[BBF Standards] Registry exchange format

[Reshma Shetty]

Just a quick note re one aspect of the current discussion...

>  I have to disagree with you on composite parts. Sadly, biological
>  contsructs are mutable. So when I sequence a composite part, and find
>  that it's different from the original parts, but it's good enough for
>  me, where do I record it? It is often the case that what you have is
>  slightly different from what you think you have. That is the basis of
>  my emphasis on unique dna=part.

When I design engineered biological systems, I don't simply write down
a DNA sequence that will encode my desired function.  Instead, I used
abstraction to compile system function to a set of devices, compile
devices into one or more standard biological parts and encode parts as
nucleic acid sequences.

Therefore, it seems as if the data representations should reflect this
engineering process: composite parts should be represented as
combinations of parts (where those parts could themselves be either
composite or basic parts.

Tim's right that mutations can happen in the course of synthesis,
assembly, or even simply propagation of parts.  I've run into this
situation myself.  My solution was to simply enter new basic parts
with new part numbers into the Registry.  The new parts had the DNA
sequences that I built (as opposed to the sequences I designed).  I
could then specify new composite parts that reflect the built
composite sequence.  Detailed info on my particular run-in with these
problems is at http://www.jbioleng.org/content/2/1/5

There's info to be gleaned from comparison of the original design
versus what could actually be built so having all these parts in the
Registry is useful.

Thanks,

Reshma