[BBF Standards] functional composition of BioBrick parts?

[Raik Gruenberg]

Mackenzie Cowell wrote:
> 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.

That sounds indeed like the most practical solution. Rather than blurring up the 
definition of a biobrick, we create a layer of relations on top of it (e.g. 
families and devices?). That would also mean we can focus on the basic/minimal 
definition first -- I guess, a biobrick either has a sequence (= basic part) or 
is defined as a "sequence" of other Biobricks (=composite part).

The issue of different formats (different prefix/suffix while equal sequence in 
between) may still deserve special treatment though. In order to reconstruct the 
exact DNA sequence of a composite part, we also need to know the scars in 
between. The brickit data model currently records either an explicitly given 
non-default scar sequence or falls back on a default scar (deducted from the 
parts' format). That implies that each biobrick has exactly one format though...

/Raik

> 
> 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 
> <mailto: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>
>      > <mailto: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>
>     <mailto: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> <http://igem.org>
>      > 231.313.9062
>      >
>      >
>      >
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> 
>     --
>     ________________________________
> 
>     Dr. Raik Gruenberg
>     http://www.raiks.de/contact.html
>     ________________________________
> 
> 
> 
> 
> -- 
> Mac Cowell
> iGEM Coordinator
> igem.org <http://igem.org>
> 231.313.9062

-- 
________________________________

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