[BBF Standards] Notes from Saturday Afternoon Workshop Discussion on White Board

[Mackenzie Cowell]

This is an interesting idea, and I could see it tying in with the 2+
discrete implementations of the standard we'll need before getting an RFC.
However, I think the test cases you are suggesting are implicitly about
testing repositories of parts, whereas the pobol standard is only concerned
with describing parts in a uniform way.

Nonetheless, we will need two repositories speaking in pobol for the RFC, so
perhaps we could develop unit tests like those you propose and include them
in the RFC somehow.  I think the current - very preliminary - plan is to
implement pobol in BrickIt and in Freebase and get those two services
sharing parts.  Additionally we might be able to work with Randy at the MIT
registry - I think he is planning on providing an outputting parts in xml
soon (maybe this summer).

Mac


On Tue, Apr 29, 2008 at 12:43 PM, Vincent Rouilly <vincent.rouilly at gmail.com>
wrote:

> Hi All,
> alongside the development of a data model for BioBrick parts, would it be
> useful to work on a series of test cases to evaluate each aspect of the
> standard.
>
> Those test cases could be designed independently of the data model, with
> only in mind the practical and functional requirements.
> Then, those test cases would be used to challenge the proposed data model
> to make sure that it fulfills our needs.
>
> In terms of methodology, it would be very close to what engineers use when
> doing unit testing.
>
> Later, those same test cases could also be useful to assess the degree of
> compliance of a given implementation with regards to the agreed standard.
>
> At this point in time, I am not too sure about the structure to adopt, any
> ideas ?
> For now I can only imagine 3 main categories:
>
> *I/ Data Entry test cases:*
> ex:  each BB should should have a unique ID, or list
> of required/optinal fields.
>
> *II /Search test cases:*
> ex: return all BB being a constitutive promoter in E.Coli, or return all
> composite sequences having a specific BB
>
> *III/ Data Flow and Data Exchange test cases:*
>
> Environment 1:  1 Person /  N Parts / 1 Registry
> - ...
>
> Environment 2:  X Persons /  N Parts / 1 Registry
> - ...
>
> Environment 3:  X Persons /  N Parts / M Registries
> - Registry 1 wants to import n1 parts from Registry 2
>
> best,
>
> Vincent.
>
>
> On 28 Apr 2008, at 15:41, Raik Gruenberg wrote:
>
> Hi Drew,
>
> this was more of an appetizer, we are in the process of preparing a better
> draft. In brief, the data model will provide a  (1) *minimal* description of
> a Biobrick and the DNA contained in an actual Sample and (2) a way to group
> Biobricks into families.
> The idea is to lay the foundation but leave things open for extension with
> more specialized vocabulary and data.
>
> stay tuned...
> Greetings,
> Raik
>
> On Mon, Apr 28, 2008 at 3:02 PM, Drew Endy <endy at mit.edu> wrote:
>
> > Mike,
> >
> > Could you provide a one paragraph narrative summary of what the
> > purpose of this standard is?  Something that would help frame or
> > direct any comments or discussion?  Also, where there any specific
> > questions or issues that came up that you would like feedback on?
> >
> > Thanks,
> > Drew
> >
> >
> >
> > On Apr 27, 2008, at 2:22 PM, Michal Galdzicki wrote:
> >
> > > Attached is a pdf of a data model, which was discussed as a group.
> > > Please make comments and discuss.
> > > mike galdzicki
> > > <BioBrock proposed data
> > > model.pdf>_______________________________________________
> > > Standards mailing list
> > > Standards at biobricks.org
> > > http://biobricks.org/mailman/listinfo/standards_biobricks.org
> >
> >
> > _______________________________________________
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> > Standards at biobricks.org
> > http://biobricks.org/mailman/listinfo/standards_biobricks.org
> >
>
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