Stories
Slash Boxes
Comments
Search

News for nerds, stuff that matters

Slashdot Log In

Log In

Create Account  |  Retrieve Password

Open source Digital Bacteria

Posted by Hemos on Mon Jun 06, 2005 11:10 AM
from the create-your-own-share-it-with-your-friends dept.
Software Science
FiReaNGeL writes "Scientists have constructed a software capable of simulating organisms at the molecular, single-cell and population levels. The program, called AgentCell, will soon be available, open sourced under a BSD license. "With AgentCell we can simulate the behavior of entire populations of cells as they sense their environment, respond to stimuli and move in a three-dimensional world". The researchers have designed their digital bacterial system in modules, so that additional components may be added later - "The hope is that people will modify the code or add some new capabilities". AgentCell has possible applications in cancer research, drug development and combating bioterrorism. Lots of movies and pictures are available, along with a detailed press release describing the program."
+ -
story
This discussion has been archived. No new comments can be posted.
The Fine Print: The following comments are owned by whoever posted them. We are not responsible for them in any way.

Open source Digital Bacteria 50 Comments More /

 Full
 Abbreviated
 Hidden
More
Loading... please wait.
  • Am I the only one the looked at the pictures and thought of core wars?
    • Am I the only one the looked at the pictures and thought of core wars?

      I haven't actually played core wars, but I know what you mean.

      What intrigues me is using this kind of bacterial model in a first-person shooter, maybe a Half-Life mod where you fight hostile bacteria in a microscopic maze. The heads-up display elements might resemble FreeAgent diagrams....

      -kgj

  • There are 10 kinds (Score:3, Funny)

    by smoyer (108342) <<ten.roc-c> <ta> <reyoms>> on Monday June 06 2005, @11:15AM (#12736969)
    of bacteria in this world ...

  • Poor server... (Score:4, Funny)

    by Cobra_666 (777517) on Monday June 06 2005, @11:15AM (#12736972)
    Saying "Lots of movies and pictures are available" in a Slashdot article is like a death sentence to the poor server running the site...

  • This Is New? (Score:5, Funny)

    by Spencerian (465343) on Monday June 06 2005, @11:16AM (#12736981) Homepage Journal
    It seems that Windows users receive free copies of stuff like this each time they connect to the Internet and get their mail.

    That, and news on free "sword sharpeners", if ya get my meaning.

    I remember the old game of "Life" that simulated growth with very simple rules. Sounds like the game has grown up.
    • I remember the old game of "Life" that simulated growth with very simple rules. Sounds like the game has grown up.

      To be technical, Life simulated cellular automata, which can demonstrate, but is not limited to, growth.

    • Re:This Is New? (Score:5, Interesting)

      by Rei (128717) on Monday June 06 2005, @11:26AM (#12737093) Homepage
      This isn't really a variant on Conway's Game of Life - it's closer to a variant on Polyworld. Of course, if you want a grown up Conway's Game of Life, I wrote one called Megaconway [daughtersoftiresias.org] a while back - massive worlds made possible by using each byte to store 8 squares and doing operations in bulk wherever possible. It also keeps entropy in the world with occasional random inputs of randomness of varying sizes. My big hope, although I doubt it will occur, is that eventually it will come up with a system that is stable, self-perpetuating, and can "heal" from random damage. Who knows... I leave it running niced to 19 at all times.

  • Great... (Score:3, Funny)

    by AnObfuscator (812343) <onering@@@phys...ufl...edu> on Monday June 06 2005, @11:17AM (#12736988) Homepage
    As if Windows didn't have to deal with enough computer viruses, now it has to deal with computer bacteria as well.

  • Let's not dis this development - (Score:5, Funny)

    by Progman3K (515744) on Monday June 06 2005, @11:17AM (#12737002)
    Bacteria may be the only culture some people have.

  • Digital disease (Score:5, Funny)

    by lilrowdy18 (870767) on Monday June 06 2005, @11:29AM (#12737117)

    Anybody know the cure for digital chlamydia?

