From anunberg at oriongenomics.com Mon May 9 11:04:36 2005 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Mon May 9 10:57:31 2005 Subject: [DAS] Question about glyph options Message-ID: 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 don?t see them listed in the documentation. Am I limited to what is listed in the DAS documentation? Andy -- Andrew Nunberg Bioinformagician Orion Genomics (314)-615-6989 www.oriongenomics.com From jws at sanger.ac.uk Tue May 10 04:39:34 2005 From: jws at sanger.ac.uk (Jim Stalker) Date: Tue May 10 04:34:20 2005 Subject: [DAS] Question about glyph options In-Reply-To: References: Message-ID: <09ccc19a32be6d074d9a87897a4e7801@sanger.ac.uk> 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 don?t 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 -- Jim Stalker Wellcome Trust Sanger Institute From anunberg at oriongenomics.com Tue May 10 10:41:26 2005 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Tue May 10 10:34:22 2005 Subject: [DAS] Question about glyph options In-Reply-To: <09ccc19a32be6d074d9a87897a4e7801@sanger.ac.uk> Message-ID: On 5/10/05 3:39 AM, "Jim Stalker" 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 don?t 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 From anunberg at oriongenomics.com Tue May 10 12:18:13 2005 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Tue May 10 12:13:49 2005 Subject: [DAS] Question about glyph options In-Reply-To: <09ccc19a32be6d074d9a87897a4e7801@sanger.ac.uk> Message-ID: On 5/10/05 3:39 AM, "Jim Stalker" wrote: Jim, I noticed ensembl has das ref servers, but none for any of the recent releases, unless I missed something The latest I see is 28_35a, Is there one for 29_35b? I would rather use ensembl rather than ucsc because I am running alocal copy of ensembl homo sapiens 29_35b Thanks > > 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 don?t 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 -- Andrew Nunberg Bioinformagician Orion Genomics (314)-615-6989 www.oriongenomics.com From girish at genet.sickkids.on.ca Fri May 27 15:38:26 2005 From: girish at genet.sickkids.on.ca (Girish Rao) Date: Fri May 27 15:31:16 2005 Subject: [DAS] LDAS Database Error Message-ID: <42977732.8020201@genet.sickkids.on.ca> Hello All, I am re-sending this post as a subscriber to the DAS Mailing List. I have chosen to install LDAS and I am currently testing it. In fact, I was able to successfully test the LDAS Server using the test data given in the installation package. However, upon creating a database containing our own data, I am getting an error message "Could not open database" when testing the LDAS Server. Actually, I was getting this error message initially with the test database, but somehow the issue resolved itself, I am not sure what was changed to fix it. When I run the dsn command, our database is displayed, so it is being recognized. If anyone could advise on this issue, it would be greatly appreciated. Thanks. Regards, Girish From girish at genet.sickkids.on.ca Fri May 27 10:42:42 2005 From: girish at genet.sickkids.on.ca (Girish Rao) Date: Wed Jun 8 23:23:08 2005 Subject: [DAS] LDAS database error Message-ID: <429731E2.9070001@genet.sickkids.on.ca> Hello All, I have chosen to install LDAS and I am currently testing it. In fact, I was able to successfully test the LDAS Server using the test data given in the installation package. However, upon creating a database containing our own data, I am getting an error message "Could not open database" when testing the LDAS Server. Actually, I was getting this error message initially with the test database, but somehow the issue resolved itself, I am not sure what was changed to fix it. Also, when I run the dsn command, our database is present in the output, so it is being recognized here. If anyone could advise on the above issue, it would be greatly appreciated. Thanks for your time. Regards, Girish