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Supercomputer Performs Simulation of Virus
moller writes to tell us Red Herring is reporting that researchers from the University of California at Irvine and the University of Illinois at Urbana-Champaign have announced that they created a computer simulation of a virus. From the article: "Using one of the world's fastest computers at the U.S. National Center for Supercomputing Applications, located at the University of Illinois at Urbana-Champaign, the researchers ran a computer program devised to reverse engineer the dynamics of all atoms making up the virus particle and a tiny drop of water containing it." Nature also has an interesting write up on the research surrounding this project.
That deleted the files on my sister's computer.
"Speaking the Truth in times of universal deceit is a revolutionary act." -- George Orwell
This is just fascinating, and precisely why we do high performance scientific computing. This quote piqued my interest in particular:
The model also shows that the virus coat collapses without its genetic material. This suggests that, when reproducing, the virus builds its coat around the genetic material rather than inserting the genetic material into a complete coat. "We saw something that is truly revolutionary," Schulten says.
So, by doing this simulation of a tiny span of time, the team was able to get new insight into the process of viral replication that would be extremely difficult to come by with experimental techniques. It also is fascinating, since we often think of viruses as little static particles that float around until they interact with a cell, and yet the simulation showed the surface pulsing. Very cool! -- Paul
OpenSource.MathCancer.org: open source comp bio
They will be writing computer simulations of spores!
Tsunami -- You can't bring a good wave down!
I sincerely hope they protected that computer with a reputable piece of anti-virus software like Norton or McAfee.
a McAfee AntiVirus update immediately wiped this program and all associated files from the face of the earth.
...I just connect an unpatched Windows machine to the internet, and wait 90 seconds. Cool!
Tubal-Cain smokes the white owl.
The virus later choked to death on a SMTP configuration file.
It must have been something you assimilated. . . .
Dear Sir or Madam: This letter is to notify you, pursuant to the provisions of the Digital Millennium Copyright Act, that we believe one of your humans is infringing God's copyrighted materials. Specifically, God is the owner of the copyright and trademarked materials, wich includes all life forms. The aforementioned human reverse engineered a virus without authorization, thereby infringing upon God's copyrights and trademarks. Accordingly, God demands that you act expeditiously immediatelly stop and remove all acquired data from that procedure in order for you to claim a safe harbor under the DMCA from liability for contributory and vicarious copyright infringement. Sincerely, God
There are millions to hundreds of millions of atoms in a typical virus. Here is interesting virus simulation info
Oh yeah, I know (hope?) you're joking, but modelling millions of atomic interactions is, as they say, nontrivial.
Man, you really need that seminar!
how about the 90%+ of dark matter that's with the virus, or at quark level :D
You don't need a supercomputer, just a Windows box.
Not quite:
Windows Box: lol this is not a virus
Supercomputer: LOL THIS IS NOT A VIRUS
(sorry, it was badly formatted)
Dear Sir or Madam:
This letter is to notify you, pursuant to the provisions of the Digital Millennium Copyright Act, that we believe one of your humans is infringing God's copyrighted materials. Specifically, God is the owner of the copyright and trademarked materials, wich includes all life forms.
The aforementioned human reverse engineered a virus without authorization, thereby infringing upon God's copyrights and trademarks.
Accordingly, God demands that you act expeditiously immediatelly stop and remove all acquired data from that procedure in order for you to claim a safe harbor under the DMCA from liability for contributory and vicarious copyright infringement.
Sincerely,
God
I once read that if you converted all the sand of the earth into processors, it would still take ages to accurately simulate the folding of a protein. Is this just "zooming out" and ignoring things like protein folding?
10 ?"Hello World" life was simple then
Just a few billion more molecules worth of computing power to go!
Bigger problems, and bigger computers to solve them on. This is certainly a fun example, and aesthetically pleasing as well.
Unfortunately, we're still a few generations of supercomputer off from being able to simulate ribosomes (at which point most of the cellular machinery will be suitable for in-silicio biochemical investigation), but this is an excellent step along the way. It's also a good to showcase Schulten's group's work on efficient parallelization of complex simulations. He's had to solve a lot of algorithmic issues in order to be able to run that simulation, so this is not just an example of "wait for a bigger computer". If you check out their web-page http://www.ks.uiuc.edu/, you'll find discussions of the underlying technology, which has required collaboration between biophysicists and computer science. My hat is off to them, especially as they not only achieved the proof of concept (we can simulate a small virus), but also gained biochemical insights (we didn't know they collapsed without the genetic payload). Bully for the Biophysicists!
