said "simulations of pron aggregation." Sign me up!
Re:Forgive my ignorance... (Score:5, Informative)
This project is designed to predict the structure of large numbers of proteins for which we know the sequence, but not the structure. The algorithms for predicting protein structure are distinct from molecular dynamics, since the end goal is very different. I believe that the particular method they are using is Rosetta, developed by at the University of Washington, with the the Institute for Systems Biology is affiliated.
Basically it boils down to the difference between protein folding (which implies studying the mechanism) and protein structure prediction. The second is solvable to reasonable accuracy with modern methods (although not perfect), but not cheap, so a grid computing approach is a nice way to tackle the problem.
The folding@home problem is MUCH more difficult, needing the distributed computing framework to study the folding of ONE small protein.
Re:Forgive my ignorance... (Score:1)
Re:Forgive my ignorance... (Score:3, Informative)
Short answer: no.
Longer answer: first, protein structures are incredibly complex, and in fact it's often much easier to sequence a big protein than to determine its structure. The first can be done (these days) by any half-competent lab tech working with relatively cheap equipment; th
Re:Forgive my ignorance... (Score:1)
No, going from sequence to structure is a big problem; see e.g. the CASP competition [llnl.gov]. The fundamental difficulty is that protein folding involves many complex interactions between amino acid side chains and solvent molecules, getting you into a world of nightmarish quantum chemistry where
Re:Forgive my ignorance... (Score:2)
This guy is right. Rosetta is being used, but has been optimized to run on desktop computers. I really encourage everyone to get this running, the paybacks will come relatively quickly, and it will give me more information to work with. Keep in mind that this sort of st
Re:Forgive my ignorance... (Score:1)
"Intellectual property" (Score:2)
Folding@Home say that the data will be released to the public. That's a start, but before I spend my CPU time on any kind of biotech project, I want a guarantee that the research won't be patented and kept from humanity the way HIV medication has been kept from people in Africa.
Re:"Intellectual property" (Score:2)
You might want to read the fine print very carefully. IBM has a rather, uh, "mixed" history with regard to such issues. You might find that the actual situation is somewhat different from what the marketing people tell you verbally.
Not that this is anything special to IBM, of course. In the past few years, we've been reading a lot of unpleasant stories abou
Re:"Intellectual property" (Score:2)
I have noticed that IBM truly has a mixed record in such things. Sometimes they have cooperated with users and developers, and supported what we now call Free Software or Open Source and independent research. Other times, they have used legal and marketing trickery to squash competitors and steal from contributors. So there is good reason for both hope and distrust. Hearing that some potential victims' lawyers have gone over the fine print and said it's ok will go a long way toward
Re:Forgive my ignorance... (Score:2)
This is the first "protein forking" I've ever seen
Re:Forgive my ignorance... (Score:2)
Maybe they're one of the "top scientific research organizations."
(Or maybe they should be.)
Re:Forgive my ignorance... (Score:1)
There are a lot of questions in different threads so:
How is this different from folding@home:
DeepStream got it right...
Folding@home aims to get at the science of how a small number of proteins of KNOWN structure fold
Trying to find diseases by using WinXX computers? (Score:5, Funny)
What if... (Score:1)
"solve complex social problems" (Score:4, Funny)
distributed.net (Score:4, Insightful)
Re:distributed.net (Score:1, Informative)
Re:distributed.net (Score:2)
I thought so too. Anyone tried this under Wine or Bochs or Virtual PC on Mac? I didn't see it in the Wine App DB.
Re:distributed.net (Score:1)
Proteomes don't fold (Score:4, Informative)
Hmmm (Score:5, Insightful)
I have plenty of unused cycles on 4-way Sun boxes with gigs of spare RAM, though.
It would be nice if they released a client in portable C.
Re:Hmmm (Score:3, Insightful)
I have plenty of unused cycles on 4-way Sun boxes with gigs of spare RAM, though.
