Domain: bakerlab.org
Stories and comments across the archive that link to bakerlab.org.
Comments · 29
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Re:Does it matter?
I run Rosetta@Home on my own computers -- I can't believe I forgot about that. Great point.
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Re:But
Yeah, here's my anecdotal evidence too!
My Mac Mini G4 has been running almost non-stop since 2005 when it replaced my K6-2 - 500. The Mini remained my primary computer until I bought a 24" iMac after the spring 2009 refresh. The Mini is whisper quiet (so is the iMac) and is currently sitting in the other room churning out work units for Rosetta@home and the World Community Grid, two distributed computing projects that strive to find cures for various diseases and model different energy and water usage patters.
Sure its slow, it can only churn out a work unit every 10-12 hours or so, but considering that the Mini doesn't use much power and would otherwise sit there doing nothing I figured I might as well use it for a good purpose. What impressed me about the Mini is that outside of power failures the machine has practically never been turned off, has been run pretty much full out the whole time and yet still keeps going. Say what you will about Apple, but their build quality is excellent and they make computers that can continue to be used long after most others would be relegated to the trash bin.
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I use Rosetta @ home and foldit
Rosetta at home is another and arguably much more efficient folding project. It actually predicts protein structures at high resolution, allows docking, and design of proteins. put your cycles there. Also if you like this kind of thing then try out foldit. it a multiplayer game in which you race others either collaboratively or in cometition to fold proteins. The games are chosen so the answers help investigators studying the protein folding process! The idea is to separate what humans do best--large scale long range geometry-- with what computers do best--fine tuning interactions.
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Re:Dupe?
In my opinion true cloud computing means that you can share processing power (e.g. Boinc) and storage (e.g. file sharing) with others. At the moment we still have somewhat centralized solutions where everyone relies on a few big companies (Google, Amazon, SAP,
...) which are providing special services. On the long term this is too limiting since those companies always need to find ways to make their service financially viable. -
Boinc
Apart from using CPU frequency scaling, shutting down unused PCs, and using thin clients, you can setup Boinc on your computer.
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Re:Donate to At Home Projects
The IT guy in me thinks that's a waste of FLOPS.
In this financial climate? Only if those projects are willing to pay you (hah!) or you really believe in supporting what they do.
The wanna-be businessman in me thinks its probably a waste of money as well.
You look like you're in a position to use virtualization to create X application servers over Y machine servers
... but you'd need all the IT staff and customer support, etc. to get that going. It's too bad you can't sell your CPUs to Amazon for their cloud computing since it's all pretty much anonymous but I guess either way I think about it you would need a pretty hefty internet connection.There's really hardly any money to speak of in plain old CPU cycles. Amazon does OK out of it, but their model relies on being really big. Most of us don't operate at that size.
OTOH, if you can offer some sort of value-add, you can charge more. For example, you might run and support specialist applications for small businesses; there's a reasonable amount to be made in that area, but you need to be thinking then in terms of not just having computers but support staff too and, indeed, a whole business. You can't do it half-assed; this isn't the tech bubble.
Have you thought about just selling the servers?
As others have explained, that may well be a solid suggestion. Right now, better to have cash in hand than servers you don't need.
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Donate to At Home Projects
The IT guy in me thinks that's a waste of FLOPS.
The wanna-be businessman in me thinks its probably a waste of money as well.
You look like you're in a position to use virtualization to create X application servers over Y machine servers
... but you'd need all the IT staff and customer support, etc. to get that going. It's too bad you can't sell your CPUs to Amazon for their cloud computing since it's all pretty much anonymous but I guess either way I think about it you would need a pretty hefty internet connection.
Have you thought about just selling the servers? -
Re:So what does it mean for PCs?
I still don't understand the problem... they are saying 1 computer with a limited throughput bus technology will be limited by adding more cores... well... duh? If it was a supercomputer, then chances are they will open the bandwidth to the processors/memory etc.
Make it a car analogy: you can transport cargo, each car = core. You can only transport 2 cargo loads down a 2 lane road, adding a 3rd car makes them go slower... if you think the engineers don't think about expanding the road is idiotic.
