[BBF Standards] functional composition of BioBrick parts?

[Mackenzie Cowell]

Perhaps we could do both?  Assuming a biobrick always has one and only one
dna sequence, perhaps we could build the data model to support organizing
biobricks into families or sets of functionally related parts?  Each family
could have one canonical biobrick associated with it that works, is
available, and exemplifies the function that the family is supposed to have.

I'm inspired by JC Anderson's library of tuned promoters:
BBa_J23100<http://parts.mit.edu/registry/index.php/Part:BBa_J23100>
.

-mac

On Feb 5, 2008 5:08 AM, Raik Gruenberg <raik.gruenberg at crg.es> wrote:

> 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/
> >
> >     _______________________________________________
> >     Standards mailing list
> >     Standards at biobricks.org <mailto:Standards at biobricks.org>
> >     http://biobricks.org/mailman/listinfo/standards_biobricks.org
> >
> >
> >
> >
> > --
> > Mac Cowell
> > iGEM Coordinator
> > igem.org <http://igem.org>
> > 231.313.9062
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Standards mailing list
> > Standards at biobricks.org
> > http://biobricks.org/mailman/listinfo/standards_biobricks.org
>
> --
> ________________________________
>
> Dr. Raik Gruenberg
> http://www.raiks.de/contact.html
> ________________________________
>



-- 
Mac Cowell
iGEM Coordinator
igem.org
231.313.9062
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