Lets see: dozens or even hundreds of ``4-way Sun boxes'' versus hundreds of thousands of ``PIII 600''. Hmm. Guess I see why they didn't start with the Solaris version.
It would be nice if they released a client in portable C.
Yep.
How does one go about making sure that nobody makes a variant client which phones home with bogus resul
Re:Hmmm (Score:2)
So the burden of creating and testing other platforms lies with the makers of the grid software, in IBM's case this is United Devices (incidentally, I work for United Devices). And since the ROI on a non-window client is
Re:Hmmm (Score:4, Insightful)
Agree with the sentiment, but put it in its right magnitude, and you can see why Windows is the sole platform here.
How many people all over the world are like you, with CPU cycles to spare on non Wintel boxes?
How many PCs are around the world, and how many run Windows?
How many of those are used at home or small business?
Don't get me wrong, I am a UNIX/Linux fan, and dislike Windows. But if you want volume, Windows is where it is at the moment. Having said that, they have to release something more portable in the future. Just like SETI and others did.
Re:Hmmm (Score:2)
The only way... (Score:1, Interesting)
Poor first impression (Score:3, Informative)
Well, not only do they not support any clients besides Windoze, but if you're operating on any reasonably secured LAN where the firewall doesn't allow you to willy-nilly connect over SSL ports (443) using proprietary protocols (gasp, imagine that), it isn't going to work.
Not really a great way to get off on the right foot with this effort. Make it impossible to use by the majority of those interested by precluding other OSes and folks on corporate networks without proxies.
Back to Folding@Home for me!
Re:Poor first impression (Score:2)
Re:Poor first impression (Score:2, Informative)
You might live instead of die. I think I would consider that a profit.
Oh, and if you look at the documentation on the site they say:
"World Community Grid, with technology and funding provided by the IBM Corporation, is making grid technology available to public and not-for-profit organi
Re:Poor first impression (Score:2)
Re:Poor first impression (Score:1)
I wonder how long it will be before MS needs something crunched and makes a distributed project part of the Windows?
Re:Poor first impression (Score:2, Insightful)
Other Clients ? (Score:3, Interesting)
I've been doing SETI@home for a while now, and was pleased to see the announcement of this in the press. I was less pleased when I went to the web site [worldcommunitygrid.org], and found out that (as it says above) the only client was for Windows. Since I use only Linux these days, I guess that leaves me out.
I hope that with IBM's involvement, and stated committment to Linux, this will change soon. I sent them a note, using the "Contact Us" form on the web site, and would encourage others to do the same.
(Incidentally, I've been running SETI@home initially on Windows, now on Linux, using the command-line client in both cases. I find I get ~50% more work units/time with Linux, and less impact on interactive use of the machine.)
Re:Other Clients ? (Score:2)
I would have expected IBM to promote the performace of their processors designs present in Macintosh G5 computers. A little optimazation can skew figures a long way..and voila their CPU really shines.
A cross-platform, CLI client would allow one development effort for MacOS X, and Linux and FreeBSD and Solaris...you get the idea.
Who benefits? (Score:2, Insightful)
Suppose it leads to the creation of a new revolutionary drug. Just exactly who will get the profits from the drug? (And who will have to travel to Canada to buy it?)
Re:Who benefits? (Score:1)
Precisely my concern! (Score:1)
If this is a problem with normal government-funded research, is will surely be an issue with products resulting from the spare CPU cycles of users.
There should be a provision limiting Intellectual Property rights of
Grid computing and the future (Score:2, Informative)
Additionally I think it's good that IBM too have an interest [ibm.com] in this area, since 1) competition is always good and 2) it makes for more accurate results. With some luck we can have peta-byte based grid by 2007.