Adding cores isn't the problem... more cores = more power regardless, there's no limit, otherwise you are saying distributed computing has an upper limit? -
Rosetta@home, not Folding@home
a client that allows you to choose out of many projects like Folding@home
Rosetta@Home, a protein folding program which has active updates from David Baker, the head of the group, runs on BOINC; Folding@Home doesn't. One benefit of BOINC is that you can run it on your system and when Rosetta@Home doesn't have more work for you to do, you can have BOINC switch over to any of a number of other projects you've attached to. . -
Umm, this is rosetta@home, not folding@home
This game is an offshoot of the rosetta@home effort to model protein folding. Folding@home is a separate effort.
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Baker heads up Rosetta
Baker already heads up Rosetta@Home , a BOINC project that has your computer fold proteins in its spare time. He's appreciated for keeping his journal up-to-date and being responsive to participants; Folding@Home is somewhat less responsive (and doesn't provide the BOINC option).
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Run Community Projects
BOINC, Tor, Freenet and/or I2P are good examples of things you can put your extra resources to some use. Here are the BOINC projects I would run if I had 100's of system's at my disposal.
Artificial Intelligence System, NanoHive@Home, Predictor@Home, Project TANPAKU, Spinhenge@Home, The Lattice Project, World Community Grid, SIMAP, Malaria Control, Proteins@Home and Rosetta@Home. -
Re:FoldingAtHomeET is more interesting to you until a very near relatives comes up with a serious illness like Cancer, AIDS
...Some poster mentioned it earlier: If you priorities is to spend youd budget on the best way to save lives then research into Cancer or AIDS isn't the best place to put it, even within the medical research field. There are other diseases that kill far more people but get far less research dollars than Cancer/AIDS already! The money goes into areas where the research companies think there will be the best return on the investment!
That said, it is a fallacy to suggest that SETI might also result in a cure for all known ills by finding the aliens who already have the cures! Again, from another poster, the best thing SETI could do is offer a wake-up call to the religiously infatuated, perhaps providing some coffee flavoured smelling salts at the same time.
FWIW, I used to run SETI, before and after BOINC. I also ran a number of other BOINC clients, including:-
SETI,
Folding,
Climate Prediction,
Einstein searching for gravitational waves,
LHC helping with the Large Hadron Collider,
Predictor trying to predict protein structure from protein sequences,
QMC,
Rosetta,
Stardust,
yada yada yada
but removed it a year or so back as it did seem to get in the way rather too often.BOINC was just too clunky. Why did you have to register individually with each BOINC project, be given yet another HUGE number, have to search for the interesting projects yourself. BOINC should have taken care of the registration once, then offered a drop-down of active projects. Selecting something interesting would do all the install stuff for you and allow you to control the shares from the Client - currently (or at least when I left it) if you wanted to alter the share of one particular project got you had to go to each Project's website rather than just set it within the client. Just clunky!
Anyway, I moved on, but I'd have to say I'm sort of interested again and may fire up SETI again for a while to see how things have progressed since I last offered some cycles!
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Re:FoldingAtHomeProtein Folding should take precedence over pointless searches for noise-in-patterns.
Distributed computing isn't an either/or proposition. Right now the BOINC infrastructure hosts at least 42 projects, and at least three of those are health related (malariacontrol.net, rosetta@home, predictor@home). When a volunteer starts BOINC and joins a project, they are presented with a list of many projects.
If SETI@home gets the 3 to 5 fold increase in volunteers that they hope for, it's a very good bet that every other BOINC based project will see significant increases in their volunteer base.
There are certainly far more than a million internet connected CPUs that are on and idle tonight. Anyone want to guess at the actual number? 10 million? 50 million? 100 million? A few percent of those would more than do all of the jobs that are available on all of the distributed computing projects that are out there.
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Re:FoldingAtHome
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Re:3 million dollars per year is a pittanceThey didn't have a lot of money, SETI@Home is born. It becomes popular, we start seeing more distributed computing apps like Folding@Home.
