[BBF Standards] functional composition of BioBrick parts?

[Jason Morrison]

/de-lurks

Mac, thanks for getting that into the wiki!  I have edited and added a few
ideas that stem from a conversation between Mac, Kim de Mora, and me.  In
particular, I think it's important to be explicit about the functional
definition, including (but not limited to) terms of inputs, outputs, and
possible side effects.

All: thoughts on my changes?

I also took some notes that I'd had ongoing at Google Docs about semantic
wikis and their possible applicability to this problem, posted them to OWW,
and linked them from the tech standards discussion.  I'd love to hear
comments on those ideas, as well.
http://openwetware.org/wiki/User:Jason_Morrison/Thoughts_on_semantic_wikis

By the way, it looks like there is/was an ontology discussion (or ideas
about one) at
http://openwetware.org/wiki/Synthetic_Biology:Semantic_web_ontology/Design.

Jason

On Feb 4, 2008 6:17 PM, Mackenzie Cowell <macowell at gmail.com> wrote:

> Hello Everyone,
>
> I seeded the BBF wiki page at
> http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technicalwith 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> 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
> > http://biobricks.org/mailman/listinfo/standards_biobricks.org
> >
>
>
>
> --
> Mac Cowell
> iGEM Coordinator
> igem.org
> 231.313.9062
> _______________________________________________
> Standards mailing list
> Standards at biobricks.org
> http://biobricks.org/mailman/listinfo/standards_biobricks.org
>
>


-- 
Jason Morrison
jason.p.morrison at gmail.com
http://jayunit.net
(585) 216-5657
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://biobricks.org/pipermail/standards_biobricks.org/attachments/20080204/def9495d/attachment.html