[BBF Standards] functional composition of BioBrick parts?

[Herbert Sauro]

I would agree. It might be worth noting that CellML already supports the 
ability to represent modules and a new version of SBML will do so as 
well, I would assume these capabilities are critical to this community. 
This doesn't meant that the synthetic bio community can't develop their 
own standards of course. We have two CellML developers and a number of 
SBML people coming to the April meeting to discuss their experiences 
with forming standards in systems biology.

Herbert Sauro

Josh Perfetto wrote:
> 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/
>>
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> 
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