Re:Grid computing and the future (Score:2)
Re:Grid computing and the future (Score:1)
Google Toolbar has distributed computing (Score:1)
It's been around for a while already too
United Devices (Score:3, Insightful)
Re:United Devices (Score:2, Informative)
Re:United Devices (Score:2, Informative)
If you are a grid.org member, then your existing client will be able to participate in the same Proteome project. (You have the option of opting out of the Proteome project if you want to continue to exclusively run the Cancer project only.)
If you download the World Com
How about millions of humans? (Score:1)
At first I thought this was going to reference millions of humans, but alas, it's the usual science-will-solve-social-problems approach.
IP rights? (Score:4, Interesting)
Bad idea (Score:2)
BOINC is better (Score:5, Informative)
Re:BOINC is better (Score:2, Informative)
Re: BOINC is better + URL (Score:2, Informative)
BOINC (and other project) URL's (Score:4, Informative)
From there you can see the five projects currently using the BOINC platform (developed by the SETI@Home team)
Cheap Computers (Score:2, Interesting)
Seems like a transparent way to get their goals accomplished.
Boinc? (Score:3, Interesting)
pollution (Score:2, Insightful)
Lets make a list first (Score:2, Interesting)
- open source
- free (as in beer)
- portable code, or multicode
- protected against buffer overflows etc. (managed code)
- signed updates of grid software, grid client software and working packages
- nice interface (including a good web server)
- only for use for non-profit organizations
- and I wan't to choose my projects
Sun (or any one else), hurry up please. I'm NOT going to run any trap that's now on the market
Re:Lets make a list first (Score:2)
Re:Lets make a list first (Score:2, Funny)
- open source
- free (as in beer)
- portable code, or multicode
- protected against buffer overflows etc. (managed code)
- signed updates of grid software, grid client software and working packages
- nice interface (including a good web server)
- only for use for non-profit organizations
- and I wan't to choose my projects
Bruce Perens called - He said, "Step off, bitch. I'm the biggest Open Source asshole
Humanitarian Grid Computing Project? (Score:1)
Gee... (Score:3, Funny)
Please Slashdot this! (Score:1)
Proteome Folding (Score:1)
To Serve Man (Score:2)
Re:To Serve Man (Score:1, Informative)
To quote:
World Community Grid is designed as a resource for research done with a philanthropic or humanitarian purpose and will only be available to projects conducted for public and not-for-profit purposes. It will serve as a useful tool for the completion of a certain stage of research, hastening the progress of projects into further phases of development. Results must be made available to the global research com
Re:To Serve Man (Score:2)
"Vegetarians eat vegetables. Humanitarians scare me."
Maybe there *is* such a thing as a free lunch
Windows only? (Score:1, Insightful)
Not all projects are truly humanitarian (Score:5, Insightful)
In the past, I've investigated a couple of projects, that upon closer scrutiny look quite troubling. They often fail to address what the actual project is specifically, and who will profit from the results financially. Instead, their websites are full of feel good graphics, but the bucks stop at a pharmaceutical company's coffers when you look at the fine details, and there's no discussion of what the findings will be specifically used for, and by whom. In some cases, the whole issue of profit and ownership is quite smoothly whitewashed.
Re:Not all projects are truly humanitarian (Score:2)
I don't care if they take this data and make a for-profit drug from it. If this data helps some pharmaceutical develop a really expensive drug that prevents some nasty disease, well, so be it. My donation consists of a few dollars of electricity, and I consider the cost of the increased risk I take on my machine to be negligible (I maintain my own equipment, and voluntarily expose myself to more risk just surfing the web.) All I ask is that
In other news.. HL2 is just released.. (Score:2, Funny)
spot heater (Score:1)
From my CPU to YOU (Score:1)
Uneconomic, foolish (Score:2, Interesting)
They cost watts, meaning money out of your pocket and increased pollution in the long term because the extra power drain will cause more coal/oil to be burned.
If you absolutely must pursure what amounts to a modern-day indulgence, do it with a cpu that delives good flops/watt performance, like a crusoe...
Re:Uneconomic, foolish (Score:2)
What most people (especially americans with their cheap power) don't realize is that those "spare" cycles aren't free at all.
