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Medicine Programming Science

Virtual Lab Rat Saves Human Lives 69

An anonymous reader writes "There is already a Virtual Physiological Human project going on in Europe, to program a simulated human that can serve as a guinea pig, but this National Institute of Health effort to program a Virtual Physiological Rat promises to help humans even more. It's too difficult to simulate humans with algorithms, but the simpler rat physiology can be easily programmed, and by hand-tweaking its virtual genes, these rats-in-an-algorithm can be set up to what-if about interventions that cure human diseases more easily that when simulating humans directly. Long live the virtual lab rat!"
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Virtual Lab Rat Saves Human Lives

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  • Another advance, to a better

    • maybe now people will start to understand that research is nowhere near the costs it is claimed to be.

      • What do you mean? I am honestly confused.

        • Testing a virtual lab rat has only the cost of the computing power.

          People try to say that research costs hundreds of billions of dollars (it used to maybe 20 years ago, but is far less today).

          It's used as an excuse to extract money.

          • Haven't done much research have you? I don't think it's the raw cost of the materials that is the major factor.

            There's facilities, support staff, the research staff itself, and all the other things you have to spend money on to be safe and regulatory-sound.

            Unless you happen to think every medical research project is done in someone's garage with the family kitchenware and a rat they trapped out by the scrapyard...

          • Testing a virtual lab rat has only the cost of the computing power.

            Plus the building to house the computers, plus data storage, plus programmers, plus tech support, plus people testing the virtual results on real rats to see if the models are correct. The researchers involved in this project were given $15 million over 5 years just to begin development on this. It is not meant to replace animal studies, but to inform future animal studies so that they can be designed better.

            People try to say that research

  • Simpler how? (Score:4, Interesting)

    by Anonymous Coward on Wednesday August 17, 2011 @06:10PM (#37123948)

    I am not a biologist, but why is rat-physiology simpler than human-physiology. Smaller yes, but simpler?

    • by h4rr4r ( 612664 )

      I agree, the mammal body plan is pretty consistent.

    • by McKing ( 1017 )

      They probably mean simpler in that the sheer volume of data makes a rat model easier to work with than a human model, even for a supercomputer. I worked on a project about 15 years ago where the scientists who were studying the effects of certain types of microwave radiation used a low resolution (5mm) rat model for their daily test runs, a higher resolution (1mm) rat model for more complex runs (2-3 days), and a low-res human model for certain runs. The low-res human runs took weeks on a seriously-beefy-

    • by Hatta ( 162192 )

      You're right, the rat isn't any simpler than a human. We just have more data on rats.

      • by Niedi ( 1335165 )
        Plus you can easily make targeted experiments to verify/falsify your model without having to fly to kuba, china or something like that...
    • Re:Simpler how? (Score:5, Informative)

      by Oligonicella ( 659917 ) on Wednesday August 17, 2011 @06:49PM (#37124252)
      I am a biologist. It's not. It's very similar. That's the word he misread - similar.
      • Seriously. Even simulating a single heart cell is a very complex, compute-intensive task. Simulating heart tissue or the entire heart is even more complicated and time consuming.

        Making it a rat heart instead of a human heart doesn't buy you very much, and it's very doubtful a "simple rat model" would be able to simulate what happens when you take certain kinds of drugs that affect, say, cell permeability to various elytes.

    • The article actually says "Due to their similar physiology...", not simpler.

    • Rat physiology is probably better understood than human physiology for two reasons:
      1. You can slice, dice, blend, and kill rats anyway necessary to study them, you can't with humans (without going to jail anyway.)

      2. You can get a genetically homogenous population of rats, keep their environments, food, and all variables identical. Treat one with a drug, and you'll know any differences from the control are probably due to the drug. With humans you get a comparatively wild variation in genetic backgroun
      • "Well, it turns out he has two extra chromesomes somehow, smokes like a chimney. And his house got foreclosed on during the test, so he probably had a massive increase in stress. He eats mostly cheeze-wiz, and I strongly suspect he does heroin."

        This is bullshit. I was assured my participation would remain confidential. Also, I'm feeling much better now.

      • But with homogeneous populations, isn't there the danger that a drug developed with them only works on those populations? Or that a working drug isn't detected as working because it just happens to not work on that particular population? Shouldn't there be testing on heterogeneous population specifically to avoid developing population-specific drugs?

        "Well, we have found a cure for cancer, but it only works on blond males between 20 and 30 who have green eyes, blood type AB, an inherited disposition for Diab

    • it is most likely not but a team of programmers needs to eat so they seem to have been able to sell it
  • before somebody starts griping that we are abusing these virtual rats?
  • by WindBourne ( 631190 ) on Wednesday August 17, 2011 @06:26PM (#37124090) Journal
    Not just rats. How about some Fungus, mollusk, reptiles, etc. And lets test various drugs on these vs. the sim. If it matches, then we find out how it matches and not. Far better to get cells down then move to simple tissues and up until we hit complex creatures. And a rat IS a complex creature.
    • by geekoid ( 135745 )

      really, you want o go from fungus to mice?
      Hint: we know MORE about mice then we do fungus. We genetically manipulate them with an incredibly high level of accuracy already.
      There is no problem with starting with a complex creature if we already understand it.