    I networked with this infected computer and didnt have my firewall turned on.

    • You've got to be careful.

      If that computer was connected to the Internet, you end up networking with everyone they network with.

      On top of that, if you're connected to the Internet you can really *screw yourself* in the end. /Rimshot

  • Pathogen games for the PS3 (Score:3, Funny)

    by CardiganKiller (854899) on Monday June 06 2005, @11:30AM (#12737123)
    "For instance, if you mix a pathogenic strain with a friendly strain, which one is going to win, and with what kind of speed?"

    I can't wait until this becomes an actual game:

    "Cell-Wars 3D. Engineer your own pathogens and destroy up to 5000 different types of organisms! Experience multiplayer action over the Internet in a race to be the quickest and most destructive pathogen.

    Be sure to enter in our annual contest. The winner will get to see their pathogen recreated in real life by our molecular engineers and injected into a mouse! Total insane action!"
  • "The hope is that people will modify the code or add some new capabilities". AgentCell has possible applications in cancer research, drug development and combating bioterrorism

    And with the addition of malware modules and networking might be used to promote cyberterrorism said lead engineer 133t h@x0r.

  • Alice: Yeah...make sure we stick 'combat terrorism' in there somewhere. That'll make sure we get the cash.

    Bob: Oooh ooh...and maybe the frontpage on some reputable internet discussion board *cough*.

    -Nano.

  • combating bioterrorism (Score:4, Interesting)

    by exp(pi*sqrt(163)) (613870) on Monday June 06 2005, @11:50AM (#12737309) Journal
    !!!

    I'd put money on this work being completely bogus. There's quite a bit of funding going to researchers from Fath^H^H^H^HHomeland Security. I'm pretty astonished by the types of reserach these people are doing which really has no practical applications whatsoever. But on paper it makes it look like the department are investing in our security. This sounds like a prime example of such a project. There simply isn't a situation involving bacteria that is both (1) something we can model on a computer and (2) relevant to combating bioterrorism. Sure, we might be able to qualitatively model a population in a petri dish, but that has nothing whatsoever to do with the reality of a terrorist releasing bacteria into the atmosphere, say. But the ignorant politicians working at the department have no way of understanding this for themselves and fund it anyway. Remember, these are the same people who think this [ready.gov] is useful.

    So...politicans might be taken in by BS about the applications of these methods, but there's no need for /. readers to be decieved the same way.

    • The thing is, anything that helps us fight infectious disease in general may also help with "combating bioterrorism." And a good simulation of the response of bacterial populations, which often show emergent behavior, respond to biochemical stimuli may very well be helpful in coming up with new methods of diagnosis and treatment. (For an understanding of why this is so, check out work on swarming behavior [nih.gov], and the research interests page of Leah Edelstein-Keshet [math.ubc.ca], one of the leading researchers in the fie
    • Strangely enough, sometimes theoretical underpinnings are crucial to end-user applications. Yes, maybe this should have been funded by a grant from NIH (new bacterial simulator), NSF (ibid), FDA/DoAg (food contamination), or DOE (model potential industrial organisms), rather than DoHS, but e. Coli is both (a) well-understood and (b) a real problem in our food supply. A good e. coli simulator could, as they've already demonstrated, teach us quite a bit about potential pathogens, or be generalized into an o

    • I'll bite. Here are two I can think of off the top of my head:

      Application one: A collection of bacterial species was selected to detect specific toxins and/or biological agents. This can quantify how they would respond, aiding in the design of a biotoxin and/or chemical detector.

      Application two: Species X is known to break down chemical agent Y. A computer model is used to determine the optimal temperature, oxygen, and other environmental settings to use this species in cleanup after a chemical attack

  • How many times have we all complained about having to use non-OSS because it was our only option that accomplished what we wanted it to. I personally have felt this way dozens of times.

