From jw12 at sanger.ac.uk Tue Jan 4 09:06:21 2011 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Tue, 4 Jan 2011 14:06:21 +0000 Subject: [DAS] DAS workshop 2011 2-4th March Message-ID: <1F1DB32E-FB2C-4D19-A53B-11789674F255@sanger.ac.uk> The 2011 DAS workshop will be held from Wednesday 2nd-Friday 5th March 2011. If you would be interested in presenting please email me jonathan.warren at sanger.ac.uk We will email a registration page for attendees. The format of the workshop is likely to be similar to last years (1st day for beginners, 2nd for both beginners and advanced users, 3rd day for advanced), information for which can be found here: http://www.biodas.org/wiki/DASWorkshop2010 If you would like to present then please send a small summary of what you would like to talk about. Thanks Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From jw12 at sanger.ac.uk Thu Jan 6 08:53:06 2011 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 6 Jan 2011 13:53:06 +0000 Subject: [DAS] DAS registry unavailable this weekend Message-ID: Due to essential maintenance at the sanger, the DAS Registry will be down from 4.30pm this Friday to Sunday afternoon. Obviously the http://www.dasregistry.org/das/sources and http://www.dasregistry.org/das/coordinatesystem web services will be down. I believe the EBI will also be affected by this down time so these documents will not be available from the EBI either. ( http://www.ebi.ac.uk/das-srv/registry/das/sources http://www.ebi.ac.uk/das-srv/registry/das/coordinatesystem ) This type of situation happens very rarely indeed, but we are very sorry for any inconvenience caused. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From andy.jenkinson at ebi.ac.uk Thu Jan 6 09:16:20 2011 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Thu, 6 Jan 2011 14:16:20 +0000 Subject: [DAS] DAS registry unavailable this weekend In-Reply-To: References: Message-ID: On 6 Jan 2011, at 13:53, Jonathan Warren wrote: > Due to essential maintenance at the sanger, the DAS Registry will be down from 4.30pm this Friday to Sunday afternoon. > Obviously the http://www.dasregistry.org/das/sources and http://www.dasregistry.org/das/coordinatesystem web services will be down. > > I believe the EBI will also be affected by this down time so these documents will not be available from the EBI either. > ( > http://www.ebi.ac.uk/das-srv/registry/das/sources > http://www.ebi.ac.uk/das-srv/registry/das/coordinatesystem > ) Just to confirm that as a result of this maintenance, the EBI mirror will indeed not be available. Most EBI web services will also be unavailable, including its DAS servers. We apologise for the inconvenience. As an aside, 2011 will see EBI content migrated to separate physical locations, making occurrences such as this even less common. Kind regards, Andy Jenkinson Information Integration Specialist European Bioinformatics Institute andy.jenkinson at ebi.ac.ul +44 (0)1223 49 2618 From jw12 at sanger.ac.uk Fri Jan 7 10:08:06 2011 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Fri, 7 Jan 2011 15:08:06 +0000 Subject: [DAS] DAS registry unavailable this weekend In-Reply-To: References: Message-ID: <61021181-620C-44EC-883B-AFEB788AF064@sanger.ac.uk> Reminder that the Sanger and EBI DAS sources along with the registry will be down from 4.30pm today until Sunday afternoon at the earliest. On 6 Jan 2011, at 13:53, Jonathan Warren wrote: > Due to essential maintenance at the sanger, the DAS Registry will be > down from 4.30pm this Friday to Sunday afternoon. > Obviously the http://www.dasregistry.org/das/sources and http://www.dasregistry.org/das/coordinatesystem > web services will be down. > > I believe the EBI will also be affected by this down time so these > documents will not be available from the EBI either. > ( > http://www.ebi.ac.uk/das-srv/registry/das/sources > http://www.ebi.ac.uk/das-srv/registry/das/coordinatesystem > ) > > This type of situation happens very rarely indeed, but we are very > sorry for any inconvenience caused. > > Jonathan Warren > Senior Developer and DAS coordinator > blog: http://biodasman.wordpress.com/ > jw12 at sanger.ac.uk > Ext: 2314 > Telephone: 01223 492314 > > > > > > > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome > ResearchLimited, a charity registered in England with number 1021457 > and acompany registered in England with number 2742969, whose > registeredoffice is 215 Euston Road, London, NW1 > 2BE._______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From prem.apa at gmail.com Fri Jan 7 11:49:04 2011 From: prem.apa at gmail.com (Prem Anand) Date: Fri, 7 Jan 2011 16:49:04 +0000 Subject: [DAS] GBrowse as DAS server+Ensembl as DAS client Message-ID: Hi We are trying to set up our GBrowse as DAS server and were testing it with ensembl as client. We have the right metadata in the datasource.conf file. GRCh_37,Chromosome,Homo sapiens The server responds for /cgi-bin/das/sources (also /cgi-bin/das/dsn) well. We also tried with different capabilities locally and it seems to be fine. In all our GFF files/gbrowse databases we name the chromosomes prefexing with 'chr' as given in the test_range. But ensembl client seems to ignore the test_range and is making the request as shown below ( from http access log) /cgi-bin/das/01_Hs_GRCh37%7CASSOC_VARIANT/features?segment=1:114355433,114415381;maxbins=872 HTTP/1.1" 200 345 "-" "Ensembl/60" And as GBrowse server doesn't recognise the region (1:114355433,114415381), it doesn't return anything back. In cgi-bin/das script, approximately at around line 860, if I prefix the $reference with 'chr', it works. foreach (@segments) { my ($reference,$refclass,$start,$stop) = @$_; if($reference !~ /^chr/){ $reference = "chr".