They cost watts, meaning money out of your pocket and increased pollution in the long term because the extra power drain will cause more coal/oil to be burned.
Assuming that you aren't running the computer just for this project, how much is the additional cost?
Most of a computer's power is lost in places other then the CPU (drives, video card, monitor, etc).
Say the average
IBM ? (Score:1)
IBM will have the right to transfer one or more of ownership, management, and control of the WCG to another entity. In that event, you agree that this agreement and its provisions will also apply to that other entity.
The possible transfer is mentioned like 3 times(!) in the (relatively short) client license. I wonder how serious is the IBM participation ?
Macs (Score:1)
What a pity, that means they can't harvest the massive power of the G5s!
It doesn't support linux either, so wave goodbye to the spare cycles of super-geek's clusters.
Oh well, I suppose that the huge numbers of windoze computers should stack up to be enough anyway..
W00T!! (Score:1)
It was a pretty fun project while I owned it (a few weeks to do my part) though the schedule seemed aggressive.
Honestly, however, I know very little about the project. To me it's just a bunch of servers.
Slashdot 'team' built (Score:3, Informative)
In the time it took me to create a Slashdot login to be able to post a message here, 4 other people have already joined the Grid 'team' for Slashdotters. Apparently they're tracking progress and awarding 'points' for tasks completed and our team is ranked 35th overall at last check.
For those interested, the team name is 'Slashdot Users' and more information can be found here [worldcommunitygrid.org]
Hate to be a nay sayer.. (Score:5, Interesting)
The truth is, I don't care whether they're in it for a profit or for posterity, but if someone's using my resources, I'd at least like to know how they're being used, and what effect, if any, it has had. The SETI project might be futile, but at least someone lets us know what's going on occasionally, which is far more than I can say for the UD projects thus far. For all I know, the cancer distributed computing project has been abandoned in favor of more promising avenues of research. Personally I'll stick with SETI.
and who gets the patent? (Score:2)
Wheres the linux clients? (Score:2)
And that pisses me off no little bit. When someone downloads a windows client for one of those things, its typically setup to run as a screen-blanker, and at full priority. It it has entertaining doodads output on the screen it wastes cpu cycles, lots of them in doing those graphics, plus it only runs when the blanker is on. Thats often less than half the time the machine is turned on.
One of t
Re:NT kernel (and up) has thread prioritisation (Score:2)
I figured this stuff was probably written more to scratch an itch than for money, which does put it into a slightly dimmer light IMO.
I've not attempted to convert to the BOINC project yet, again it seems that a linux client is something they only do when all the other projects for winderz are caught up. Sad, really.
CHeers, Gene
WCF -- Salvo against HP "Global Grid Exchange" (Score:2, Informative)
http://www.globalgridexchange.com/ [globalgridexchange.com]
It's interesting to me that IBM would feel pressured to "play catch up" against HP (Should we expect one from Sun next month?) Obviously both companies have been percolating SOME sort of "Killer App" Grid Initiative for some time now. Perhaps the Grid Wars are finally starting to heat up!
(The name "World Community Grid" DOES sound like a blatant copy of "Global Grid Exchange", IMHO. C
Get a dictionary! (Score:2)
OTOH I'd like to see a grid take on greed, apathy, irrational hatred, illiteracy/innumeracy/general ignorance, and the like.
Human grids? (Score:2)
If you were part of a human distributed computing grid would the postman occasionally deliver a letter saying "when you have some spare time, what is 645 times 821?"
Re:Great! (Score:3, Funny)
Re:Great! (Score:1)
Re:Great! (Score:1)
Re:seriously (Score:1, Insightful)
Re:seriously (Score:3, Funny)
When you are finished with your tin-foil hat can I borrow it for a moment? I have to write a paper on the JFK assassination.
Re:seriously (Score:4, Funny)
Re:seriously (Score:1)