[Santa-rosa-pm] Modeling synthetic biological software approaches

William Heath wgheath at gmail.com
Wed Oct 31 14:22:16 PDT 2007

Hi All,

Regardless of what language we use fundamentally I think we have
agreed that this is a constraints based algorithm that should be used
to model how cells work.  I just talked with a physics phd friend I
have and he mentioned that is really a constraint minimization
problem.  I saw some truth to this in that the cell itself is always
trying to minimize differentials between itself and the outside world
via endocytosis, osmosis etc...  Proteins fold based on minimizing
free energy usage.  How does that sound to you all?


On 31 Oct 2007 13:10:00 -0800, Ken McGlothlen <mcglk at artlogix.net> wrote:
> Hi, Tim (or William).
> It sounds like you're working on a fascinating project.  I don't really have
> that much to add, per se, to the biological modeling, as you're in well over my
> understanding of DNA operands.  :)  However . . .
> | I also asked at my perl programming group what they felt was the best
> | language to model/simulate a cell working.  They thought it was prolog as a
> | cell basically is composed of a system of constraints.  What do you all
> | think?
> Welllllll, Prolog would work.  I've used Prolog, and I liked using it---and
> yes, you could probably hammer out a program in it that would simulate this.
> I'm not sure that Prolog is the best language for it, though.  While this might
> be a biased statement based on my nascent enthusiasm for the language, I would
> probably still recommend looking into Haskell.
>         http://haskell.org/haskellwiki/Introduction
> Like Prolog, Haskell allows you to specify what should be computed, without
> specifying sequence or enforcing a strict order.  Haskell itself will work out
> the dependencies for you, and its syntax (while a bit regular-expressionish at
> times) will allow you to write the rules of your system relatively concisely.
> It will also allow you to change the rules a bit more easily than a lot of
> other languages would (but on a par with Prolog, I think).
> Do check it out.
>                                                         ---Ken

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