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Supercomputing Medicine Science Technology

Computing a Cure For HIV 89

Posted by Soulskill from the petaflops-for-science dept.
aarondubrow writes: The tendency of HIV to mutate and resist drugs has made it particularly difficult to eradicate. But in the last decade scientists have begun using a new weapon in the fight against HIV: supercomputers. Using some of the nation's most powerful supercomputers, teams of researchers are pushing the limits of what we know about HIV and how we can treat it. The Huffington Post describes how supercomputers are helping scientists understand and treat the disease.
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Computing a Cure For HIV More

Computing a Cure For HIV

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  • Bitcoin mining? (Score:3, Interesting)

    by Anonymous Coward on Saturday June 21, 2014 @01:53PM (#47289207)

    Imagen if all that computer power was put to use such as finding the cure of HIV.... We would be done by lunch time.

    • Re:Bitcoin mining? (Score:5, Insightful)

      by Anonymous Coward on Saturday June 21, 2014 @02:07PM (#47289261)

      It isn't lack of computing power that is holding back most theoretical biophysics research.. it's the lack of people who have the rare combination of skills of a programmer, mathematician, chemist, biologist and drug engineer coming up with novel and unique ideas to combat disease who will sacrifice industry paychecks to work in academic fields.

      • who will sacrifice industry paychecks to work in academic fields.

        Why do researchers have to sacrifice an industry paycheck to do it? In other words, why won't industrial pharma hire more talented scientists. They seem instead to be more interested in hiring salespeople, lawyers and MBAs, then contracting with academia so they can take advantage of "cheap labor" due to the overabundant supply of low-paid graduate students and post-docs. But then they wonder why the amount of NDAs (New Drug Applications) has been declining.

        • Re:Bitcoin mining? (Score:5, Insightful)

          by gnupun ( 752725 ) on Saturday June 21, 2014 @02:54PM (#47289433)

          Why do researchers have to sacrifice an industry paycheck to do it? In other words, why won't industrial pharma hire more talented scientists. They seem instead to be more interested in hiring salespeople, lawyers and MBAs...

          Perhaps, it has something to do with the high failure rate of such research. Would you pay a salary to 1000 employees, of which only one employee gives you solid results and the remaining fail? That's not very business friendly. This type of research is more feasible under govt. grants.

          • Re:Bitcoin mining? (Score:5, Insightful)

            by bmo ( 77928 ) on Saturday June 21, 2014 @03:56PM (#47289655)

            Perhaps, it has something to do with the high failure rate of such research. Would you pay a salary to 1000 employees, of which only one employee gives you solid results and the remaining fail?

            >implying that this is bad

            Typical bean-counter/MBA attitude.

            That's not very business friendly.

            Companies like HP, Xerox, etc, built empires on that kind of research.

            They declined when they spun off or closed their research divisions because management failed to see the value/use the output of the research labs. The HP example is particularly striking - they went from an advanced technology company to a schlock printer seller, one that is sneered at and loathed, in a handful of years. Xerox is also striking in that PARC laid the foundation for a lot of modern computing but management only saw money to be made in copiers and filing paper and thusly ignored most of PARC's output, ceding the computer revolution to other companies.

            It is also part of a larger problem. Because of the emphasis on short-term profits (quarters are too long!) at the expense of everything else, we in the West are so enthusiastic at shoving all our production to the Chinese and others saying "We can't be arsed to get our hands dirty; we want to just do the high-level stuff like design and company management" totally ignoring the fact where the production goes, so does the engineering development, science research, and eventually even upper-management. This was learned by Samuel Slater, Francis Cabot Lowell, and others who founded the "silicon valley" (Blackstone Valley) of the Industrial Revolution. A lesson forgotten through complacency, greed, and snobbery.

            Alexander Graham Bell is shouting at you from his grave calling you a moron.

            --
            BMO

            • Re: (Score:1)

              by Anonymous Coward

              Typical bean-counter/MBA attitude.

              And who do you think makes those decisions?
              Research only gives a pay off for the next CEO. Fuck that guy. It's much better to downsize everything, cut down costs and jump with a golden parachute and repeat the formula elsewhere.

              Industry doesn't wants theoretical results that might be useful ten years from now. They want results for this quarter. So while they do invest in crazy ideas, small improvements is more their thing. It goes the other way around for academicals: even if it isn't a viable solution rig

              • Re: (Score:2)

                by pepty ( 1976012 )

                Research only gives a pay off for the next CEO. Fuck that guy.

                But the stock price moves based on the latest clinical trial results and letters from the FDA. What's a CEO to do?

