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

[Ken McGlothlen]

| 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.

Oh, no, I agree perfectly with that.  Life itself is more or less a constraint
minimization issue, after all---everything free to work within the limitations
of their nature, or adaptation or death must occur.

I was also doing some thinking about your bottle-cap-forming cell problem, and
another computer language possibility occurred to me:  breve.  In breve, you
define the behaviors of agents in a 3D space, and creating visualizations of
those is relatively easy.  It should be people to create constraint-based
simulations for each object on multiple levels (genomic, cellular, etc.).  You
can check that out at

        http://www.spiderland.org/

One nice thing about breve is that it's easier than Haskell, and getting a
visual of what's going on is also a lot easier as well.

It's open-source, and available for Linux, OS X and Windows.

                                                        ---Ken