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Simulating the cell in software.

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  • Simulating the cell in software.

    In the January 2014 issue of Scientific American is an interesting article about simulating a cell in software.

    It seems that scientists are getting pretty good at it.

    A researcher who has done a lot in the field, Markus Covert, writes about their most recent attempt at this. Unlike many previous attempts, this group concentrated on a single cell, and they used the most simple cell, Mycoplasma genitalium. Scouring the literature for anything concerning the structure, behaviour, energetics and biochemistry of the organism, they built their simulator over a number of years, and now, given that it works so well, find that it can inform them on things about the organism in such a manner that:-

    1) they learn new things, and

    2) can direct their research to verify things discovered or suggested by simulator runs.

    The Sci Am article is referenced here:-

    Scientists Successfully Model a Living Cell with Software

    An online research report describing the work is here:-

    A whole-cell computational model predicts phenotype from genotype

    The Sci Am article was fascinating, although a read of the research article might end up being more rewarding.

    Among other things, what I found fascinating were the following:-

    Underlying random processes

    As an example of this, proteins don’t necessarily bind to DNA securely. The are often getting knocked off their regulatory regions by the random battering from other proteins. This can happen up to 30,000 times per 9 hour cell cycle. The researchers were surprised to see this.

    Emergent phenomena

    The particular cell they simulated has a cell cycle period, time between cell divisions, of around 9 hours. Their software cell also divides at that time. Interestingly, this proved to be an emergent phenomenon caused by “the interaction of two distinct phases of replication, each of which varies wildly in duration”.


    Anyway, for those who are interested - it’s a good read.

  • #2
    Too much of this was over my head, I'm afraid, but it was very interesting nonetheless. I think it's cool that they could model all of the separate sections independently and then meld them together with a reasonably accurate picture of what's happening.

    Thanks for this.
    I'm not here anymore.

    Comment


    • #3
      Originally posted by Carrikature View Post
      Too much of this was over my head, I'm afraid, but it was very interesting nonetheless. I think it's cool that they could model all of the separate sections independently and then meld them together with a reasonably accurate picture of what's happening.

      Thanks for this.
      Yeah. The Sci Am article was very readable and makes for a better read for the layperson. I have not read the technical article yet and will most likely struggle as did you.

      Comment


      • #4
        Originally posted by rwatts View Post
        Yeah. The Sci Am article was very readable and makes for a better read for the layperson. I have not read the technical article yet and will most likely struggle as did you.
        I don't have a subscription to Sci Am. I'm not sure if I would use it enough to justify the cost, but maybe it's something I really need.
        I'm not here anymore.

        Comment


        • #5
          Originally posted by Carrikature View Post
          I don't have a subscription to Sci Am. I'm not sure if I would use it enough to justify the cost, but maybe it's something I really need.
          If you can get to a library or a news agent and over a few months, flip through some issues, and see what you think.

          Comment

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