[DAS2] Fwd: DAS/2 code sprint next week!

Andrew Dalke dalke at dalkescientific.com
Mon Aug 14 16:20:03 UTC 2006

Begin forwarded message:

> From: Andrew Dalke <dalke at dalkescientific.com>
> Date: August 14, 2006 6:00:30 PM GMT+02:00
> To: "Helt,Gregg" <Gregg_Helt at affymetrix.com>
> Subject: Re: DAS/2 code sprint next week!
>> We’re hosting another DAS/2 code sprint next week at Affy Santa 
>> Clara, to coincide with the CSB meeting at Stanford.  Will you be 
>> able to join in?  If not in person, then we’re having a daily 9 AM 
>> PST conference call you could join.
> I'll be there.  It starts in a few minutes.  I'm in a cybercafe in
> Cape Town.
>>  I’m wondering what the status of the DAS/2 writeback spec is.
> It's unchanged.  I'll be working on that over the sprint.
> I've spent most of the last, month+ catching up on the latest in
> web development systems for Python, and learning various libraries.
> Including giving a 2 week course on it.  As my test case I've
> been working on a DAS2 server.  I have a reference server nearly
> finished and a few things came up during it:
>   - I'm iffy about the current SEGMENTS document.  It lists
> "title" and "reference" for each segment but not for the list of
> segments as a whole.  Does it make sense allowing those to be
> specified if they have reasonable names?  (I know they don't always.)
> It's part of that separation between the sources document, which
> describes these, and the segments document.
>   - did we specify that the sequence is in upper-case, lower-case,
> etc.?
>   - I would like some experience with an agp or other assembly format.
> I'm concerned about how a client can piece together segment names
> from that document with the URIs we're using.  It seems to me that
> most places use a local name ("yeast_1" or somesuch) which is not
> exposed via the web.  If the assembly document, fasta file, etc.
> use the local name and not the URL then it's hard to tie them together.
>   - There are two different segment titles I've come across.  One
> is the name you want to see in a pull-down menu, etc. while the
> other is the text you want in the FASTA header .  These could be the
> same but I don't think they are always the same.
					dalke at dalkescientific.com

More information about the DAS2 mailing list