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Software Science

Open source Digital Bacteria 125

Posted by Hemos
from the create-your-own-share-it-with-your-friends dept.
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."
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Open source Digital Bacteria

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  • True AI? (Score:1, Insightful)

    by AviN456 (863971)
    This brings up the question of could this be used to create a true AI, or perhaps even a way to store a human conciousness, which would have useful applications for people with major illnesses or injuries.
    • Re:True AI? (Score:4, Insightful)

      by Rei (128717) on Monday June 06, 2005 @12:16PM (#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.gmail@com> on Monday June 06, 2005 @12:33PM (#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

          • Your math is off:
            1 500 000 000 000 000 = 1.5 x 1014
            There are 14 zeros there. Remove them all and you get 15 x 10^14, or 1.5 x 10^15.

            But then I went and calculated your first calculation, and that's where the error was; you added one too many zeros, but then took one away with the exponential. So the rest of the numbers are valid, and it's just a typo, not a math error as I at first thought.

  • Incentive? (Score:1, Insightful)

    by m50d (797211)
    Why are those who improve this going to release their changes? Hopefully some real open source people will pick it up and add good things to the public version, but I wonder about a big company making their own version and keeping it propriety. Big biotech is hardly a historically open environment, is it?
    • Re:Incentive? (Score:3, Insightful)

      by ScentCone (795499)
      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.

  • 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
  • Huh? (Score:1, Funny)

    by yanndug (832046)
    Will my anti-virus interfere with this software?
  • by smoyer (108342) <smoyer64@@@gmail...com> on Monday June 06, 2005 @12:15PM (#12736969)
    of bacteria in this world ...
  • by Cobra_666 (777517) on Monday June 06, 2005 @12:15PM (#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...
    • Maybe that was the whole plan. Competitors Post site on slashdot... destory servers... Info is not lost to the world... 3. Profit
      Sounds like a good plan to me.

      (Maybe not Competitor.. but government?!)

      This is of course just speculation.
    • I'm getting 159 KB/sec. Seems to be working fine so far. :)
    • by Anonymous Coward
      Oh boy, I can't wait until that "joke" is repeated again in the *next* article. :-/
  • by Spencerian (465343) on Monday June 06, 2005 @12:16PM (#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 @12:26PM (#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.
      • I tried to run your program from the link, but there wasn't a Setup.exe. Just a bunch of strange files.

        I think maybe you have a virus.

      • Sigh, I just wrote a long message and then closed the browser tab... here goes again.

        First, nice program, it looks huge and very fast. I like to play with CA too, but in java (quite a difference.) I came up with a variation on Conway's which doesn't tend to die of "heat death" as I call it, but it also tends to be a little too chaotic to develop anything real as well.

        Here is a link to the Java sim I wrote... [skeeze.net] My documentation sucks, but if you click on the "Fill" button until it reads "Life2", then cl
  • Great... (Score:3, Funny)

    by AnObfuscator (812343) <onering@phys. u f l .edu> on Monday June 06, 2005 @12:17PM (#12736988) Homepage
    As if Windows didn't have to deal with enough computer viruses, now it has to deal with computer bacteria as well.
  • It looks very cool, but it also looks like it could make a neat programming game.
  • by Progman3K (515744) on Monday June 06, 2005 @12:17PM (#12737002)
    Bacteria may be the only culture some people have.
  • Can I run the bacteriosim inside my favorite online game [slashdot.org]?
  • Hey thats the game of life http://www.math.com/students/wonders/life/life.htm l [math.com]. I remember programming that one for multiple school classes. One of my friends even made it his screen saver.
  • by lilrowdy18 (870767) on Monday June 06, 2005 @12:29PM (#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
  • I think I'll add a modification to this code to make all the little bacteria make the space invaders noise...'VOOMP-voomp-voomp-voomp-VOOMP-voomp-vomp- voomp....CHUH-CHUH-CHUH-CHUH-CHUH-DZZZZ...' You've been eaten.
  • by CardiganKiller (854899) on Monday June 06, 2005 @12:30PM (#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.

  • ...who's going to write the open-source simulator code to model the Fritos crumbs, dirty socks, and body soil and sweat for the sim-bacteria to feed on, and who's going to write the sim anti-bacterial spray to clean it up and... will anyone get the message?

  • If it were GPL, it'd be a digital virus.
  • by nanoakron (234907) on Monday June 06, 2005 @12:47PM (#12737281)
    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.
  • Ahhh yes, one step closer to having myself cloned into a virtual sim, this way I can see whether or not I will survive a gunshot, fall or if I should procreate....
  • by exp(pi*sqrt(163)) (613870) on Monday June 06, 2005 @12:50PM (#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

      • Yes, these sound completely plausible. That's why the grants get given. I spent 2 years working for a pharmaceutical company (GlaxoWellcomeSmithKlineBeecham... or whatever it's called these days). I don't think I believe anything I read about the modeling of biological systems by computer. You can generate plausible models, but the reality, outside of a lab, is almost always different.
  • 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 @12:58PM (#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.

    • No, but I am the only one that predicted that someone would misread it like that and scrolled down to search for that post.

      Now, before you say you predicted that someone would predict that it would be misread as orgasms... that's impossible, that would require a brain the size of a jumbojet.

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

      Man, think about something else. You'll go friggin' blind or somethin'. :-P
  • 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....
  • Read the title and thought it was another of those "the GPL is a virus" rants/FUD articles...
  • 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.

  • If IBM ran AgentCell on their virtual brain [slashdot.org], perhaps we could find ways to reduce the damage caused by brain infections
  • >> 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.
  • Why is it that when some interesting new technology is developed, the first question that gets asked is "How can we use it for the military?"
  • in true...this is just an initial step in biological modelling. We yet need more experimental data to develop reliable models, and build oriented models. Real biological systems are much more complex than our modelling capacity today. References?? http://www.nature.com/msb/index.html [nature.com] http://www.fosbe.org/ [fosbe.org] http://ieeexplore.ieee.org/xpl/RecentIssue.jsp?puN umber=9270 [ieee.org]
  • I've recently implemented a small (6 node) openmosix [sourceforge.net] cluster.
    I'll have to try this out on it.
  • now that we have open source bacteria, i guess ballmer was right when he said "linux is a cancer..."
  • How could they possibly simulate bacteria, if they are not completely understood yet? You would have to simulate every single molecule of the bacteria. A quick guess is, that bacteria have several billion molecules (a bacteria has a size of about 1 micrometer; that are 1000 to 10000 atoms, which taken to the third power are 10^9 - 10^12. roughly).
    Fully calculating all those parts' movement in all 3 degrees of freedom could prove tricky. Especially taking quantum effects into account.
    Even if they do simula

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