Note: I don't work for them, but I admire the scale of simulations they do, and their willingness to make available to the community the tools they use.
the more accurate the calculations became, the more the concepts tended to vanish into thin air. R. S. Mulliken
From TFA the virus so simple as to need a second more complex virus in order to replicate. Even so, the simulation only covered 50 billionths of a second, or about 50,000 frames. The Nature article stated that in the next 5 years it may be possible to simulate more complex viruses. Its amazing to see how complex life is that even the most powerful computers we have come up short.
The simulations followed the life of the satellite tobacco mosaic virus, but only for a very brief time,
The nature article mentions a runtime of 50 times a billionth of a second, which I guess is 50 nanosecond, or 50 femtosecond, depending on how you define 'billion'. 50 nanoseconds is pretty good for a simulation nowadays, especially for a system of that size.
Look, it al seems very nice that they did this, fancy pictures and nature paper garantueed, but this really won't help us much further. This is no big scientific step forward. Virus processes happen at least in the micro/millisecond timescale, there's a lot of protein diffusion and refolding going on. Since the short simulation done here was an immense effort, it means that going to the timescales studying the real important processes is still way too far away. But who knows, maybe in ten years.
Right now, you could better use the same computer power used for this single project to study a lot more smaller projects that actually will give us insight into real molecular processes. Or maybe I'm just jealous ;)
molmod.com - computing tips from a molecular modeling
Yeah, but does it run Linux?
In Soviet Russia, Viruses simulate Computers.
I think Melissa was the first distributed super computing simulation of a virus. At least a simulation of how it spreads: TCP/IP
The Cough, Phlem. Infected Pus.
Oh You POS
Are you sure you didn't mean Adam sims, considering it's a ColecoVision you are talking about?
This space unintentionally left blank.
Since it is now possible to simulate what a virus will do if we know how it's built and what its environment looks like (on a molecular level), can we extend such a simulation to more sophisticated lifeforms?
The article talks about more complex virii, we could also, given more computing power, probably simulate the behavior of bacteria. But following in this fashion, computational biologists should be able to simulate more and more complex animals, up to and including humans.
Since the world is quite deterministic in any large enough scale, wouldn't that mean that given enough data about the surrounding of any person we would be able to predict everything he/she will do?
So this is what you get when you uninstall your Anti-Virus software?
I realize that the /. crowd is going to fellate any researcher who uses high-performance computing to draw pretty pictures, but from the Nature summary this sounds like a classic scientific case of showboating.
The researchers were using a technique called molecular dynamics, which attempts to model the movements of atoms in a 3D structure by integrating over Newton's equations. Force, however, is calculated using a coarse, empirical function of atom positions and their chemical properties. This model is weak, and it fails to produce physically-reasonable results on a whole variety of smaller problems, so it's an exaggeration to suggest that this simulation produced anything of physical or experimental relevance. And drawing strong physical conlusions from it? That's just crazy.
Before I get flamed by the MD crowd, I'll say that I am NOT suggesting that MD is useless. It's just that, it has a very short track record on problems of this size, and even in much smaller systems (i.e. fewer atoms), it's success rate is questionable. We can't even predict the dynamics of a single protein with this stuff -- it's absurd to suggest that it will work on an entire virus.
In short: don't be fooled. This experiment got into Nature because of its hubris and glamour, not necessarily because of its science.
P.S. I work in this field, so I'm posting anonymously.
...will it be intense as hacking the Gibson?
...on finding a lawyer. I hear most of them end up downstairs.
They need a supercomputer to simulate a virus? Crap, just get an XP box, give one of my coworkers admin rights, and you'll have the real thing in 15 minutes!
Futher proof of Windows' superiority.
See my journal for slashdot ID's by year. Mine created in 2005. http://slashdot.org/journal/289875/slashdot-ids-by-year
Why do I read "nod32" and think of the little wooden boy who isn't Pinocchio?
FTFA: This particular virus can only replicate in a cell which has already been infected by another virusthe tobacco mosaic viruswhich commonly attacks tomato plants.
Tomacco.
"There are no facts, only interpretations." --Friedrich Nietzsche.
Finally, I can say this for real: Imagine a Beowulf cluster (link is to Biowulf) of these!
The modeling software they used is called NAMD, free open source "parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems" that will run on commodity clusters of tens of Linux PCs on gigabit ethernet. In other words, you too can run the virus simulation on your own Beowulf cluster, if you don't mind it taking some years to run. According to NCSA's own press release about the virus simulation, it "only" took 35 processor-years, so if you have a 100 fast Linux PCs on a gigabit network lying around you can do it yourself in not much more than 4 months.
1. The full research page for this project is here. This is a lot better than the stuff linked through Nature and such.
2. The image was actually generated by our group, and specifically Anton Arkhipov, using our software package VMD. NCSA didn't have anything to do with it.
