[BBF Standards] Amorphous languages for bio fabs

[Bryan Bishop]

On Tuesday 19 February 2008, Deepak Chandran wrote:
> As far as development of a new language, the intent was to allow
> people from different disciplines to communicate without having to
> cross hurdles. Pictures are generally the easiest way to summarize a
> model (i.e. device or systems). So, the idea was to create a format
> that is similar to what one would see in a picture and yet contain
> sufficient information. This format would be converted to other
> standard formats such as XML in the end, but it would still allow
> someone who is not not accustomed to XML to contribute. But if there
> are no hurdles to cross in the first place (which I don't know the
> answer to), then there is no need to a new language.

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. This has been my interest as of late. A BioCAD-like 
development environment will be needed, and then a way to translate the 
linear instructions into parallel instructions. This is going to 
require computer science and is very much like modern compiler 
optimization techniques, except relying on what we know about certain 
problem spaces in computer science. I have preliminary language 
information over at:
 http://biohack.sf.net/wiki/index.php/Amorphous_computing 
* i.e., growth direction language. Check out the PDF.

make head;
make body;
make clothing;
is not sufficient to make a doll with bacteria or MNT. 

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, which perhaps would be matched in a 
database O(n) search??

- Bryan
________________________________________
Bryan Bishop
http://heybryan.org/