[BBF Standards] functional composition of BioBrick parts?

[Raik Gruenberg]

Thanks Mac for setting up the wiki!

 > And here is a BioBrick part data model question: should there be a
 > one-to-one relationship between a part 's functional definition and its
 > sequence?  What if you introduce a silent mutation into a BioBrick - is
 > there a "different sequence, different part" doctrine, even if the two
 > are functionally equivalent?  Additionally, how are codon-optimized
 > sequences for the same function related to one another?  Families of

Or put differently -- What *is* a biobrick?
We right now seem to follow the unspoken rule that a part is defined by its 
exact DNA sequence. Any modification creates a new part, which is kind of 
logical to the experimentalist because it maps a biobrick to exactly one DNA 
fragment (which you either have in your freezer or not) and vice versa.

But you are right, things are getting murky if you codon optimize a protein part 
(should the biobrick be defined by the amino acid sequence instead?). Even more 
extreme: You can have the "same" Biobrick in different formats, e.g. with 
prefix/suffix from one of the two suggested protein fusion formats. Now the 
sequence is exactly the same, but having a sample of biobrick X with biofusion 
flanks may be of no use if the other biobricks in you freezer are formatted 
differently. Or you could have a composite part A-B-C and another one A~B~C with 
the same parts but different scars in between.

On the other hand, you don't care about format or even detailed sequence if you 
DNA-synthesize your whole assembly from scratch.

 > tuned promoters?  Is this a source code vs. compiled code issue?
...or specification versus implementation

So what shall we do?

A) keep/fix the sequence-based definition but introduce relations like "ortholog 
to", "equivalent to", etc.

A') define "reference biobricks" and link variants to them

B) find a more abstract definition (still based on reference sequences of DNA, 
AA, or Biobrick letters?) and create the concept of BB 'implementation' or 
'instance'.

B may actually have some legal implications (e.g. no need to copyright sequence 
but copyright higher-level description and protect the whole family from being 
patent-snatched).

Opinions?
Raik

Mackenzie Cowell wrote:
> Hello Everyone,
> 
> I seeded the BBF wiki page at 
> http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical 
> with some of the main points of the recent discussion.
> 
> You can also navigate to a "dewikified" version of the page from the BBF 
> homepage at http://biobricks.org/, or directly via 
> http://bbf.openwetware.org/Standards/Technical.html.
> 
> And here is a BioBrick part data model question: should there be a 
> one-to-one relationship between a part 's functional definition and its 
> sequence?  What if you introduce a silent mutation into a BioBrick - is 
> there a "different sequence, different part" doctrine, even if the two 
> are functionally equivalent?  Additionally, how are codon-optimized 
> sequences for the same function related to one another?  Families of 
> tuned promoters?  Is this a source code vs. compiled code issue?
> 
> -Mac
> 
> On Jan 31, 2008 10:01 PM, Bryan Bishop <kanzure at gmail.com 
> <mailto:kanzure at gmail.com>> wrote:
> 
>     On Thursday 31 January 2008, "Julius B. Lucks" wrote:
>      > 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.
> 
>     I certainly see the need to be able to reference other sub-ontologies
>     related to understanding the experimental methods for testing the
>     brick, or the specifications for the computational evidence etc.
> 
>     - Bryan
>     ________________________________________
>     Bryan Bishop
>     http://heybryan.org/
> 
>     _______________________________________________
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> 
> 
> 
> 
> -- 
> Mac Cowell
> iGEM Coordinator
> igem.org <http://igem.org>
> 231.313.9062
> 
> 
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-- 
________________________________

Dr. Raik Gruenberg
http://www.raiks.de/contact.html
________________________________