All they needed to do was start with a fresh installation of Win2k and stay online for a couple of days....
Oh, you wanted it simulated?
Does running under VMware count?
To simulate the spreading/infection rate of the virus, it just uploads it to WOW...
What about the fact that virii aren't usually considered to be alive, not being capable of reproduction outside of a host cell?
No matter how you define a billion, 50 billionths of a second would not be 50 femtoseconds (it could either be 50 picoseconds or 50 nanoseconds). Besides, "billion" generally refers to 10^9 in most English-speaking countries, including the UK. In particular, since the article and the research are both from the United States, it is unlikely that it is anything but 50 nanoseconds.
it said that they will eventually be able to simulate more complex organisms...that run on dna....that means full computer sims of us :D :D
Somebody please shoot this man.
Sorry, but I don't see how this is insightful. Anyone...?
I pretend to know more than I really do by mooching off google and wikipedia.
Speaking of which, what kind of screensaver do you use on a supercomputer?
I already figured it would most likely be 50 nanoseconds, but of course they might have used the wrong one on purpose to make it look like a bigger number :)
In the process I also found a very nice wiki on the history of the word 'billion': http://en.wikipedia.org/wiki/Billion
molmod.com - computing tips from a molecular modeling
oh, and another error: the actual paper was not in nature but in structure. I wonder if they tried Nature first...
molmod.com - computing tips from a molecular modeling
You can't shoot him. He's Neo, he'll just stop the bullets in mid-air and stare blankly at you.
That means I can play Spore on it!
How much does the Macafee virus scanner run for that system? Really a shame when you can't even connect your super computer to the Internet without it getting a virus. Of course it begs the question, why were they not using a firewall?
Go Chambana.
Did something change?
I could have sworn that they went, thousand, million, thousand-million, billion in Britain.
(A friend got me one of those mensa books in high school, but it was British, and I remember being really confused by the different way of counting large numbers)
Maybe I hallucinated it?
I guess that means the 3 body orbital dynamics problem is solved too.
I can't wait to get my hands on this game (legally). I loved Sim Ant, Sim Earth and the earlier, simpler versions of Sim City and Civ. This will really be a joy to pick up, play and have fun without too much of a learning curve. Sort of what Sid 's people did for the Pirates remake, I hope this game, and Nintendo Revolution lead to a new trend of addictive titles for casual gamers looking to recapture their youth.
Folding@Home.
I agree. It's just another "computer stunt" paper. The supercomputer centers love these things, as they (sort of) justify their existence. I think if they tore apart these big parallel machines and gave a small piece to small research groups around the country, a lot more science would get done. It takes a _lot_ of simulations to really learn anything, not just one moon shot hero run. The idea of these grand challenge computational problems soaking up all of the resources is so 80's. You can load up a 2-way dual core (for 4 cores) system (say, Operton or G5) and load up 16GB of RAM and get a lot of science done. This was even true more than 10 years ago: it was faster to run on a RISC workstation than to submit a job to a remote CRAY somewhere, where it sits in a queue for a few hours of cpu time. And debugging was a lot easier, too. I do think there are a few problems that really do require a large, dedicated system - but not very many.
This has been covered: http://www.simulation-argument.com/simulation.html
Supercomputer: $12,000,000.00
Pathogen Simulation Script: $145,000.00
Power Button (ATX style): $2.59
Watching a room full of nerds giddy about a virus: Priceless
BOINC can easily network thousands of PC and Unix servers to run simulation of this kind. http://boinc.berkeley.edu/
SKYNET not only simulated a virus but it actually infected computer systems.
It is a little disappointing to see people talking about "showboating" in this case. The NAMD program is a fantastic md program for biological systems that has been designed from the bottom up to be scaleable. The same group has also developed a graphics program VMD that allows one to analyze results from MD runs and even interact with a simulation while it is in progress... The folks at the University of Illinois are WORLD CLASS in this area and deserve congratulations for making it widely available. You can download NAMD and VMD for your pc (if you want to) or your Mac and have a heckuva simulation system. What is nice is that you can use any little toy program files that you develop for calculations on supercomputers at Pittsburgh or San Diego, say. The NAMD program won the Gordon Bell program a few years ago. Check it out!
You could have the surviving humans turn into creatures with hyper-reactive DNA to protect themselves against the constantly changing virus patterns. Call them muties or something. They have to constantly test one another's behaviors to make sure a new virus hasn't slipped through.
Cool.
That's our life, the big wheel of shit. - The Fat Man, Blue Tango Salvage
Here. They're just looking at what holds together the structure of the virus.
"The White House is not an intelligence-gathering agency," -- Scott McClellan, Whitehouse spokesman.