$reference; } We are not happy with this fix and wondering if it is a ensembl client issue or gbrowse server issue. Shouldn't ensembl make the right request figuring out the right url from 'test_range'? OR If GBrowse server has to handle it in a better way? Any directions would help. Many Thanks Prem From andy.jenkinson at ebi.ac.uk Fri Jan 7 12:33:06 2011 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Fri, 7 Jan 2011 17:33:06 +0000 Subject: [DAS] GBrowse as DAS server+Ensembl as DAS client In-Reply-To: References: Message-ID: <2B36018B-91DD-4130-B91A-3BA28447A14D@ebi.ac.uk> Hi Prem, Each DAS coordinate system (e.g. GRCh_37 chromosomes) should always use the same sequence names between all DAS servers. In fact, compatibility between DAS servers is the primary reason for coordinate systems to exist. This allows all clients and servers to be sure that if they use the same coordinates then they can communicate with each other without having to know anything about each particular client/server. In truth the difference between the sequence names used by different genome browsers is a headache, and the net result is that coordinates are effectively defined by whoever uses them first (in this case being Ensembl). So, the GRCh37 coordinates use names like 1, 2, 3, X, MT as defined by Ensembl's reference server. So gbrowse will need to detect this if it is to work properly, and also report a test_range without the "chr" prefix. As an aside, I believe UCSC (who also use the chrX format) do this conversion in their DAS server and can handle both formats. Cheers, Andy On 7 Jan 2011, at 16:49, Prem Anand wrote: > Hi > > We are trying to set up our GBrowse as DAS server and were testing it with > ensembl as client. > > We have the right metadata in the datasource.conf file. > > authority="GRCh" test_range="chr1:114356433..114414381" taxid="9606" > version="37" source="Chromosome">GRCh_37,Chromosome,Homo > sapiens > > The server responds for /cgi-bin/das/sources (also /cgi-bin/das/dsn) well. > We also tried with different capabilities locally and it seems to be fine. > > In all our GFF files/gbrowse databases we name the chromosomes prefexing > with 'chr' as given in the test_range. > > But ensembl client seems to ignore the test_range and is making the request > as shown below ( from http access log) > > /cgi-bin/das/01_Hs_GRCh37%7CASSOC_VARIANT/features?segment=1:114355433,114415381;maxbins=872 > HTTP/1.1" 200 345 "-" "Ensembl/60" > > > And as GBrowse server doesn't recognise the region (1:114355433,114415381), > it doesn't return anything back. > In cgi-bin/das script, approximately at around line 860, if I prefix the > $reference with 'chr', it works. > > foreach (@segments) { > my ($reference,$refclass,$start,$stop) = @$_; > > if($reference !~ /^chr/){ > $reference = "chr".$reference; > } > > > We are not happy with this fix and wondering if it is a ensembl client issue > or gbrowse server issue. > > Shouldn't ensembl make the right request figuring out the right url from > 'test_range'? > OR > If GBrowse server has to handle it in a better way? > > Any directions would help. > > Many Thanks > Prem > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das From prem.apa at gmail.com Fri Jan 7 12:56:37 2011 From: prem.apa at gmail.com (Prem Anand) Date: Fri, 7 Jan 2011 17:56:37 +0000 Subject: [DAS] GBrowse as DAS server+Ensembl as DAS client In-Reply-To: <2B36018B-91DD-4130-B91A-3BA28447A14D@ebi.ac.uk> References: <2B36018B-91DD-4130-B91A-3BA28447A14D@ebi.ac.uk> Message-ID: Thanks Andy, You are right about the compatibility issues. However, I thought the clients could also handle this as for example, the ensembl client first queries the server for /das/sources/, and as it already has all the information it needs to make a das request properly from the 'test_range' and other attributes, it can make the request suiting the server as well. Anyway, we have to see what gbrowse developers have to say. Cheers Prem On Fri, Jan 7, 2011 at 5:33 PM, Andy Jenkinson wrote: > Hi Prem, > > Each DAS coordinate system (e.g. GRCh_37 chromosomes) should always use the > same sequence names between all DAS servers. In fact, compatibility between > DAS servers is the primary reason for coordinate systems to exist. This > allows all clients and servers to be sure that if they use the same > coordinates then they can communicate with each other without having to know > anything about each particular client/server. In truth the difference > between the sequence names used by different genome browsers is a headache, > and the net result is that coordinates are effectively defined by whoever > uses them first (in this case being Ensembl). So, the GRCh37 coordinates use > names like 1, 2, 3, X, MT as defined by Ensembl's reference server. > > So gbrowse will need to detect this if it is to work properly, and also > report a test_range without the "chr" prefix. As an aside, I believe UCSC > (who also use the chrX format) do this conversion in their DAS server and > can handle both formats. > > Cheers, > Andy > > On 7 Jan 2011, at 16:49, Prem Anand wrote: > > > Hi > > > > We are trying to set up our GBrowse as DAS server and were testing it > with > > ensembl as client. > > > > We have the right metadata in the datasource.conf file. > > > > > authority="GRCh" test_range="chr1:114356433..114414381" taxid="9606" > > version="37" source="Chromosome">GRCh_37,Chromosome,Homo > > sapiens > > > > The server responds for /cgi-bin/das/sources (also /cgi-bin/das/dsn) > well. > > We also tried with different capabilities locally and it seems to be > fine. > > > > In all our GFF files/gbrowse databases we name the chromosomes prefexing > > with 'chr' as given in the test_range. > > > > But ensembl client seems to ignore the test_range and is making the > request > > as shown below ( from http access log) > > > > > /cgi-bin/das/01_Hs_GRCh37%7CASSOC_VARIANT/features?segment=1:114355433,114415381;maxbins=872 > > HTTP/1.1" 200 345 "-" "Ensembl/60" > > > > > > And as GBrowse server doesn't recognise the region > (1:114355433,114415381), > > it doesn't return anything back. > > In cgi-bin/das script, approximately at around line 860, if I prefix the > > $reference with 'chr', it works. > > > > foreach (@segments) { > > my ($reference,$refclass,$start,$stop) = @$_; > > > > if($reference !~ /^chr/){ > > $reference = "chr".$reference; > > } > > > > > > We are not happy with this fix and wondering if it is a ensembl client > issue > > or gbrowse server issue. > > > > Shouldn't ensembl make the right request figuring out the right url from > > 'test_range'? > > OR > > If GBrowse server has to handle it in a better way? > > > > Any directions would help. > > > > Many Thanks > > Prem > > _______________________________________________ > > DAS mailing list > > DAS at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/das > > From andy.jenkinson at ebi.ac.uk Fri Jan 7 13:21:37 2011 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Fri, 7 Jan 2011 18:21:37 +0000 Subject: [DAS] GBrowse as DAS server+Ensembl as DAS client In-Reply-To: References: <2B36018B-91DD-4130-B91A-3BA28447A14D@ebi.ac.uk> Message-ID: <056AEDBF-6831-497D-A13A-43C0BD597D99@ebi.ac.uk> Hi Prem, The test range does not really provide enough information - it only provides a single identifier, and does not help identify which of Ensembl's sequences that refers to and so cannot be a generic solution. It's true that Ensembl could make some assumptions and