[Hplusroadmap] Fwd: Re: [BBF Standards] functional composition of BioBrick parts?

[Bryan Bishop]

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Subject: Re: [BBF Standards] functional composition of BioBrick parts?
Date: Thursday 31 January 2008
From: Bryan Bishop <kanzure at gmail.com>
To: standards at biobricks.org

On Thursday 31 January 2008, "Josh Perfetto" <josh at maulikai.com> wrote:
> I'm sure that high-throughput screening may have a role to play in
> testing part compatibility.  I'm not sure that this alone would ever
> be sufficient alone, though I'd love to be proved wrong.

I too would love to be proved wrong as I hold that same notion. Here's 
what I started to think about upon reading your message. Obviously, in 
any massive-screening operation, there is going to have to be a lot of 
measurement utilities to make sure that there are, at the very least, 
the basic results that are to be expected. This is where lab-on-a-chip 
tech will come in handy. If we have a LOA-chip that serves basically as 
an FPGA, we can reconfigure the LOA for many, many experiments. Each 
time we have new possible library to screen through, we configure the 
LOAs for each of their roles given the combinations of BioBrick parts. 
The BioBrick parts themselves -- in their XML file format -- would 
specify what sort of measurement utilities should be used, in some 
cases maybe PCR on a LOA chip or in other cases maybe visual processing 
with the onboard STM (who knows). Granted, this does not allow us to 
catch for emergent effects, but it does significantly cut down on 
pathetically incompatible parts. As for emergent phenomena resulting 
from different BioBricks interacting together, that's going to be the 
real trick, isn't it? I am not sure if we even have protocols for human 
comprehension of emergent genetic results, there's so very much data to 
sort through and then how do we encode what we know about anything 
emergent of the system? 

I can't help but think that it would be far more easy if we had a much 
larger knowledge base (kb) to work off of, so that we may summarize and 
make generalizations about important trends in incompatabilities. But 
maybe somebody can provide a proof that we can start off without this 
KB and still be able to make in silico specifications that turn out to 
be mostly correct?  After all, whatever data format we choose will 
determine what we can later record in that format, so if we miss some 
important characteristics or are unable to graph various chemical 
reactions, then we're screwed and would have to rewrite software many 
times. Perhaps there is an organic chemistry data format for the 
description of chemical reactions? And then, using this, we can help to 
describe (even vague) reaction networks in BioBrick standardized files, 
which would be complimentary to the ontology files, therefore further 
specifying known research on each of the bricks. Further automation can 
be developed at the LOA chip screening technique that I suggested, 
especially if we can automate protein isolation methods for the 
determination of cause/effect in biology through common methods (a sort 
of 'meta experimental design' research journal might be helpful here).

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