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

Ken McGlothlen mcglk at artlogix.net
Wed Oct 31 14:10:00 PDT 2007

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.


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.


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