implement an ad-hoc solution for this specific case (similar to the hack you have applied) but this would not be compliant with the DAS specification and would be confusing for other DAS clients. In the past we have found that supporting non-standard functionality has been very confusing for others and is a major reason for inconsistency of DAS implementation today. For that reason, I would suggest that it is better to do the conversion in the server. I'm actually surprised it does not do this already, as I seem to remember when Lincoln was working on updating gbrowse for DAS 1.6 that things worked OK with Ensembl. Cheers, Andy On 7 Jan 2011, at 17:56, Prem Anand wrote: > Thanks Andy, > > You are right about the compatibility issues. However, I thought the clients could also handle this as for example, the ensembl client first queries the server for /das/sources/, and as it already has all the information it needs to make a das request properly from the 'test_range' and other attributes, it can make the request suiting the server as well. > > Anyway, we have to see what gbrowse developers have to say. > > Cheers > Prem > > > On Fri, Jan 7, 2011 at 5:33 PM, Andy Jenkinson wrote: > Hi Prem, > > Each DAS coordinate system (e.g. GRCh_37 chromosomes) should always use the same sequence names between all DAS servers. In fact, compatibility between DAS servers is the primary reason for coordinate systems to exist. This allows all clients and servers to be sure that if they use the same coordinates then they can communicate with each other without having to know anything about each particular client/server. In truth the difference between the sequence names used by different genome browsers is a headache, and the net result is that coordinates are effectively defined by whoever uses them first (in this case being Ensembl). So, the GRCh37 coordinates use names like 1, 2, 3, X, MT as defined by Ensembl's reference server. > > So gbrowse will need to detect this if it is to work properly, and also report a test_range without the "chr" prefix. As an aside, I believe UCSC (who also use the chrX format) do this conversion in their DAS server and can handle both formats. > > Cheers, > Andy > > On 7 Jan 2011, at 16:49, Prem Anand wrote: > > > Hi > > > > We are trying to set up our GBrowse as DAS server and were testing it with > > ensembl as client. > > > > We have the right metadata in the datasource.conf file. > > > > > authority="GRCh" test_range="chr1:114356433..114414381" taxid="9606" > > version="37" source="Chromosome">GRCh_37,Chromosome,Homo > > sapiens > > > > The server responds for /cgi-bin/das/sources (also /cgi-bin/das/dsn) well. > > We also tried with different capabilities locally and it seems to be fine. > > > > In all our GFF files/gbrowse databases we name the chromosomes prefexing > > with 'chr' as given in the test_range. > > > > But ensembl client seems to ignore the test_range and is making the request > > as shown below ( from http access log) > > > > /cgi-bin/das/01_Hs_GRCh37%7CASSOC_VARIANT/features?segment=1:114355433,114415381;maxbins=872 > > HTTP/1.1" 200 345 "-" "Ensembl/60" > > > > > > And as GBrowse server doesn't recognise the region (1:114355433,114415381), > > it doesn't return anything back. > > In cgi-bin/das script, approximately at around line 860, if I prefix the > > $reference with 'chr', it works. > > > > foreach (@segments) { > > my ($reference,$refclass,$start,$stop) = @$_; > > > > if($reference !~ /^chr/){ > > $reference = "chr".$reference; > > } > > > > > > We are not happy with this fix and wondering if it is a ensembl client issue > > or gbrowse server issue. > > > > Shouldn't ensembl make the right request figuring out the right url from > > 'test_range'? > > OR > > If GBrowse server has to handle it in a better way? > > > > Any directions would help. > > > > Many Thanks > > Prem > > _______________________________________________ > > DAS mailing list > > DAS at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/das > > From prem.apa at gmail.com Fri Jan 7 13:49:34 2011 From: prem.apa at gmail.com (Prem Anand) Date: Fri, 7 Jan 2011 18:49:34 +0000 Subject: [DAS] GBrowse as DAS server+Ensembl as DAS client In-Reply-To: <056AEDBF-6831-497D-A13A-43C0BD597D99@ebi.ac.uk> References: <2B36018B-91DD-4130-B91A-3BA28447A14D@ebi.ac.uk> <056AEDBF-6831-497D-A13A-43C0BD597D99@ebi.ac.uk> Message-ID: Thanks Andy. If there is no other alternative, then we will fix it on our side. Cheers Prem On Fri, Jan 7, 2011 at 6:21 PM, Andy Jenkinson wrote: > Hi Prem, > > The test range does not really provide enough information - it only > provides a single identifier, and does not help identify which of Ensembl's > sequences that refers to and so cannot be a generic solution. It's true that > Ensembl could make some assumptions and implement an ad-hoc solution for > this specific case (similar to the hack you have applied) but this would not > be compliant with the DAS specification and would be confusing for other DAS > clients. In the past we have found that supporting non-standard > functionality has been very confusing for others and is a major reason for > inconsistency of DAS implementation today. For that reason, I would suggest > that it is better to do the conversion in the server. I'm actually surprised > it does not do this already, as I seem to remember when Lincoln was working > on updating gbrowse for DAS 1.6 that things worked OK with Ensembl. > > Cheers, > Andy > > On 7 Jan 2011, at 17:56, Prem Anand wrote: > > > Thanks Andy, > > > > You are right about the compatibility issues. However, I thought the > clients could also handle this as for example, the ensembl client first > queries the server for /das/sources/, and as it already has all the > information it needs to make a das request properly from the 'test_range' > and other attributes, it can make the request suiting the server as well. > > > > Anyway, we have to see what gbrowse developers have to say. > > > > Cheers > > Prem > > > > > > On Fri, Jan 7, 2011 at 5:33 PM, Andy Jenkinson > wrote: > > Hi Prem, > > > > Each DAS coordinate system (e.g. GRCh_37 chromosomes) should always use > the same sequence names between all DAS servers. In fact, compatibility > between DAS servers is the primary reason for coordinate systems to exist. > This allows all clients and servers to be sure that if they use the same > coordinates then they can communicate with each other without having to know > anything about each particular client/server. In truth the difference > between the sequence names used by different genome browsers