    Now, it seems the tables have turned. OSS has turned into the exact thing that it despises. I personally think this article raises some interesting issues, particularly concerning living organisms being forced to use open source just because that is the only option available to them.

  • OK, someone was actually given a research grant to produce a new version of Life?

    Yes, I'll have what they're smokin', thank you.

  • Orgasms? (Score:3, Funny)

    by c0d3h4x0r (604141) on Monday June 06 2005, @11:58AM (#12737371) Homepage Journal
    Scientists have constructed a software capable of simulating organisms at the molecular, single-cell and population levels.

    Am I the only one who had to read that thrice to verify that it in fact did not say "orgasms"?

    Imagine the military applications of software capable of simulating orgasms at the population level!

    Maybe I just need caffeine.

  • Aha! I knew OSS supports terrorists, communists, and is anti-American. What else would a digital bacteria be for?! Other than to infect the computers of law-abiding, copyright-fearing, Windows users?! Isn't that what all bacterias do after all....
  • Sounds like it should be one of those Tom Clancey videogames for the Xbox where you walk around with night-vision goggles and shoot people.

  • >> The researchers have designed their digital bacterial system in modules, so that additional components may be added later

    K00l!!! Do they have a level editor? I'll do the "capture the flag" mod.

    • Re:True AI? (Score:4, Insightful)

      by Rei (128717) on Monday June 06 2005, @11:16AM (#12736987) Homepage
      Seems to just be a more realistic version of something like PolyWorld [beanblossom.in.us]. Still quite interesting.

      If you want a "AI" that borders on a consciousness, you don't want to start at this level - that's way too much work. You want to algorithmicly be simulating entire cells or even groups of cells at once, instead of components of cells. The higher up you can shift the behavior, the more computation you can get done.

      Hmm... this may tempt me to play with Framsticks and [alife.pl] Avida [caltech.edu] some more. :)

      • Re:True AI? (Score:5, Insightful)

        by AKAImBatman (238306) * <(akaimbatman) (at) (gmail.com)> on Monday June 06 2005, @11:33AM (#12737147) Homepage Journal
        If you want a "AI" that borders on a consciousness, you don't want to start at this level - that's way too much work. You want to algorithmicly be simulating entire cells or even groups of cells at once, instead of components of cells.

        Except for one problem: You're assuming that we actually know how the brain functions. Neural networks are interesting, but to date they've failed to show the levels of intelligence of a comparable animal. On top of that, they don't actually model the brain's neural patterns correctly.

        Experiments at a lower level may produce greater insight, especially if we're missing something tricky such as encoded waveforms in neural pulses. Lower level simulations would allow us to explore the differences between the simulation and the real thing, thus producing loads of data on things we might be missing.
        • From Man and Machine [capcollege.bc.ca] An average human brain contains about 100 Billion neurons, although, at this point in your life, you may have fewer.

          An average neuron has 1500 signal connections to other neurons.There are about 0.15 quadrillion of these "synapses" in the brain.

          The senses transduce external stimuli into neural action which modifies the states of connected neurons. Each of the 100 Billion neurons in your brain is in a changing state at every instant

          It is interesting to estimate how many arith

          • Not going to happen. Your scenarios require eliminating every other possibility, which is clearly impossible. Even if we could precisely simulate this universe, and had the preposterous amount of CPU necessary to simulate an entire universe, the number of "possibilities" at each step along the way rules out practicable encountering of the specific route that led to our existance.

            The further distanced you get from precisely simulating our universe, the less of the potential search space you're covering.
          • I don't think anything like that is holding anybody back. The problem is that we simply don't know enough about how the brain functions to get a good model that we could transfer over to silicon (or whatever material we end up building computers out of). The brain is not a piece of end-user engineering. It's a complicated organ that has gone through a lot of modification during its evolutionary history, and it's pretty tough to reverse engineer something like that.
    • Hopefully some real open source people

      Because people who work for companies are fake open source people? Sometimes the only people who can still eat, have a roof over their head, and still be able to put in 14 hours a day on a large project (open source or otherwise) are those working for an organization with some actual money to spend. Some of those are (gasp!) corporations.

