BioBrick Parts Catalog
Cesar A. Rodriguez
Thanks to the efforts of Altay Guvench and Gabe Smedresman, the
"BioBrick Parts Catalog" is starting to take form:
Please take it for a spin. ALL comments are welcome.
Thanks!
Cesar
Deepak Chandran
Deepak
Yizhi Cai
Nice job. Is this build on top of the MIT registry or another database
elsewhere?
Cheers,
Patrick
------------
Yizhi Cai, GBCB Ph.D Candidate
Virginia Bioinformatics Institute
Virginia Tech,Blacksburg, VA 24061
Email: c...@vt.edu
Google Voice Number: (540) 200-8224
Michal Galdzicki
later,
mike
On Fri, Nov 13, 2009 at 2:24 AM, Cesar A. Rodriguez
<one.se...@gmail.com> wrote:
>
Cesar A. Rodriguez
It's a Python/Django/MySQL app...
Cesar
Michal Galdzicki
Are Altay Guvench and Gabe Smedresman on this mailing list? I'd like to create a way for SBOL semantic to read (later write) data from/ to biobrickparts.org . Excellent work, btw.
mike
Altay Guvench
Gabe Smedresman
Mike -- we're thinking through the API right now (what's currently on the website is just a first step), trying to figure out how to best support SBOL and also data formats of the future. We'd love your help...if you could detail your ideal use case, that would be really helpful!
Ditto on Altay's comment about being web developers -- if there's anything on the site that doesn't seem right, *let us know* and we'll do something about it right away.
Happy to be working with you!
-Gabe
From: Altay Guvench <aguv...@gmail.com>
To: synb...@googlegroups.com
Sent: Fri, November 13, 2009 11:59:58 AM
Subject: Re: BioBrick Parts Catalog
Herbert Sauro
standard?
Herbert Sauro
Gabe Smedresman wrote:
> Yep I'm here!
>
> Mike -- we're thinking through the API right now (what's currently on
> the website is just a first step), trying to figure out how to best
> support SBOL and also data formats of the future. We'd love your
> help...if you could detail your ideal use case, that would be really
> helpful!
>
> Ditto on Altay's comment about being web developers -- if there's
> anything on the site that doesn't seem right, *let us know* and we'll
> do something about it right away.
>
> Happy to be working with you!
>
> -Gabe
>
> ------------------------------------------------------------------------
> *From:* Altay Guvench <aguv...@gmail.com>
> *To:* synb...@googlegroups.com
> *Sent:* Fri, November 13, 2009 11:59:58 AM
> *Subject:* Re: BioBrick Parts Catalog
>
> Yup, we're here. =) (I'm assuming you're on the list too, Gabe?)
>
> Michael: There's an API in the works -- documentation is at
> http://biobrickparts.org/api -- although we're playing around with the
> data model so some things might change around. Can you tell us a
> little more about how you'd like to access the data?
>
> Yizhi: We've seeded it with data from the MIT registry, but we'd like
> to aggregate all the data and make it available via a common interface.
>
> Our expertise is web development, not biology, so we'd really like for
> there to be a tight feedback loop between us and the folks who will be
> using the site+dat. So everyone, please let us know how we can make
> it better!
>
> Altay
>
>
> On Fri, Nov 13, 2009 at 7:26 PM, Michal Galdzicki
> <mgal...@u.washington.edu <mailto:mgal...@u.washington.edu>> wrote:
>
> great i was just looking at django, as Raik had recommend it in
> the past.
> Are Altay Guvench and Gabe Smedresman on this mailing list? I'd
> like to create a way for SBOL semantic to read (later write) data
> from/ to biobrickparts.org <http://biobrickparts.org> . Excellent
> work, btw.
>
> mike
>
>
> On Fri, Nov 13, 2009 at 11:12 AM, Cesar A. Rodriguez
> <one.se...@gmail.com <mailto:one.se...@gmail.com>> wrote:
>
>
> Mike,
>
> It's a Python/Django/MySQL app...
>
> Cesar
>
>
>
> On Nov 13, 2009, at 9:14 AM, Michal Galdzicki wrote:
>
>
> pretty sweet and fast, what kind of architechture does it
> run on?
>
> later,
> mike
>
>
> On Fri, Nov 13, 2009 at 2:24 AM, Cesar A. Rodriguez
> <one.se...@gmail.com <mailto:one.se...@gmail.com>>
Michal Galdzicki
retrieve all of the hosted data at once, and then get pushed new
entries when updates occur.
in the mean time take a look at the SBOL core data model
(http://tinyurl.com/y9xz6ph), using the terminology described there is
very helpful as it is intended as a community standard.
Of course if you are willing I would help you setup export into RDF
using SBOL Semantic (http://tinyurl.com/ya5vksd), which follows the
core data model.
I'll get back to you this weekend with a more detailed use case,
mike
Gabe Smedresman
-Gabe
----- Original Message ----
From: Herbert Sauro <hsa...@u.washington.edu>
To: synb...@googlegroups.com
Sent: Fri, November 13, 2009 1:43:27 PM
Subject: Re: BioBrick Parts Catalog
Herbert Sauro
standard for synth bio. However the standard is provisional at the
moment so changes at this stage can be made but if you do make changes
let the community know so that discussion can follow.
Cesar A. Rodriguez
The goal is to support the Synthetic Biology Data Transfer Protocol
(SB/DTP):
http://openwetware.org/wiki/Endy:Notebook/Synthetic_Biology_Data_Transfer_Protocol
for data model-independent GETs and SBOL for data model-centric GETs
and POSTs.
We're committed to making the BioBrick Parts Catalog an open-source,
collaborative venture that encourages innovation...
Cesar
Cesar A. Rodriguez
A process has to be developed for incorporating contributions to the
app. Gabe is presently keeping the code at:
http://github.com/gabesmed/biobricks_repository
We also have to share the cost for hosting the app. Presently, Altay
and Gabe are contributing cycles from their account at SliceHost:
Lots of work ahead...
Cesar
Cesar A. Rodriguez
The data was acquired by scraping the MIT Registry.
Cesar
MadraghRua
Cesar A. Rodriguez
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