is a headache, > and the net result is that coordinates are effectively defined by whoever > uses them first (in this case being Ensembl). So, the GRCh37 coordinates use > names like 1, 2, 3, X, MT as defined by Ensembl's reference server. > > > > So gbrowse will need to detect this if it is to work properly, and also > report a test_range without the "chr" prefix. As an aside, I believe UCSC > (who also use the chrX format) do this conversion in their DAS server and > can handle both formats. > > > > Cheers, > > Andy > > > > On 7 Jan 2011, at 16:49, Prem Anand wrote: > > > > > Hi > > > > > > We are trying to set up our GBrowse as DAS server and were testing it > with > > > ensembl as client. > > > > > > We have the right metadata in the datasource.conf file. > > > > > > > > authority="GRCh" test_range="chr1:114356433..114414381" taxid="9606" > > > version="37" source="Chromosome">GRCh_37,Chromosome,Homo > > > sapiens > > > > > > The server responds for /cgi-bin/das/sources (also /cgi-bin/das/dsn) > well. > > > We also tried with different capabilities locally and it seems to be > fine. > > > > > > In all our GFF files/gbrowse databases we name the chromosomes > prefexing > > > with 'chr' as given in the test_range. > > > > > > But ensembl client seems to ignore the test_range and is making the > request > > > as shown below ( from http access log) > > > > > > > /cgi-bin/das/01_Hs_GRCh37%7CASSOC_VARIANT/features?segment=1:114355433,114415381;maxbins=872 > > > HTTP/1.1" 200 345 "-" "Ensembl/60" > > > > > > > > > And as GBrowse server doesn't recognise the region > (1:114355433,114415381), > > > it doesn't return anything back. > > > In cgi-bin/das script, approximately at around line 860, if I prefix > the > > > $reference with 'chr', it works. > > > > > > foreach (@segments) { > > > my ($reference,$refclass,$start,$stop) = @$_; > > > > > > if($reference !~ /^chr/){ > > > $reference = "chr".$reference; > > > } > > > > > > > > > We are not happy with this fix and wondering if it is a ensembl client > issue > > > or gbrowse server issue. > > > > > > Shouldn't ensembl make the right request figuring out the right url > from > > > 'test_range'? > > > OR > > > If GBrowse server has to handle it in a better way? > > > > > > Any directions would help. > > > > > > Many Thanks > > > Prem > > > _______________________________________________ > > > DAS mailing list > > > DAS at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/das > > > > > > From jw12 at sanger.ac.uk Tue Jan 18 05:25:46 2011 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Tue, 18 Jan 2011 10:25:46 +0000 Subject: [DAS] Registrations for DAS Workshop 2011 Message-ID: DAS is currently being used to share annotations on genomes, protein alignments, structural and interaction information. If you are interested in sharing biological information the DAS workshop below may be of interest to you. Registration is open for the 2011 DAS workshop (2,3,4th March) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.ebi.ac.uk//training/onsite/110302DAS.html and register via the web link at the bottom of the page. This workshop will cater for novice to expert DAS users as each day is optional. Please register early as places will be limited. Registration closes 18 February 2011 (17:00). If you are interested in giving a 15 minute talk on the second day please email Jonathan Warren using jonathan.warren at sanger.ac.uk Many thanks The Sanger/EBI DAS team. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From hk3 at sanger.ac.uk Wed Jan 19 05:45:17 2011 From: hk3 at sanger.ac.uk (Hashem Koohy) Date: Wed, 19 Jan 2011 10:45:17 +0000 Subject: [DAS] Histogram Stylesheet Message-ID: Dear DAS masters, I need to create a histogram stylesheet but I don?t know how to that. I have looked at: http://www.dasregistry.org/extension_stylesheet_histogram.jsp But there is only an output example of a histogram. I don?t see any documentation about how to do that or any template. I will really appreciate any help. Thanks Hashem -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From thomas.a.down at gmail.com Wed Jan 19 06:26:04 2011 From: thomas.a.down at gmail.com (Thomas Down) Date: Wed, 19 Jan 2011 11:26:04 +0000 Subject: [DAS] Histogram Stylesheet In-Reply-To: References: Message-ID: Hi Hashem, There are some examples in the new DAS/1.6 spec: http://www.biodas.org/documents/spec-1.6.html#glyphid Typical use is something like: 0 3 60 white black 2 Thomas. On Wed, Jan 19, 2011 at 10:45 AM, Hashem Koohy wrote: > Dear DAS masters, > I need to create a histogram stylesheet but I don?t know how to that. I > have > looked at: > http://www.dasregistry.org/extension_stylesheet_histogram.jsp > But there is only an output example of a histogram. I don?t see any > documentation about how to do that or any template. > I will really appreciate any help. > Thanks > Hashem > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > > > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das > From andy.jenkinson at ebi.ac.uk Wed Jan 19 06:26:11 2011 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Wed, 19 Jan 2011 11:26:11 +0000 Subject: [DAS] Histogram Stylesheet In-Reply-To: References: Message-ID: Hi Hashem, What kind of information are you looking for? The DAS 1.6 specification explains in more detail what the various stylesheet fields mean (type, category, glyphs etc), and has details of histograms: http://www.biodas.org/documents/spec-1.6.html#stylesheet http://www.biodas.org/documents/spec-1.6.html#glyphid Which server are you using? Since the stylesheet is a static document, for most servers you just construct it manually and tell the server where to find it. Cheers, Andy On 19 Jan 2011, at 10:45, Hashem Koohy wrote: > Dear DAS masters, > I need to create a histogram stylesheet but I don?t know how to that. I have > looked at: > http://www.dasregistry.org/extension_stylesheet_histogram.jsp > But there is only an output example of a histogram. I don?t see any > documentation about how to do that or any template. > I will really appreciate any help. > Thanks > Hashem > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > > > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das From thomas.a.down at gmail.com Thu Jan 20 05:02:05 2011 From: thomas.a.down at gmail.com (Thomas Down) Date: Thu, 20 Jan 2011 10:02:05 +0000 Subject: [DAS] New DAS client paper Message-ID: Bioinformatics has just published a new Application Note about DAS and the Dalliance genomic client: http://bioinformatics.oxfordjournals.org/content/early/2011/01/19/bioinformatics.btr020.abstract If