      Now, if you're suggesting that "big biotech" is going to deliberately break a license clause, that's another story. But the big

      • Umm... The BSD license doesn't have to be broken in order for some random person or company to close up their version. The software isn't licensed under the GPL, which would prevent this.

      • No, exactly, no one has to release any changes. That makes me wonder whether anyone will. So their "hope" may be unfounded.

    • Re:What about us? (Score:5, Funny)

      by ScentCone (795499) on Monday June 06 2005, @11:23AM (#12737052)
      And just how do we know our entire reality isn't simply a large scale version of this? Is our universe simply the inside of a box? Does it even matter?

      Well, first, no - if we're in a giant box, and the laws of physics defined therein cause us to see and experience what we're seeing and experiencing, then... no. That's the framework of our universe. We can't operate outside of that framework, so kvetching about it isn't very productive.

      And second, you'll be getting the munchies very soon, I'm guessing.
        • Trouble is, in The Matrix, Neo's brain (and, for that matter, a functional body) are physically outside the simulation.

          It's also possible to have a simulation that's good enough to simulate matter behaving as a brain, in which case any life being simulated has no existence at all outside of the simulation. It's not impossible for that life to be intelligent, conscious, or self aware, and there would be no way for them to tell they were in a simulation, other than by saying that things looked like someone d
          • Look up Stanislaw Lems 'Non Serviam' for an excellent short story on this topic.

            It features in Hoffstader & Dennett 'Minds I'
          • That's like saying you're "outside" a video game. I think Neo's body and mind were always right there in the normal physical universe, bounded by all of the normal rules, and he was just (along with everyone else) unusually plugged into a particularly good simulation. You're not in the simulation, the simulation's in you (perceptually, cognitively). So, dreaming (no matter how convincingly) you're superman and can fly doesn't change the laws of physics. My two cents' worth, anyway.
    • No. We're on top.
      Daylight and everything.
    • Maybe for the professional navel gazers out there, but the practical applications of such knowledge are nil. Except maybe to stick our tongues every once in a while at some uber unix geek observing our universe.
      • But it is a lousy simulation! Doesn't quantum uncertainty look like a kludge? Doesn't the strong force look like it's been played with to make things work nicely?

        (No I am not a creationist)
    • Rather, how long before the nice Men in Black show up at their door, confiscate the code, throw them all in jail, and get Con-gress to pass a law against this sort of thing, on the grounds that it could be used to ADVANCE bioterrorism?

      Why is that tinfoil-clad perspective any better (more likely) than wondering how long it will be before they're offered jobs at Fort Dietrich or at any of a number of big contractors that are working on exactly this sort of stuff with defense in mind? They can't hire good p

    • Blockquoth the article:

      "As soon as this is done the code will be available for download. Stay tuned."

      Besides, the MiB don't operate on the entire planet. Perhaps that's the best argument for releasing something which may have questionable applications as open source - you can't undo it once it's done.
    • It looks more like Microbiologists are lazy people who are just trying to save a little bit work.

      Yeah, and nuclear scientists are too lazy to build a gazillion particle accelerators so instead of doing hard work, as they SHOULD, they try their tests in a computer simulation, instead. This is outrageous! There's nothing worse than a lazy scientist! [/sarcasm]

    • There are many reasons. For one thing, not all physical quantities are easily and accurately measurable. But in a situation like this, you can measure whatever you simulated and gain new insights, right down to the molecular level. Chemical reaction rates in individual cells, intracellular pressures and mechanical stresses, the effects of different mutation rates, the distribution of nutrient concentrations both within the cells and between them, and so forth.

      Then there's the issue of experimental cont

All trademarks and copyrights on this page are owned by their respective owners. Comments are owned by the Poster. The Rest © 1997-2009 Geeknet, Inc.