[DAS] Question about glyph options

[Andrew Nunberg]

On 5/10/05 3:39 AM, "Jim Stalker" <jws at sanger.ac.uk> wrote:

> 
> On 9 May 2005, at 16:04, Andrew Nunberg wrote:
> 
>> I am in the process of setting up a local das annotation server to be
>> used
>> with a local mirror of ensembl.
>> 
>> I wanted to display some microarray data using some of the glyphs from
>> Bio::Graphics package that I had used in Gbrowse, however I don¹t see
>> them
>> listed in the documentation.  Am I limited to what is listed in the DAS
>> documentation?
> 
> Hi Andy,
> 
> The Ensembl DAS renderers don't use the Bio::Graphics package, and so
> custom glyphs from Gbrowse will not necessarily be available in Ensembl
> (of course, the converse is also true).  The only set of glyphs that
> are specified are, as you say, listed in the DAS documentation, but
> you'll probably find implementation differences between DAS clients
> here too: the stylesheet spec is rather open to interpretation.  Then
> again, it's only supposed to provide "hints to clients on how the
> annotations should be rendered visually".
> 
> On the upside, new glyphs are pretty straightforward to implement in
> Ensembl, and I'd be happy to help if you have specific requirements.
> The Ensembl web guys would undoubtedly be happy to add new glyphs into
> the distribution if they are generally useful.
> 
> Regards,
> 
> Jim
Because there is a time crunch I have decided to go with Gbrowse completely
as a das client/server.
Point it to a das reference server of the human genome(either ucsc or
ensembl) and set up my array data annotations locally.

The glyph is the Bio::Graphics  xyplot

If that glyph is supported on the EnsEMBL das client in the future, then I
can switch over

Thanks for the offer!
-- 
Andrew Nunberg
Bioinformagician
Orion Genomics
(314)-615-6989
www.oriongenomics.com