[DAS] DAS setup questions

[James Freeman]

Dear Graeme,

If you are trying to view your annotations on the public ensembl website
(http:://www.ensembl.org/), there is an some easy ways to do it,
depending on your time constraints.

Get your annotations matched to the sequences in:

ftp://ftp.ensembl.org/pub/human-4.28/data/fasta/dna/Homo_sapiens.latestgp.fa.gz

Once you know where your annotations are relative to the above, you
there are two options that I recommend:

The fastest by far is to upload your data directly into ensembl:

http://www.ensembl.org/Homo_sapiens/helpview?se=1&kw=upload

or if you want to set up your own client neutral (i.e. not just Ensembl,
but also Omnigene, Geodesic, et al.) das annotation service, try the
following:

http://www.biodas.org/servers/
http://www.ensembl.org/Dev/Lists/das/msg01042.html
http://www.ensembl.org/Dev/Lists/das/msg01056.html

If you are trying to create an internal version of the distributed
Ensembl website, follow the instructions on the website and I suggest a
Dazzle reference server and an LDAS annotation server, each of which are
excellent at their particular jobs.

Good luck,

Jim Freeman
Senior Scientist
Variagenics, Inc.

Graeme Campbell wrote:
> 
> Hi there,
> 
> I have been attempting to set up a sample DAS installation using the
> document "Setting up a Ensembl DAS Server"
> (http://www.ensembl.org/Docs/das_server_v1.2.pdf), but have been
> stumbling a bit and I was hoping someone could offer some advice.
> 
> I'm confused about the dazzle-webapp-skeleton
> (http://www.biojava.org/download/dazzle/dazzle-webapp-skeleton-0.95.tar.gz).
> I get a welcome page when I point my browser at localhost:8080/das/.
> I'm also able to get back XML (in compressed format) by pointing my
> browser at localhost:8080/das/dsn.  However, it comes with "test" and
> "tss" data sources.  What exactly should I be able to do with these
> sources once they are installed?  Should I be able to connect to my
> local das webapp from the Ensembl website and view test annotations
> online?
> 
> I've also set up the test database, loaded the sample data, and
> configured another sample web-app
> (http://www.biojava.org/download/ensembl-das/ensembl-das-webapp-20020214.tar.gz)
> as specified in the setup document.  From this, I'm able to get back XML
> from a DSN request that lists my new datasource, and I'm able to add the
> das source to the web-viewer on the ensembl.org site.  However, when I
> browse the AC000041 contig region, there are no annotations, just a
> message saying "No * Ensembl Te.. features in this region."  I believe
> the test data from the setup document is all in this region though - but
> I may be misunderstanding things.
> 
> Any guidance you could give me would be appreciated.
> 
> Thanks,
> 
> Graeme
> 
> --
> Graeme Campbell                         phone:  (604) 875-3868
> Bioinformatics Core Facility            e-mail: graemeca@cmmt.ubc.ca
> Centre for Molecular Medicine and Therapeutics
> Vancouver, BC. Canada.
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