you haven't tried Dalliance in the last month or two, major enhancements include better DAS/1.6 support and direct export of browser graphics (in SVG or PDF formats). We're also gearing up for a major new release, hopefully in the next month or so, with substantial performance and navigation improvements. If you've got any requests or suggestions, please drop me a line, or open a ticket on our Github page: https://github.com/dasmoth/dalliance Thomas Down. From andy.jenkinson at ebi.ac.uk Thu Jan 20 05:23:18 2011 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Thu, 20 Jan 2011 10:23:18 +0000 Subject: [DAS] New DAS client paper In-Reply-To: References: Message-ID: <37CE1614-54D0-4935-8D89-2603E03A4CA2@ebi.ac.uk> Good stuff Thomas! On 20 Jan 2011, at 10:02, Thomas Down wrote: > Bioinformatics has just published a new Application Note about DAS and the > Dalliance genomic client: > > > http://bioinformatics.oxfordjournals.org/content/early/2011/01/19/bioinformatics.btr020.abstract > > If you haven't tried Dalliance in the last month or two, major enhancements > include better DAS/1.6 support and direct export of browser graphics (in SVG > or PDF formats). We're also gearing up for a major new release, hopefully > in the next month or so, with substantial performance and navigation > improvements. If you've got any requests or suggestions, please drop me a > line, or open a ticket on our Github page: > > https://github.com/dasmoth/dalliance > > Thomas Down. > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das From jw12 at sanger.ac.uk Mon Jan 31 11:18:34 2011 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 31 Jan 2011 16:18:34 +0000 Subject: [DAS] Workshop Discussions Message-ID: <524D5A98-7356-443D-97A7-0EDF3A963542@sanger.ac.uk> Hi All This years DAS workshop is not far away now (less than 5 weeks away, deadline for registrations 18th Feb). If you haven't registered and would like to come - please do so here: http://www.ebi.ac.uk//training/onsite/110302DAS.html There is also a preliminary schedule up here: http://www.biodas.org/wiki/DASWorkshop2011 For Day 2 presentations we now have at least half of a days talks. Thanks to those who have volunteered already. If you have new software or made updates to software that uses DAS extensively, please volunteer to give a short talk? Whether you are attending or not, it would be good to get suggestions from the community as to what should be discussed on Day 3. There is a place on the wiki for suggestions: http://www.biodas.org/wiki/DASWorkshop2011#Suggested_Topics please add any suggestions you have and if you feel comfortable add your name next to your suggestion. My guess is that topics will arise during the workshop, but it is helpful to get an idea of peoples hopes/ joys/concerns about the DAS project beforehand. Thanks in advance, looking forward to seeing many of you in a few weeks. Jonathan. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From jw12 at sanger.ac.uk Tue Jan 4 14:06:21 2011 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Tue, 4 Jan 2011 14:06:21 +0000 Subject: [DAS] DAS workshop 2011 2-4th March Message-ID: <1F1DB32E-FB2C-4D19-A53B-11789674F255@sanger.ac.uk> The 2011 DAS workshop will be held from Wednesday 2nd-Friday 5th March 2011. If you would be interested in presenting please email me jonathan.warren at sanger.ac.uk We will email a registration page for attendees. The format of the workshop is likely to be similar to last years (1st day for beginners, 2nd for both beginners and advanced users, 3rd day for advanced), information for which can be found here: http://www.biodas.org/wiki/DASWorkshop2010 If you would like to present then please send a small summary of what you would like to talk about. Thanks Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From jw12 at sanger.ac.uk Thu Jan 6 13:53:06 2011 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 6 Jan 2011 13:53:06 +0000 Subject: [DAS] DAS registry unavailable this weekend Message-ID: Due to essential maintenance at the sanger, the DAS Registry will be down from 4.30pm this Friday to Sunday afternoon. Obviously the http://www.dasregistry.org/das/sources and http://www.dasregistry.org/das/coordinatesystem web services will be down. I believe the EBI will also be affected by this down time so these documents will not be available from the EBI either. ( http://www.ebi.ac.uk/das-srv/registry/das/sources http://www.ebi.ac.uk/das-srv/registry/das/coordinatesystem ) This type of situation happens very rarely indeed, but we are very sorry for any inconvenience caused. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From andy.jenkinson at ebi.ac.uk Thu Jan 6 14:16:20 2011 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Thu, 6 Jan 2011 14:16:20 +0000 Subject: [DAS] DAS registry unavailable this weekend In-Reply-To: References: Message-ID: On 6 Jan 2011, at 13:53, Jonathan Warren wrote: > Due to essential maintenance at the sanger, the DAS Registry will be down from 4.30pm this Friday to Sunday afternoon. > Obviously the http://www.dasregistry.org/das/sources and http://www.dasregistry.org/das/coordinatesystem web services will be down. > > I believe the EBI will also be affected by this down time so these documents will not be available from the EBI either. > ( > http://www.ebi.ac.uk/das-srv/registry/das/sources > http://www.ebi.ac.uk/das-srv/registry/das/coordinatesystem > ) Just to confirm that as a result of this maintenance, the EBI mirror will indeed not be available. Most EBI web services will also be unavailable, including its DAS servers. We apologise for the inconvenience. As an aside, 2011 will see EBI content migrated to separate physical locations, making occurrences such as this even less common. Kind regards, Andy Jenkinson Information Integration Specialist European Bioinformatics Institute andy.jenkinson at ebi.ac.ul +44 (0)1223 49 2618 From jw12 at sanger.ac.uk Fri Jan 7 15:08:06 2011 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Fri, 7 Jan 2011 15:08:06 +0000 Subject: [DAS] DAS registry unavailable this weekend In-Reply-To: References: Message-ID: <61021181-620C-44EC-883B-AFEB788AF064@sanger.ac.uk> Reminder that the Sanger and EBI DAS sources along with the registry will be down from 4.30pm today until Sunday afternoon at the earliest. On 6 Jan 2011, at 13:53, Jonathan Warren wrote: > Due to essential maintenance at the sanger, the DAS Registry will be > down from 4.30pm this Friday to Sunday afternoon. > Obviously the http://www.dasregistry.org/das/sources and http://www.dasregistry.org/das/coordinatesystem > web services