Consider also the increase in awareness of grid computing, and not just the individual apps. This led to BOINC, leading to the ease of installing and multitasking between World Community Grid, Rosetta@Home, and so many other projects with 'practical' applications that have produced real results -- projects that to date didn't have a grid computing infrastructure to harness for their needs. That infrastructure sprung from the mindshare generated by SETI@Home.
So let SETI keep searching for E.T. As far as I'm concerned, if the only thing that ever came out of Seti was SETI@Home, and the only thing of value that came out of that was BOINC, that's enough of a contribution to society to justify its continued existence.
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Re:Randomize the clock
What about always using 100% of your CPU? I run the BOINC client for the Rosetta@HOME project and tell it to crunch as much data as it can with idle CPU time. It is ALWAYS up and running. So, if I have this running on a machine that also uses Tor then the "create extra CPU load" method would fail.
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Distributed Computing Wins Again!
Individuals contributing their spare processor cycles via BOINC are currently producing over 380 TeraFLOPS putting them clearly in first place (if such distributed systems were counted).
SETI@Home is now operated exclusively through BOINC and it alone is doing over 167 TeraFLOPS right now, putting the SETI@Home network in second place, only behind BlueGene/L (if such distributed systems were counted).
You can contribute your spare processor cycles too by downloading the BOINC client and attaching to a cool project such as Rosetta@Home which folds proteins as part of an effort to cure human diseases. Join the biggest "supercomputer" today! -
Re:And yet, other researchers disagree
"As you can see by their actions, rather than their words... Notably at Stanford University, Washington University, Munich University, Scripps Research Institute, Oxford University etc.
http://folding.stanford.edu/about.html
http://boinc.bakerlab.org/rosetta/rah_about.php
http://boinc.bio.wzw.tum.de/boincsimap/project.php
http://predictor.scripps.edu/about_team.php
http://www.grid.org/projects/cancer/index.htm
So... Who are you again? Yeah, you're a guy reading Slashdot... Getting much research done?"
Grr....I can't let this go.....
I'm a guy who was once associated with one of labs/projects mentioned above. I was working on the problem for years, and have a great deal of expertise in the area.
I can also tell you that the project is complete and utter crap, from a scientific perspective. The PI routinely misrepresents the project goals, claiming "possible" results that could never, ever come from the type of research performed. In general, the "science" is poorly-conceived and improperly controlled, and most of the "experiments" are methodologically flawed. I can't post my name here...it would be career suicide.
As one of the authorities to whom you seem so desperate to appeal, let me assure you: if you are devoting your resources to this project, the world would be a better place if you simply turned your computer off. -
And yet, other researchers disagree
As you can see by their actions, rather than their words... Notably at Stanford University, Washington University, Munich University, Scripps Research Institute, Oxford University etc.
http://folding.stanford.edu/about.html
http://boinc.bakerlab.org/rosetta/rah_about.php
http://boinc.bio.wzw.tum.de/boincsimap/project.php
http://predictor.scripps.edu/about_team.php
http://www.grid.org/projects/cancer/index.htm
So... Who are you again? Yeah, you're a guy reading Slashdot... Getting much research done? -
Re:BOINCBio-related projects that use BOINC:
IBM's World Community Grid: http://www.worldcommunitygrid.org/
investigate protein-related diseases: http://predictor.scripps.edu/
Rosetta@home: http://boinc.bakerlab.org/rosetta/
Cell Computing http://www.cellcomputing.net/
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Re:Why is it... here is the link to help
Sorry, here's the Baker Lab link, for the Biochemical Structure prediction effort, folding proteins with your home computer. They also have another Beta for a different project as well.
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Re:outsourcing, or why I learned to Fold Proteins
I am concerned about sending my spare CPU time overseas, i mean, they say they are "climate modeling", but could they not just as easily be selling this "distributed" computer network to the black market, or Iran, or doing nuclear weapons simulations?
You could always donate your CPU cycles to help Fold Proteins at the Baker Lab here at the University of Washington.
Then you'd know your CPU cycles were doing good American scientific research.
And Prof. Baker is a neat guy, very slashdot. -
Re:Understanding protein structure..
The computer programs that predict protein structure from its primary structure are getting better. So there is a way....
