From kim750 at ggbio.com Sun Jun 5 04:35:55 2005 From: kim750 at ggbio.com (kim750@ggbio.com) Date: Wed Jun 8 23:23:15 2005 Subject: [DAS] Das2GFF.plfailure Message-ID: <20050605.AAA1117960398@ggbio.com> Hi! I am testing das server on window. How can I execute ldas_load.pl on window? Thanks for kind responses in advance. Yeon-Ki Yeon-Ki Kim, Ph.D. Director GreenGene Biotech, inc. Myongji University 38-2 Namdong Yongin Kyonggido 449-728 Korea URL:http://www.ggbio.com E-mail:kim750@ggbio.com kim750a11@hotmail.com Phone:82-31-330-6276 Fax: 82-31-321-6355 GreenGene BioTech Inc. From frank.potthast at fgcz.ethz.ch Wed Jun 8 10:11:04 2005 From: frank.potthast at fgcz.ethz.ch (Potthast, Frank) Date: Wed Jun 8 23:23:16 2005 Subject: [DAS] das chromosome location focussed annotation file, web-upload, error ? Message-ID: <2AAC8C52F33BCC4080610382C0873D2F0128EC12@EX5.d.ethz.ch> Hi, We are trying to annotate C.Elegans in ensemlbl using e.g. http://www.ensembl.org/Caenorhabditis_elegans/contigview?l=I:5555-5555 when we upload a file containing lines like that below, (tab separated, 10 columns, chromosome location focussed), we get a timeout error on the DAS server. Anything obvious we're doing wrong? In the example below, we try to map a peptide to chromosome I bp-positions 5906577 to 5906618. 20020050415_S2_51_54.3496.3496.2 ETVQSESNQICLSK pepnailer identity I 5906577 5906618 + . 100 Greetings from Zurich ... Frank --------------------------------- Functional Genomics Center Zurich Frank Potthast, PhD Senior Research Scientist Proteome Informatics frank@fgcz.ethz.ch +41 79 46 180 72 skype.com: frank.potthast --------------------------------- From ak at ebi.ac.uk Thu Jun 9 05:17:43 2005 From: ak at ebi.ac.uk (Andreas Kahari) Date: Thu Jun 9 05:17:14 2005 Subject: [DAS] das chromosome location focussed annotation file, web-upload, error ? In-Reply-To: <2AAC8C52F33BCC4080610382C0873D2F0128EC12@EX5.d.ethz.ch> References: <2AAC8C52F33BCC4080610382C0873D2F0128EC12@EX5.d.ethz.ch> Message-ID: <20050609091743.GA5191@ebi.ac.uk> Dear Frank, The hardware involved with the user uploaded data is currently being relocated. We are aware of the disruption and we are working to restore this service ASAP. Regrads, Andreas On Wed, Jun 08, 2005 at 04:11:04PM +0200, Potthast, Frank wrote: > Hi, > > We are trying to annotate C.Elegans in ensemlbl using e.g. > http://www.ensembl.org/Caenorhabditis_elegans/contigview?l=I:5555-5555 > when we upload a file containing lines like that below, (tab separated, 10 columns, chromosome location focussed), > we get a timeout error on the DAS server. Anything obvious we're doing wrong? > In the example below, we try to map a peptide to chromosome I bp-positions 5906577 to 5906618. > > 20020050415_S2_51_54.3496.3496.2 ETVQSESNQICLSK pepnailer identity I 5906577 5906618 + . 100 > -- Andreas K?h?ri EMBL-EBI/ensembl www.ensembl.org 1024D/C2E163CB F4C4 A41A 665B 448A 3FA9 6AEA 12E3 39DA C2E1 63CB From hvdspek at liacs.nl Thu Jun 30 18:29:23 2005 From: hvdspek at liacs.nl (Harmen van der Spek) Date: Thu Jun 30 18:20:42 2005 Subject: [DAS] xyplot glyph in Ensembl genome browser Message-ID: <1120170563.10016.23.camel@athene> I am currently working on CGH data visualisation (DAS annotation server). The idea is to draw a histogram or another kind of plot. I came across the xyplot glyph, which is being used in gbrowse. In the archives of May I found a post about the same problem, namely microarray data visualisation. Ensembl doesn't support the xyplot glyph yet. I've been playing around a bit with the source code of Ensembl and found out that I could add glyphs myself in the Bio/Ensembl/Glyph/Symbol directory. I am able to use my own xyplot class to draw features, but I can't make it plot histograms or line plots. In das.pm, I modified get_featuredata in such a way that it returns the score feature (which I need to plot) entry too. I still have some problems with rendering. Is someone else working on the same matter or can anyone give some help to get me on the right track. Is there still interest to include the xyplot glyph in the main Ensembl distribution? Regards, Harmen van der Spek Leiden Institute of Advanced Computer Science P.S. If I don't reply to mails, it's not because I'm impolite, but because I'm having a short holiday. From meuleman at gmail.com Thu Jun 30 19:07:25 2005 From: meuleman at gmail.com (Wouter Meuleman) Date: Thu Jun 30 18:58:33 2005 Subject: [DAS] xyplot glyph in Ensembl genome browser In-Reply-To: <1120170563.10016.23.camel@athene> References: <1120170563.10016.23.camel@athene> Message-ID: On 6/30/05, Harmen van der Spek wrote: > I am currently working on CGH data visualisation (DAS annotation > server). The idea is to draw a histogram or another kind of plot. I came > across the xyplot glyph, which > is being used in gbrowse. In the archives of May I found a post about > the same problem, namely microarray data visualisation. Ensembl doesn't > support the xyplot glyph yet. > > I've been playing around a bit with the source code of Ensembl and found > out that I could add glyphs myself in the Bio/Ensembl/Glyph/Symbol > directory. I am able to use my own xyplot class to draw features, but > I can't make it plot histograms or line plots. > In das.pm, I modified get_featuredata in such a way that it returns the > score feature (which I need to plot) entry too. > > I still have some problems with rendering. Is someone else working on > the same matter or can anyone give some help to get me on the right > track. Is there still interest to include the xyplot glyph in the main > Ensembl distribution? > Dear Harmen, Questions to do with Ensembl are perhaps better asked on the ensembl-dev list. A few weeks ago this topic was addressed there by Andrew Nunberg doing, I think, something comparable. The question and subsequent responses by Ewan Birney and Steve Taylor follow. If this is what you mentioned, please ignore (I wasn't sure which archives you meant). ============================= >> Is there a relatively simply way to display microarray data in ensembl? >> I have a local copy running and I am exploring using DAS, except I do not >> think that DAS supports the xyplot glyph. > > I don't think there is something out of the box, but being able to show > "wiggle plots" via DAS is on our agenda - which I think it what you want. > > If you want to hack Ensembl, the GC glyph is the place to start whcih is > a wiggle plot. > > James and/or Eugene might comment more about wiggle plots via DAS (we could > use the Score slot, right?) > I know of several groups would be really interested in seeing this. It would be useful if you could load 'wiggle' format data via URL as you can in the UCSC Genome Browser (as well as via DAS). ============================= In addition, James Smith mentioned the following on the ensembl-dev list: > By the September release we will also have "score-based" > rendering on the sequence level displays, in the form of > "wiggle-lines", "histograms" and colour based scoring. Hope this helps. -Wouter Meuleman.