    • by interkin3tic ( 1469267 ) on Wednesday August 17, 2011 @07:53PM (#37124656)
      Biologists generally do work on the simplest model organisms they can. Cheaper, generally easier to study, fewer variables to screw up the results, and cheaper again. There's a reason you probably never hear about drug tests in chimpanzees: they're more complicated and hideously expensive to keep compared to e.coli, frogs, fish, mice, or rats.

      The driving force behind this project itself is probably economics, someone got tired of wasting money on real rats when virtual ones might suffice.
      • Not just that. Basically, by doing a virtual animal, plant, etc, we can find out what is missing from our understanding. That allows us to know WHERE to look. With large genomes, we know that they turn on and off at various times, but we have not way to know WHEN they do (or exactly what they do, what triggers, etc). With a virtual animal, we figure out how these model and if not quite right, where to look. Basically, Biology is finally moving from a soft science into a hard science. And I say that as some
  • That must be the understatement of the decade. Nothing is easy about simulating a rat, or nobody would use them anymore.

  • by Anonymous Coward

    Virtual Peta is going to be all over this.
    "What do you mean you just stopped the simulation..."

  • We can only simulate what we fully understand; beyond that, we're just guessing. This will do something between 'jack' and 'squat' for testing things like the effect of novel pharmaceuticals. There are too many unknowns when it comes to cellular biology.

    Hell, just recently we discovered that removing the spleen caused a significant increase in diabetes; turns out that spleens create islet cells. We didn't know that. I'm skeptical of the usefulness of models that contain so many unknowns. Hell, we're lucky i

    • I agree it won't be useful for proving new drugs work, nor will it be good for discovering new things, but it -could- be a useful compendium for knowledge, and -could- help prevent some needless wastes of research money.

      You have a new chemical cocktail that looks like it fights cancer in a petri dish. You are just about to spend a lot of money to make significant amounts of the components and order the rats when you decide to run it virtually through this rat.

      Surprise! Program tells you that it woul
      • and -could- help prevent some needless wastes of research money.

        This type of projects is not particularly known to be cheap. Supercomputers are expensive and cost quite a bit just to have them powered and maintained (I heard 1 mio US$/yr electricity bill for a IBM Blue Gene). Plus all these projects are run by a large consortium. Most experienced scientists tend to think of them as expensive useless toys and I tend to agree for all the reasons the parent has mentioned. We are nowhere near understanding rodent physiology well enough to create a model that has any relevan

        • This type of projects is not particularly known to be cheap. Supercomputers are expensive and cost quite a bit just to have them powered and maintained

          On the other hand, it's a parallelisable, and scale nicely with processing power (like number of nodes on the cluster or Moore's law and newer CPU/GPU).

          You could use the virtual model to test not 2 chemicals - like GP mentionned - but tens of thousands of candidate.

          It's currently done at the molecular level: You can throw a database of thousands of molecule and a bunch of know 3D structure or a bunch of chemicals for which we know precisely how much each is efficient. And see what sticks. And thus have an i

    • We can only simulate what we fully understand; beyond that, we're just guessing. This will do something between 'jack' and 'squat' for testing things like the effect of novel pharmaceuticals. There are too many unknowns when it comes to cellular biology.

      There's only one use case in scientific history that I know of where simulations have COMPLETELY supplanted experimentation, and that would be nuclear weapons testing, per the Nuclear Test Ban Treaty. That treaty, and the necessary maintenance of our existing nuclear stockpile have done a lot to drive the supercomputing "arms race" in the last couple of decades. The vRat is most certainly not going to replace the meat version, but it will provide an adjunctive tool. In the real world, biomedical research w

  • simulations can only be accurate if we understand the entire system, in this case it's a rat. when we fully understand how a rat works down to the atomic level THEN we can make a proper rat simulator. however, by that time we will have discovered how to do the same with humans.

  • the effort looks very worthwhile and may well be quite helpful, ie PROMISES... but the notion that rat physiology is EASILY programmed is so ridiculous as to be laughable. Perhaps some broad, gross strokes, which might be good for some things, but certainly not in any detailed, thorough way at the level of subtlety that many disease operate at. And yes, rat physiolog is very similar to human physiology, certainly at these levels and below. When the genome is 90+% identical, so is the physiology.

  • If they can use the simulation to keep real rats from experiments, then the virtual rat is saving the lives of real rats before any humans are affected.

  • I propose a special moderation line in the pulldown with the value of -2 for usage of the line "Saves Human Lives"

    • by Livius ( 318358 )

      The headline did overstate the matter. I was expecting to learn about virtual rats escaping their simulation and carrying people out of burning buildings.

  • Pfft. What good is a rat emulator without a good place to get ROMs?
  • from Virtual PETA.
    • Queue the protests
      • No, GP had it right. Queue is to enter something into a sequence, to be served sequentially in order of insertion. Cue is an action or event that signals something to occur. This coming to fruition (event) would cue the protests to begin. Queuing the protests would be asking them to stand in a line and complain indivually one after the other.
        • Technically you're correct, however I was just going with the majority usage of the word here. English is a living language...
          • Indeed it is. Personally it annoys the hell out of me that it so many homophones. Makes it far to easy to know what you want to say but still say it incorrectly. :-/
  • To clarify the summary, the virtual rat project is being done at the Medical College of Wisconsin (Milwaukee). NIH is just funding the project.

"The eleventh commandment was `Thou Shalt Compute' or `Thou Shalt Not Compute' -- I forget which." -- Epigrams in Programming, ACM SIGPLAN Sept. 1982