"moller writes to tell us that Red Herring is reporting that researchers ... have announced ..."
Indeed.
Discuss. ;)
(That's what I believe, anyway; at a fundamental level, life is something unique that cannot entirely be modeled via biochemical process modeling. Still can't wait to see the results once this gets better...)
Aren't there more important things to be doing? Like searching for aliens?
I am a computational chemist, and although this is a good piece of work, it's really not a big deal compared to what everyone else out there is doing. There are also a few caveats here...
First off, this is not actually a virus perse, it's a satallite virion which can only reproduce during cocontaminant Tobacco-Mosaic Virus infection, and does not have the ability to infect anything itself. It is also only a fraction of the size of most viruses.
Second, Molecular Dynamics is a purely emperical, non-precise method for doing molecular simulation. Although to be fair, ab initio or Density functional theory approaches to this kind of a problem are impossible at this time. But there are some QM semi-emperical methods that are gaining popularity in the biology world.
Third, this is a tiny, minute time-scale for such a large chemical system. It's one thing to be working femtosecond timescale when you are simulating electron exchange between to small molecules, but on a system of this size means very little, especially when using an imprecise measure such as MM.
I guess I should also point out that it's not that hard to set up a simulation such as this when you are starting out with a hi-res x-ray crystal structure for you're starting coordinates. It's really just how much computational capacity you have.
Any thoughts?
-Ryan
It takes a _lot_ of simulations to really learn anything,
still you have to do one before you can do a lot. Maybe those opterons would even exist with out people grand-standing on a super-computer a decade ago.
Apocalypse Cancelled, Sorry, No Ticket Refunds
As far as force field calculations go, it depends on the protein, however I'd jump up and down for an efficient and accurate force field system. I'm betting that as the simulation gets larger, the artifacts become less important to the large picture, and that the large scale interactions can drown out the noise( pure intuition YMMV ). And in this case, determining the assembly of TMV, it's the most convincing game in town.
Storm
There is no text. Nothing to see here, move along.... ;)
Supercomputer Performs Simulation of Virus, Accidentally Deletes Own Harddrive.
They're using their grammar skills there.
a windows machine goes one better. instead of just simulating an infection, with windows you get the real thing.
In premed, I tried to produce a 4D graphic animation of a virus being reproduced from an RNA, protein by protein, in a host cell. My advisor told me it would be too hard - I should use the newfangled computer to instead process huge (1980s megabyte) datasets of genetic drift data. I thought he was too shortsighted based on his pessimism for the animation, so I just made PR animations of cameraviews flying around a double helix, which I reused as a lightshow for the psychedelic rock band I lived with.
Turns out I'd have spent at least 20 years on that animation. And that genetic drift project would have trapped me in COBOL programmer Mesozoic. The lightshow, however, had immediate effect on my chromasomes.
--
make install -not war
Thank you Randall, that was the joke.
Rex is 09 F9 11 02 9D 74 E3 5B D8 41 56 C5 63 56 88 C0
Everyone is running simulations on some sort of a batch queuing system. This system may have been more obnoxiously huge than most, but it's not atypical. Or are you just saying that the processors should be broken up into (mumble, I didn't RTFA) smaller systems and spread around? It would still be a batch queuing system, I'd guess.
My research group isn't really starved for computing horsepower right now, but we may not be typical.
no, actually it's a different joke. you're not being a careful reader. neither are you, person who modded him up.
This is an interesting coincidence because I used to reflect deeply on this exact subject a few years ago: what if a supercomputer could simulate a human ? I'll be honest here: I am literally _astounded_ to discover that this scientific team has successfuly simulated a virus. I didn't thought supercomputers were powerful enough for such a task. I just finished reading some articles about the experience and I now understand why this has been possible: they used some empirical functions instead of implementing exact physical laws (would have required much more computing power) and they also simulated the virus for only 50 billionths of a second. But still, they seem to have successfuly simulated life.
Most people don't realize the significance of this event, it means that given enough computing resources we could theoretically simulate humans ! One day we will have enough computing power to run such a simulation. And when it will be done, this human life simulation will have the potential to prove (or disprove) that humans are "just" a bunch of atoms following physical laws and nothing more.
This is huge. Think about it. I know this may sound sad, but personally I am convinced that any life form, including humans, is just that a complex assembly of atoms following physical laws, there is no soul, no afterlife, etc. This human life supercomputer will prove I am right :)
System weighing only 50-100kg handles motion of every atom in human body in real time.
User interface found to be cumbersome.
Believing something doesn't make it true. Not believing something doesn't make it false.
You are stoned !
Now that we've simulated a virus, you can actually catch a virtual STD from pr0n!
Is that x386 Processor years or AMD64 processor years?