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Why prime numbers ?I'm just wondering, what's the point to calculate the largest possible prime number? I mean, there are a lot of distributed computing projects that sound more... useful : Climate Prediction (Hello Katrina), research protein-related diseases or another doing wider research on human diseases. That's just to name a few projects using the Berkeley Open Infrastructure for Networks.
So I'm not being sarcastic here, my genuine questions is : why should I spend my free computing power on calculating prime numbers instead of research to cure cancer?
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Quite easyJust download the client package, eg:
wget http://boinc.berkeley.edu/dl/boinc_5.2.8_i686-pc-
Extract it, eg:l inux-gnu.sh
sh boinc_5.2.8_i686-pc-linux-gnu.sh
Start it, eg:cd BOINC
Then sign up for whatever projects you want and you will get an email with a project url and an account key in it. Once you have that just execute: ./run_client &./boinc_cmd --project_attach [project_url] [project_key]
for each project and that's it. You might want to pipe the output from the run_client to a file so you can tail it if you want to see what it's been doing. -
Re:FolditWhile I agree that folding@home is more useful than seti@home, I think that Rosetta@home. It's also focused on protein folding, but the difference is that Rosetta has consistently outperformed folding@home at the CASP (Critical Assessment of Structure Prediction) competitions. Check out the CASP website to see the raw results. Or, check out a summary from the Baker Lab website. Also, Dr. David Baker (head of the lab where Rosetta has been developed) is very involved in the community of users that run Rosetta@home, check the messageboards on the Rosetta@home site.
Disclaimer: I'm a student in David's lab. But that doesn't mean that I'm wrong, or mindlessly plugging my own Kool-Aid.
:) I really believe that Dr. Baker and his lab have a strong chance to solve the protein folding prediction problem.Whatever project you choose to donate your cycles to in the end, protein science is a cool field with far-reaching implications for humans in general, and the scientists in the field really appreciate your cycles. Thanks to all those who are donating and will donate in the future.
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Re:FolditWhile I agree that folding@home is more useful than seti@home, I think that Rosetta@home. It's also focused on protein folding, but the difference is that Rosetta has consistently outperformed folding@home at the CASP (Critical Assessment of Structure Prediction) competitions. Check out the CASP website to see the raw results. Or, check out a summary from the Baker Lab website. Also, Dr. David Baker (head of the lab where Rosetta has been developed) is very involved in the community of users that run Rosetta@home, check the messageboards on the Rosetta@home site.
Disclaimer: I'm a student in David's lab. But that doesn't mean that I'm wrong, or mindlessly plugging my own Kool-Aid.
:) I really believe that Dr. Baker and his lab have a strong chance to solve the protein folding prediction problem.Whatever project you choose to donate your cycles to in the end, protein science is a cool field with far-reaching implications for humans in general, and the scientists in the field really appreciate your cycles. Thanks to all those who are donating and will donate in the future.
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Re:Lose membersTruthfully I doubt that they will lose members.
And I dont think the transition is a problem, you simply create an account on the new Seti@home site and link it to your old one so that your credit is transferred over, Then download Boinc and insert your project and ID code and it does the rest.
I switched over to Boinc in March or April and since then have had no problems at all. old Seti credit is transported across when you sign into the Boinc account version of Seti, and you can compile and run optimized clients for your architecture, something the old seti never really had.
I got a 35% performance increase by switching to an optimized client.Boinc itself isn't really a replacement for seti though, it is simply a manager
You choose which projects you wish to subscribe to, and how long you want any particular project to hog resources for and away you go.
At first i ran seti alone, but recently I have been running the Einstein@home and LHC@Home client on a 33% resource share basis with Seti.
Einstein, looks for spinning Pulsars and the LHC is a client from CERN running simulations of particles spinning around the new Six Track large hadron colider.
The LHC project has just finished sadly, but I think I'll move onto the Rosetta project, which is looking to work out various protein structures and interactions and how they can be used.If, like me, you always fancied running a few other projects other than Seti but didnt want the hassle of manually deciding which client ot run then Boinc is a real boon and well worth the few minutes needed to set it up.
Have a go, I think you will like it!