[DAS] "DAS/0.5" -- a different way of doing it

Ian Holmes ihh@fruitfly.org
Fri, 21 Dec 2001 12:23:59 -0800 (PST)

Lincoln Stein wrote:

> Hi All,
> Over the past couple of days I've been experimenting with a variant of DAS, 
> and have implemented it on the GMOD Generic Genome Browser.  I'm calling it 
> the DAS/0.5 protocol, since it represents a deevolutionary step from DAS/1 
> and DAS/2 .
> You can see what I've been working on at 
> http://www.wormbase.org/db/seq/gbrowse
> The user experience is as follows:
> 	1) she browses her favorite region of the genome
> 	2) she decides to annotate genbank entry AB12345
> 	3) she creates a space or tab-delimited text file that looks like this:
> 	reference = AB12345.1
> 	Gene  "Predicted gene 1"      518-616,661-735,3187-3365  "Zinc-finger domain"
> 	Gene  "Predicted gene 2"      5513-6497,7968-8136,8278-8383   "Unknown"
> 	Gene  "Predicted gene 3"      16626-17396,17451-17597 "7-transmembrane"

Lincoln --- this is *way* cool --- like Wiki for DAS!

> So I'm not proposing this as a replacement for DAS/1->DAS/2 development, but 
> rather as an alternative architectural style that addresses the same use 
> cases that DAS/1 does, and does it in a much more lightweight fashion.
> Thoughts?

I love the idea that it is an architectural pattern rather than a strict
spec. (cf Wiki)

I am not sure exactly what information the various tab-delimited fields in
the edit box are conveying (perhaps I am not up to speed on the DAS
ontology). the range field (518-616,661-735 etc) is clear enough but.. the