                ILOS: in license, out source. It's much faster to buy a promising drug candidate (in license) then to herd your own to phase II. It may also be less risky. Hence Valeant trying to buy Allergan. For your remaining pipeline outsourcing R &D to contract labs can cut your R&D budget nicely, and it's the investors looking at R&D spending as a black hole into which their money disappears t

                • They might try not publicly trading. There's no shareholders to yank your leash around. Don't jump into the pool if you don't want to get wet.

                  • Re: (Score:2)

                    by pepty ( 1976012 )
                    Shareholders are hard to avoid. A new drug approval might cost just $200M (Optimer's Dificid), but on average companies are racking up ~$4B in R&D per new drug. (by new drug I mean new molecule, not new dose/formulation/indication for an old one). If you take venture capital they will be looking for a payout well before a drug is approved, probably by either selling the company or its ideas to a big pharma. Keeping it closely held has worked in the past - but you may need vasty deep (10 figure deep) po

            • Re: (Score:2)

              by pepty ( 1976012 )

              Companies like HP, Xerox, etc, built empires on that kind of research.

              Tech research is a lot less risky and has a much shorter wait til revenue then Pharma/Biotech (these days).

            • You rolled all of R&D into one pile, so horseshit.

              Drug R&D is way different from tech R&D. Microsoft is sitting on billions of unmonetized discoveries. They could, if they converted 10% of the non-operational Microsoft Research into marketable assets, push Apple off the map.

              In comparison, look at the price for a cure for HCV. $100 per pill, or $90,000+ in total. It seems to be a solved problem, and not one of those things where big pharma hides a cure because long-term treatment is financia

          • This is the reason that most major medical research is done by government grant (historically). Big pharma companies like to tell everyone they are the solution but really they are only the endpoint in the process.

            • Re: (Score:2)

              by pepty ( 1976012 )
              Year in, year out, 75-80% of new drugs are invented privately in biotechs/pharma. The remainder are invented by academia. In terms of money and sheer manpower required to get from "what causes this disease?" to "new drug approval" the pharma/biotech portion often isn't the short end of the stick either.

              • Year in, year out, 75-80% of new drugs are invented privately in biotechs/pharma. The remainder are invented by academia.

                Correct; what government grants pay for is the majority of the basic research that informs efforts to find a cure. Naturally, private companies are (mostly) free to use this information when searching for new drugs - this is part of the point of federal funding for basic research. The vast majority of that research won't directly lead to a cure, of course, but it does contribute to our

                • Re: (Score:2)

                  by pepty ( 1976012 )

                  In contrast, I've heard the drug development process at some companies compared to "piling up stacks of money and setting it on fire", which is why I'm really, really glad the universities and governments don't try to get deeply into the drug development business.

                  Lots of folks express that exact feeling about the NIH's efforts to get into translational medicine, which is establishing centers to do preclinical and clinical development. I'm pretty sanguine about that too. I could see some payouts happening though even if not many new drugs get made: 1, having publicly funded (and disclosed) research into how to conduct pharma R&D might improve the whole industry; 2, a stable funding source could allow really, really long clinical trials, which could be critical f

        • Industry does do a lot of research. There's money to be made in curing HIV, after all. They do shy away from the purely theoretical though, because there's no money to be made if you don't get a patentable drug at the end of it.

          • Re: (Score:2)

            by pepty ( 1976012 )
            You don't always need a patentable drug, just FDA exclusivity. If you find a new indication for an old generic drug and do the research to back it up you can get market exclusivity for a while and charge out the wazoo for it.
          • The true cure of HIV is a genetic mutation in a human, with HIV resistant genes. The highest likelihood of such a mutation emerging is in an area ravaged by HIV deaths, such as South Africa. If HIV doesn't really cause death (i.e. does not really increase mortality) then it's not really a disease worth mutating against. There are probably a gazillion kinds of bacteria and viruses that live in you, that do nothing special, and these HIV FUD (fear, uncertainty, doubt) spreading people will use one of these st

            • I'm trying to figure out what you are saying, but I find your post rambling and self-contradictory.

              The test for HIV doesn't use an electron microscope. It's a form of the ELISA test, using specific antibodies that attach only to HIV. Are you trying to claim that HIV is actually harmless, or accusing scientists of fabricating the tests where no virus exists? Because either way, there are about 35 million corpses that disagree with you.

            • Comment removed based on user account deletion

              • So do you have a control group to present to us that didn't buy into the HIV bullshit?

