[BBF Standards] functional composition of BioBrick parts?

[Julius B. Lucks]

It sounds like there needs to be an annotation system in place that  
would allow compatibility evidence to be labeled as experimentally or  
computationally generated (or both).  We might even consider the  
possibility of digitally signing the annotations to associate  
experiments or calculations with known labs.  The preliminary  
question would be whether or not the annotations would be a part of  
the main parts ontology, or would it be a separate ontology itself.

Julius

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On Jan 31, 2008, at 4:25 PM, Josh Perfetto 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.
>
> My point really was that we should be thinking about what we can do  
> to model parts in a way that will allow *some* incompatibilities to  
> be identified through modeling, even if we cannot identify *all*  
> incompatibilities in this manner with  current technologies.  That  
> is still valuable in that it cuts down on the NxN combinations,  
> even if the resulting possibilities still need to be followed up by  
> further screening as you suggest, or simply by trial and error.   
> It's cheaper when incompatibilities can be identified in silico.
>
> -Josh
>
> -----Original Message-----
> From: standards-bounces at biobricks.org [mailto:standards- 
> bounces at biobricks.org] On Behalf Of Bryan Bishop
> Sent: Thursday, January 31, 2008 3:36 PM
> To: standards at biobricks.org
> Subject: Re: [BBF Standards] functional composition of BioBrick parts?
>
> On Thursday 31 January 2008, Josh Perfetto wrote:
>> 1.       While it may not be currently possible to say with certainty
>> which parts will work well together through modeling, NxN
>> combinatorial testing is not practical.  It is therefore of great
>> value to know which parts would not be expected to work together
>> through the use of modeling.  Information to help us do that (i.e.
>> information about the small molecules used internally for starters)
>> should be included in the data model of a part.
>
> Actually, I have done some thinking on combinatorial testing, and  
> isn't
> this basically what we do with arraying systems? The trick is to run a
> massive library experiment in parallel on the cheap and a way to
> *select* the results so that we can figure out which ones are
> producing 'bad' effects and those that are producing 'good' effects.
>
> - Bryan
> ________________________________________
> Bryan Bishop
> http://heybryan.org/
>
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