[DAS] Dazzle with Ensembl 3.26.1

[Tony Cox]

On Fri, 15 Feb 2002, Stefano Tine wrote:

Hi Stefano,

one thing to consider is whether this region has become a lot more "busy" in
terms of visible annotations. Maybe the server is shifting a lot more data now?

Is it only DAS that slows it down? - maybe you have a junked index in ensembl
somewhere. 7-fold slowdown seems suspiciously bad....

Tony


+>
+>Well, I tried forgetting our own DAS service
+>and just requesting a contigview with one of the
+>predefined DAS services on (=LINE repeat):
+>
+>http://localhost/Homo_sapiens/contigview?chr=chr15&vc_start=61218530&vc_end=
+>61938748
+>
+>this takes 5 seconds with 1.2.0
+>this takes 35 seconds with 3.26.1
+>
+>Since in both cases I am calling an external DAS service (which
+>I assume uses its own reference data) I would expect them to be 
+>equally fast (or slow) independent of a potentially screwed up 
+>install of 3.26.1 here, or am I missing something?
+>
+>Anyway, I will try reinstalling 3.26.1 data/software from scratch,
+>since I suppose by now that Dazzle/Tomcat is not the issue here but
+>Ensembl is.
+>
+>Thanks
+>
+>Stefano
+>
+>
+>
+>
+>-----Original Message-----
+>From: Tony Cox [mailto:avc@sanger.ac.uk]
+>Sent: Friday, February 15, 2002 11:54 AM
+>To: Thomas Down
+>Cc: Stefano Tine; das@biodas.org
+>Subject: Re: [DAS] Dazzle with Ensembl 3.26.1
+>
+>
+>On Fri, 15 Feb 2002, Thomas Down wrote:
+>
+>+>On Fri, Feb 15, 2002 at 10:21:29AM -0000, Stefano Tine wrote:
+>+>> 
+>+>> Thanks for the quick release.
+>+>> 
+>+>> I have now:
+>+>> 
+>+>> Dazzle 0.95
+>+>> Tomcat 4.0.2
+>+>> Ensembl 3.26.1 (with human_trace.pm and mouse_trace.pm
+>+>> still desaparecidos)
+>+>> 
+>+>> and.. I still have the long loading times even with the
+>+>> simple (one DAS service) dazzlecfg.xml listed below :-((
+>+>> 
+>+>> 31" just for a random call such as
+>+>>
+>/Homo_sapiens/contigview?chr=5&highlight=&vc_start=82457556&vc_end=82557555
+>+>> 
+>+>> with one SNP-type DAS service on. This only takes a couple seconds
+>+>> when using 1.2.0 schema and Ensembl 1.2.0 distribution.
+>+>
+>+>
+>+>Hmmm, worrying...
+>+>
+>+>How big is your snps.gff file?
+>+>
+>+>I'm still not sure I understand what's going on here.  It
+>+>makes me wonder if maybe an index got lost when you loaded
+>+>tables into your database (the Java code uses the database
+>+>in a slightly different way to the Perl, so it's possible that
+>+>an indexing change could clobber biojava-ensembl, but still
+>+>leave contigview running normally).
+>
+>I gave up on GFF-based data sources. I tried them for some repeat data and
+>after
+>a certain file size (can't remember what) the data source just bogs down
+>completely.
+>
+>Try changing the data to a simple generic feature source. Worked for me.
+>
+>Tony
+>
+>+>
+>+>Anyone else got any ideas about this?
+>+>
+>+>    Thomas.
+>+>_______________________________________________
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+>+>
+>
+>******************************************************
+>Tony Cox			Email:avc@sanger.ac.uk
+>Sanger Institute		WWW:www.sanger.ac.uk
+>Wellcome Trust Genome Campus	Webmaster
+>Hinxton				Tel: +44 1223 834244
+>Cambs. CB10 1SA			Fax: +44 1223 494919
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******************************************************
Tony Cox			Email:avc@sanger.ac.uk
Sanger Institute		WWW:www.sanger.ac.uk
Wellcome Trust Genome Campus	Webmaster
Hinxton				Tel: +44 1223 834244
Cambs. CB10 1SA			Fax: +44 1223 494919
******************************************************