                One of the earliest public cases of HIV was a elementary school kid in Indiana that got it through a blood transfusion. That helped push for higher standards in blood donations. It also pushed for higher standards in dealing with spilled bodily fluids. Before all this though the general public thought was only a STD that the gay community passed around.

                Remember that real bullshit is pretty green grass before being consu

        • Why do researchers have to sacrifice an industry paycheck to do it? In other words, why won't industrial pharma hire more talented scientists.

          There is more money in treating a medical condition than in curing it. Once a disease is cured, there is no need to take expensive medications anymore. The financial incentives for both doctors and pharmaceutical companies is to keep a patient in treatment for as long as possible.

          • There is more money in treating a medical condition than in curing it.

            Not for the insurance companies or government, there isn't. And given the immense cost of long-term treatment for many conditions, pharma companies would be able to charge much more for a drug that completely stopped a disease.* In reality, the reason most medications merely treat rather than cure diseases is that actually eliminating the root cause of a disease without debilitating side effects, for instance death of the patient, is us

      • Re: (Score:1)

        by Anonymous Coward

        And yet, many people do just that - when given a choice between doing good for humanity and making money, they choose to do good.
        It's almost weird.

      • Re: (Score:2)

        by pepty ( 1976012 )
        Sort of. Basically we need someone to invent a force field (mathematical model) that can simulate proteins, protein-substrate interactions, and protein-protein interactions so well that it can make accurate and useful de novo predictions about drug candidates and disease models. After that we've got plenty of med chemists, structural biologists, etc., ready to make use of it.

      • it's the lack of people who have the rare combination of skills of a programmer, mathematician, chemist, biologist and drug engineer coming up with novel and unique ideas to combat disease who will sacrifice industry paychecks to work in academic fields.

        Guess what: there are vastly more jobs like this available in academic groups than in industry. (I know this firsthand, because I work in a related field and am basically stuck in academia unless I can change careers somehow.) The bigger problem is that gi

    • Is computational biology really looking to compute a lot of SHA hashes?

    • Computational drug design and bitcoin miners have in common that both run best on custom hardware. The crux is, that both require very different types of hardware. As an example, please refer to Anton [wikipedia.org], designed by DE Shaw Research exactly for molecular dynamics (MD) codes.

      Bitcoin mining is classified as a so called embarrassingly parallel algorithm, while MD is a tightly coupled problem. Hence an efficient parallelization for MD codes is much harder to speed up: communication gets in the way, and communicat

      • It's not that specialized. It's just plenty of DSPs strapped together on a torus.
        Unlike what wikipedia claims, you could probably achieve comparable performance using a more classical and general-purpose supercomputer setup with GPU or Xeon Phi accelerators, provided the network topology is well tuned to address this sort of communication scheme (most recent supercomputers don't use tori)

        • It's not that specialized. It's just plenty of DSPs strapped together on a torus.

          Actually Anton uses ASICS, their cores are specially geared at MD codes. This goes way beyond just "strapping together DSPs". They have IIRC ~70 hardware engineers on site. (Source: I've been to DE Shaw Research last year).

          Unlike what wikipedia claims, you could probably achieve comparable performance using a more classical and general-purpose supercomputer setup with GPU or Xeon Phi accelerators, provided the network topology is well tuned to address this sort of communication scheme

          No, you can't, and here is why: Anton is built for strong scaling of smallish, long running simulations. If you ran the same simulations on a "x86 + accelerator" system (think ORNL's Titan) then you'd observe two effects:

          • The GPU itself might idle a lot as each timestep only involves few

          • Indeed, the GPU constrained programming model is ill-suited for this, but a Xeon Phi isn't. And the next-gen Xeon Phi will have very low latency networking on board, too.

            My bad about tori, the supercomputers I have had access to lately were all fat tree.

    • HIV is easy to erradicate. Just use mandatory testing, sterilization, and quarantine, and no mater how it mutates, it will be gone in two generations.

    • Imagen if all that computer power was put to use such as finding the cure of HIV.... We would be done by lunch time.

      If anyone wants to contribute to computer research on HIV with their own systems then there is a World Community Grid [worldcommunitygrid.org] project called Fight Aids At home (FAAH) that uses your computer's spare cycles to work on AIDS research, using the BOINC platform.

      There are versions for Windows, Apple, Linux, and Android software.

    • Re: (Score:2)

      by ClioCJS ( 264898 )
      No, we would not.

  • Because we don't get out much.

  • We bothered about HIV for decades while we just had to run supercomputers to get rid of it. I wonder why nobody thought about it before.
  • Condoms. Cheap, plentiful, and 99% effective.

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