[BBF Standards] functional composition of BioBrick parts?

[Josh Perfetto]

My initial instinct is also that a separate ontology will be needed to
properly describe BioBricks.  However I would expect it would be both
conceptually and practically desirable to be able to transform such models
into SBML models-- both to make use of the vast amounts of systems biology
software, as well as to model systems which are only partly engineered.

-Josh

-----Original Message-----
From: standards-bounces at biobricks.org
[mailto:standards-bounces at biobricks.org] On Behalf Of Herbert Sauro
Sent: Wednesday, January 30, 2008 8:20 PM
Cc: standards at biobricks.org
Subject: Re: [BBF Standards] functional composition of BioBrick parts?

Yes definitely, there are a bunch of new ontologies coming up in systems 
biology and I think they will have some relevance here, though I suspect 
there could still be a need for something specifically related to 
synthetic biology.

The existence of these ontologies makes human readable formats difficult 
to deal with and XML is the proper place for them. However, as humans, 
we also need a human readable face and I think there has to be some kind 
of two way world, or at least each software application will present 
parts and devices in their own human readable format even if the 
back-end is ultimately XML. This is the way SBML and CellML work. We are 
seeing however a proliferation of human readable formats in systems 
biology, both visual and text based but which are largely 
interchangeable through SBML or CellML.

Herbert Sauro

Bryan Bishop wrote:
> On Wednesday 30 January 2008, "Josh Perfetto" <josh at maulikai.com> wrote:
>> Yes, I think ease of processing and the representational power of the
>> format is more important nowadays than human readability.  We need
>> standard representations that can be adopted by software developers
>> to build powerful processing systems for BioBricks.  We can expect
>> such software to present a more human-usable interface to manipulate
>> the BioBricks than a file format ever could.
> 
> Have you ever heard of these 'ontologies' that have jumped up?
> http://www.biomodels.net/
> http://obofoundry.org/
> 
> I wonder how this might be useful.
> 
> - Bryan
> ________________________________________
> Bryan Bishop
> http://heybryan.org/
> 
> _______________________________________________
> Standards mailing list
> Standards at biobricks.org
> http://biobricks.org/mailman/listinfo/standards_biobricks.org


_______________________________________________
Standards mailing list
Standards at biobricks.org
http://biobricks.org/mailman/listinfo/standards_biobricks.org