will be down. > > I believe the EBI will also be affected by this down time so these > documents will not be available from the EBI either. > ( > http://www.ebi.ac.uk/das-srv/registry/das/sources > http://www.ebi.ac.uk/das-srv/registry/das/coordinatesystem > ) > > This type of situation happens very rarely indeed, but we are very > sorry for any inconvenience caused. > > Jonathan Warren > Senior Developer and DAS coordinator > blog: http://biodasman.wordpress.com/ > jw12 at sanger.ac.uk > Ext: 2314 > Telephone: 01223 492314 > > > > > > > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome > ResearchLimited, a charity registered in England with number 1021457 > and acompany registered in England with number 2742969, whose > registeredoffice is 215 Euston Road, London, NW1 > 2BE._______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From prem.apa at gmail.com Fri Jan 7 16:49:04 2011 From: prem.apa at gmail.com (Prem Anand) Date: Fri, 7 Jan 2011 16:49:04 +0000 Subject: [DAS] GBrowse as DAS server+Ensembl as DAS client Message-ID: Hi We are trying to set up our GBrowse as DAS server and were testing it with ensembl as client. We have the right metadata in the datasource.conf file. GRCh_37,Chromosome,Homo sapiens The server responds for /cgi-bin/das/sources (also /cgi-bin/das/dsn) well. We also tried with different capabilities locally and it seems to be fine. In all our GFF files/gbrowse databases we name the chromosomes prefexing with 'chr' as given in the test_range. But ensembl client seems to ignore the test_range and is making the request as shown below ( from http access log) /cgi-bin/das/01_Hs_GRCh37%7CASSOC_VARIANT/features?segment=1:114355433,114415381;maxbins=872 HTTP/1.1" 200 345 "-" "Ensembl/60" And as GBrowse server doesn't recognise the region (1:114355433,114415381), it doesn't return anything back. In cgi-bin/das script, approximately at around line 860, if I prefix the $reference with 'chr', it works. foreach (@segments) { my ($reference,$refclass,$start,$stop) = @$_; if($reference !~ /^chr/){ $reference = "chr".$reference; } We are not happy with this fix and wondering if it is a ensembl client issue or gbrowse server issue. Shouldn't ensembl make the right request figuring out the right url from 'test_range'? OR If GBrowse server has to handle it in a better way? Any directions would help. Many Thanks Prem From andy.jenkinson at ebi.ac.uk Fri Jan 7 17:33:06 2011 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Fri, 7 Jan 2011 17:33:06 +0000 Subject: [DAS] GBrowse as DAS server+Ensembl as DAS client In-Reply-To: References: Message-ID: <2B36018B-91DD-4130-B91A-3BA28447A14D@ebi.ac.uk> Hi Prem, Each DAS coordinate system (e.g. GRCh_37 chromosomes) should always use the same sequence names between all DAS servers. In fact, compatibility between DAS servers is the primary reason for coordinate systems to exist. This allows all clients and servers to be sure that if they use the same coordinates then they can communicate with each other without having to know anything about each particular client/server. In truth the difference between the sequence names used by different genome browsers is a headache, and the net result is that coordinates are effectively defined by whoever uses them first (in this case being Ensembl). So, the GRCh37 coordinates use names like 1, 2, 3, X, MT as defined by Ensembl's reference server. So gbrowse will need to detect this if it is to work properly, and also report a test_range without the "chr" prefix. As an aside, I believe UCSC (who also use the chrX format) do this conversion in their DAS server and can handle both formats. Cheers, Andy On 7 Jan 2011, at 16:49, Prem Anand wrote: > Hi > > We are trying to set up our GBrowse as DAS server and were testing it with > ensembl as client. > > We have the right metadata in the datasource.conf file. > > authority="GRCh" test_range="chr1:114356433..114414381" taxid="9606" > version="37" source="Chromosome">GRCh_37,Chromosome,Homo > sapiens > > The server responds for /cgi-bin/das/sources (also /cgi-bin/das/dsn) well. > We also tried with different capabilities locally and it seems to be fine. > > In all our GFF files/gbrowse databases we name the chromosomes prefexing > with 'chr' as given in the test_range. > > But ensembl client seems to ignore the test_range and is making the request > as shown below ( from http access log) > > /cgi-bin/das/01_Hs_GRCh37%7CASSOC_VARIANT/features?segment=1:114355433,114415381;maxbins=872 > HTTP/1.1" 200 345 "-" "Ensembl/60" > > > And as GBrowse server doesn't recognise the region (1:114355433,114415381), > it doesn't return anything back. > In cgi-bin/das script, approximately at around line 860, if I prefix the > $reference with 'chr', it works. > > foreach (@segments) { > my ($reference,$refclass,$start,$stop) = @$_; > > if($reference !~ /^chr/){ > $reference = "chr".$reference; > } > > > We are not happy with this fix and wondering if it is a ensembl client issue > or gbrowse server issue. > > Shouldn't ensembl make the right request figuring out the right url from > 'test_range'? > OR > If GBrowse server has to handle it in a better way? > > Any directions would help. > > Many Thanks > Prem > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das From prem.apa at gmail.com Fri Jan 7 17:56:37 2011 From: prem.apa at gmail.com (Prem Anand) Date: Fri, 7 Jan 2011 17:56:37 +0000 Subject: [DAS] GBrowse as DAS server+Ensembl as DAS client In-Reply-To: <2B36018B-91DD-4130-B91A-3BA28447A14D@ebi.ac.uk> References: <2B36018B-91DD-4130-B91A-3BA28447A14D@ebi.ac.uk> Message-ID: Thanks Andy, You are right about the compatibility issues. However, I thought the clients could also handle this as for example, the ensembl client first queries the server for /das/sources/, and as it already has all the information it needs to make a das request properly from the 'test_range' and other attributes, it can make the request suiting the server as well. Anyway, we have to see what gbrowse developers have to say. Cheers Prem On Fri, Jan 7, 2011 at 5:33 PM, Andy Jenkinson wrote: > Hi Prem, > > Each DAS coordinate system (e.g. GRCh_37 chromosomes) should always use the > same sequence names between all DAS servers. In fact, compatibility between > DAS servers is the primary reason for coordinate systems to exist. This > allows all clients and servers to be sure that if they use the same > coordinates then they can communicate with each other without having to know > anything about each particular client/server. In truth the difference > between the sequence names used by different genome browsers is a headache, > and the net result is that coordinates are effectively defined by whoever > uses them first (in this case being Ensembl). So, the GRCh37 coordinates use > names like 1, 2, 3, X, MT as defined by Ensembl's reference server. > > So gbrowse will need to detect this if it is to work properly, and also > report a test_range without the "chr" prefix. As an aside, I believe UCSC > (who also use the chrX format) do this conversion in their DAS server and > can handle both formats. > > Cheers, > Andy > > On 7 Jan 2011, at 16:49, Prem Anand wrote: > > > Hi > > > > We are trying to set up our GBrowse as DAS server and were testing it > with > > ensembl as client. > > > > We have the right metadata in the datasource.conf file. > > > > > authority="GRCh" test_range="chr1:114356433..114414381" taxid="9606" > > version="37" source="Chromosome">GRCh_37,Chromosome,Homo > > sapiens > > > > The server responds for /cgi-bin/das/sources (also /cgi-bin/das/dsn) > well. > > We also tried with different capabilities locally and it seems to be > fine. > > > > In all our GFF files/gbrowse databases we name the chromosomes prefexing > > with 'chr' as given in the test_range. > > > > But ensembl client seems to ignore the test_range and is making the > request > > as shown below ( from http access log) > > > > > /cgi-bin/das/01_Hs_GRCh37%7CASSOC_VARIANT/features?segment=1:114355433,114415381;maxbins=872 > > HTTP/1.1" 200 345 "-" "Ensembl/60" > > > > > > And as GBrowse server doesn't recognise the region > (1:114355433,114415381), > > it doesn't return anything back. > > In cgi-bin/das script, approximately at around line 860, if I prefix the > > $reference with 'chr', it works. > > > > foreach (@segments) { > > my ($reference,$refclass,$start,$stop) = @$_; > > > > if($reference !~ /^chr/){ > > $reference = "chr".$reference; > > } > > > > > > We are not happy with this fix and wondering if it is a ensembl client > issue > > or gbrowse server issue. > > > > Shouldn't ensembl make the right request figuring out the right url from > > 'test_range'? > > OR > > If GBrowse server has to handle it in a better way? > > > > Any directions would help. > > > > Many Thanks > > Prem > > _______________________________________________ > > DAS mailing list > > DAS at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/das > > From andy.jenkinson at ebi.ac.uk Fri Jan 7 18:21:37 2011 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Fri, 7 Jan 2011 18:21:37 +0000 Subject: [DAS] GBrowse as DAS server+Ensembl as DAS client In-Reply-To: References: <2B36018B-91DD-4130-B91A-3BA28447A14D@ebi.ac.uk> Message-ID: <056AEDBF-6831-497D-A13A-43C0BD597D99@ebi.ac.uk> Hi Prem, The test range does not really provide enough information - it only provides a single identifier, and does not help identify which of Ensembl's sequences that refers to and so cannot be a generic solution. It's true that Ensembl could make some assumptions and implement an ad-hoc solution for this specific case (similar to the hack you have applied) but this would not be compliant with the DAS specification and would be confusing for other DAS clients. In the past we have found that supporting non-standard functionality has been very confusing for others and is a major reason for inconsistency of DAS implementation today. For that reason, I would suggest that it is better to do the conversion in the server. I'm actually surprised it does not do this already, as I seem to remember when Lincoln was working on updating gbrowse for DAS 1.6 that things worked OK with Ensembl. Cheers, Andy On 7 Jan 2011, at 17:56, Prem Anand wrote: > Thanks Andy, > > You are right about the compatibility issues. However, I thought the clients could also handle this as for example, the ensembl client first queries the server for /das/sources/, and as it already has all the information it needs to make a das request properly from the 'test_range' and other attributes, it can make the request suiting the server as well. > > Anyway, we have to see what gbrowse developers have to say. > > Cheers > Prem > > > On Fri, Jan 7, 2011 at 5:33 PM, Andy Jenkinson wrote: > Hi Prem, > > Each DAS coordinate system (e.g. GRCh_37 chromosomes) should always use the same sequence names between all DAS servers. In fact, compatibility between DAS servers is the primary reason for coordinate systems to exist. This allows all clients and servers to be sure that if they use the same coordinates then they can communicate with each other without having to know anything about each particular client/server. In truth the difference between the sequence names used by different genome browsers is a headache, and the net result is that coordinates are effectively defined by whoever uses them first (in this case being Ensembl). So, the GRCh37 coordinates use names like 1, 2, 3, X, MT as defined by Ensembl's reference server. > > So gbrowse will need to detect this if it is to work properly, and also report a test_range without the "chr" prefix. As an aside, I believe UCSC (who also use the chrX format) do this conversion in their DAS server and can handle both formats. > > Cheers, > Andy > > On 7 Jan 2011, at 16:49, Prem Anand wrote: > > > Hi > > > > We are trying to set up our GBrowse as DAS server and were testing it with > > ensembl as client. > > > > We have the right metadata in the datasource.conf file. > > > > > authority="GRCh" test_range="chr1:114356433..114414381" taxid="9606" > > version="37" source="Chromosome">GRCh_37,Chromosome,Homo > > sapiens > > > > The server responds for /cgi-bin/das/sources (also /cgi-bin/das/dsn) well. > > We also tried with different capabilities locally and it seems to be fine. > > > > In all our GFF files/gbrowse databases we name the chromosomes prefexing > > with 'chr' as given in the test_range. > > > > But ensembl client seems to ignore the test_range and is making the request > > as shown below ( from http access log) > > > > /cgi-bin/das/01_Hs_GRCh37%7CASSOC_VARIANT/features?segment=1:114355433,114415381;maxbins=872 > > HTTP/1.1" 200 345 "-" "Ensembl/60" > > > > > > And as GBrowse server doesn't recognise the region (1:114355433,114415381), > > it doesn't return anything back. > > In cgi-bin/das script, approximately at around line 860, if I prefix the > > $reference with 'chr', it works. > > > > foreach (@segments) { > > my ($reference,$refclass,$start,$stop) = @$_; > > > > if($reference !~ /^chr/){ > > $reference = "chr".$reference; > > } > > > > > > We are not happy with this fix and wondering if it is a ensembl client issue > > or gbrowse server issue. > > > > Shouldn't ensembl make the right request figuring out the right url from > > 'test_range'? > > OR > > If GBrowse server has to handle it in a better way? > > > > Any directions would help. > > > > Many Thanks > > Prem > > _______________________________________________ > > DAS mailing list > > DAS at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/das > > From prem.apa at gmail.com Fri Jan 7 18:49:34 2011 From: prem.apa at gmail.com (Prem Anand) Date: Fri, 7 Jan 2011 18:49:34 +0000 Subject: [DAS] GBrowse as DAS server+Ensembl as DAS client In-Reply-To: <056AEDBF-6831-497D-A13A-43C0BD597D99@ebi.ac.uk> References: <2B36018B-91DD-4130-B91A-3BA28447A14D@ebi.ac.uk> <056AEDBF-6831-497D-A13A-43C0BD597D99@ebi.ac.uk> Message-ID: Thanks Andy. If there is no other alternative, then we will fix it on our side. Cheers Prem On Fri, Jan 7, 2011 at 6:21 PM, Andy Jenkinson wrote: > Hi Prem, > > The test range does not really provide enough information - it only > provides a single identifier, and does not help identify which of Ensembl's > sequences that refers to and so cannot be a generic solution. It's true that > Ensembl could make some assumptions and implement an ad-hoc solution for > this specific case (similar to the hack you have applied) but this would not > be compliant with the DAS specification and would be confusing for other DAS > clients. In the past we have found that supporting non-standard > functionality has been very confusing for others and is a major reason for > inconsistency of DAS implementation today. For that reason, I would suggest > that it is better to do the conversion in the server. I'm actually surprised > it does not do this already, as I seem to remember when Lincoln was working > on updating gbrowse for DAS 1.6 that things worked OK with Ensembl. > > Cheers, > Andy > > On 7 Jan 2011, at 17:56, Prem Anand wrote: > > > Thanks Andy, > > > > You are right about the compatibility issues. However, I thought the > clients could also handle this as for example, the ensembl client first > queries the server for /das/sources/, and as it already has all the > information it needs to make a das request properly from the 'test_range' > and other attributes, it can make the request suiting the server as well. > > > > Anyway, we have to see what gbrowse developers have to say. > > > > Cheers > > Prem > > > > > > On Fri, Jan 7, 2011 at 5:33 PM, Andy Jenkinson > wrote: > > Hi Prem, > > > > Each DAS coordinate system (e.g. GRCh_37 chromosomes) should always use > the same sequence names between all DAS servers. In fact, compatibility > between DAS servers is the primary reason for coordinate systems to exist. > This allows all clients and servers to be sure that if they use the same > coordinates then they can communicate with each other without having to know > anything about each particular client/server. In truth the difference > between the sequence names used by different genome browsers is a headache, > and the net result is that coordinates are effectively defined by whoever > uses them first (in this case being Ensembl). So, the GRCh37 coordinates use > names like 1, 2, 3, X, MT as defined by Ensembl's reference server. > > > > So gbrowse will need to detect this if it is to work properly, and also > report a test_range without the "chr" prefix. As an aside, I believe UCSC > (who also use the chrX format) do this conversion in their DAS server and > can handle both formats. > > > > Cheers, > > Andy > > > > On 7 Jan 2011, at 16:49, Prem Anand wrote: > > > > > Hi > > > > > > We are trying to set up our GBrowse as DAS server and were testing it > with > > > ensembl as client. > > > > > > We have the right metadata in the datasource.conf file. > > > > > > > > authority="GRCh" test_range="chr1:114356433..114414381" taxid="9606" > > > version="37" source="Chromosome">GRCh_37,Chromosome,Homo > > > sapiens > > > > > > The server responds for /cgi-bin/das/sources (also /cgi-bin/das/dsn) > well. > > > We also tried with different capabilities locally and it seems to be > fine. > > > > > > In all our GFF files/gbrowse databases we name the chromosomes > prefexing > > > with 'chr' as given in the test_range. > > > > > > But ensembl client seems to ignore the test_range and is making the > request > > > as shown below ( from http access log) > > > > > > > /cgi-bin/das/01_Hs_GRCh37%7CASSOC_VARIANT/features?segment=1:114355433,114415381;maxbins=872 > > > HTTP/1.1" 200 345 "-" "Ensembl/60" > > > > > > > > > And as GBrowse server doesn't recognise the region > (1:114355433,114415381), > > > it doesn't return anything back. > > > In cgi-bin/das script, approximately at around line 860, if I prefix > the > > > $reference with 'chr', it works. > > > > > > foreach (@segments) { > > > my ($reference,$refclass,$start,$stop) = @$_; > > > > > > if($reference !~ /^chr/){ > > > $reference = "chr".$reference; > > > } > > > > > > > > > We are not happy with this fix and wondering if it is a ensembl client > issue > > > or gbrowse server issue. > > > > > > Shouldn't ensembl make the right request figuring out the right url > from > > > 'test_range'? > > > OR > > > If GBrowse server has to handle it in a better way? > > > > > > Any directions would help. > > > > > > Many Thanks > > > Prem > > > _______________________________________________ > > > DAS mailing list > > > DAS at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/das > > > > > > From jw12 at sanger.ac.uk Tue Jan 18 10:25:46 2011 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Tue, 18 Jan 2011 10:25:46 +0000 Subject: [DAS] Registrations for DAS Workshop 2011 Message-ID: DAS is currently being used to share annotations on genomes, protein alignments, structural and interaction information. If you are interested in sharing biological information the DAS workshop below may be of interest to you. Registration is open for the 2011 DAS workshop (2,3,4th March) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.ebi.ac.uk//training/onsite/110302DAS.html and register via the web link at the bottom of the page. This workshop will cater for novice to expert DAS users as each day is optional. Please register early as places will be limited. Registration closes 18 February 2011 (17:00). If you are interested in giving a 15 minute talk on the second day please email Jonathan Warren using jonathan.warren at sanger.ac.uk Many thanks The Sanger/EBI DAS team. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From hk3 at sanger.ac.uk Wed Jan 19 10:45:17 2011 From: hk3 at sanger.ac.uk (Hashem Koohy) Date: Wed, 19 Jan 2011 10:45:17 +0000 Subject: [DAS] