[BBF Standards] Amorphous languages for bio fabs

[Jake Beal]

> As for a new language, it was my understanding that amorphous computing 
> (and amorphous fabrication on top of that) would require a new way of 
> programming. 
> [snip]
> But I suspect that any such compiler will not be directly working with 
> biobricks, since amorphous fabrication is a *general* problem and 
> biobricks are a specific solution

You may be interested in a talk I gave to the MIT Synthetic Biology
lunch last month, on "Programming Cell Aggregates."  There is a copy
online at: http://web.mit.edu/jakebeal/www/Talks/SynthBio08.pdf

As work has continued in the amorphous computing group here at MIT,
we've developed techniques for global-to-local compilation based on an
appropriate choice of space/time primitives and a continuous space
abstraction.  These can be expressed succinctly in our language,
Proto; a nice introduction to the approach can be found in our paper,
"Infrastructure for Engineered Emergence on Sensor/Actuator Networks"
(http://people.csail.mit.edu/jrb/stp/proto-isys-2006.pdf) though the
language has gotten much more concise since that paper was written.

If we apply these techniques to BioBricks, then we should be able to
largely separate the problems "tissue"-level programming of cell
aggregates from the composition problems of implementing those spatial
programs using BioBricks.  Although there are significant engineering
obstacles (surveyed briefly in the talk slides), the basic
computational structure of genetic regulatory networks appears to
match well with the Proto / Amorphous Medium approach to spatial
computing.

Thanks,
-Jake