[BBF Standards] functional composition of BioBrick parts?

[Drew Endy]

Hang tight for ~18 hours if you can.  I'll be able to straighten out  
the permissions and get the wikis properly organized tonight.

Thanks!
Drew


On Jan 31, 2008, at 9:42 AM, Raik Gruenberg wrote:

> Hi all ,
>
> I see two pretty independent questions waiting to be answered for  
> the data
> exchange standardization:
>
> 1) What is the minimal data set needed to describe a biobrick?  
> (including What
> is a Biobrick?)
> 2) What is the best format / technology for exchange?
>
> It would be good if we could capture the main suggestions and  
> arguments on a
> wiki page -- I would be happy to take care of that but didn't manage  
> to create
> one on http://parts.mit.edu/registry. Could someone with the  
> permissions please
> add some empty page to the community portal box (like the ones for  
> the other RFC
> groups)?
>
> Anyway, we have started discussing 2). Suggestions were roughly:
>
> a) create a new XML format
> b) adapt existing CellML, SBML XML formats
> c) create a custom file format
> d) use Turtle/N3 notation for semantic web documents
>
> If we get a wiki page, we could put up a little section on each  
> possibility and
> collect pro's and cons.
>
> Does anyone have the needed permissions to create a page on the  
> registry wiki?
> Or perhaps i just overlooked the right link?
>
> Greetings,
> Raik
>
> 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
>> -Josh
>>
>
>> 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
>>
>> Herbert Sauro
>
>>> 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/
>
>
> -- 
> ________________________________
>
> Dr. Raik Gruenberg
> http://www.raiks.de/contact.html
> ________________________________
>
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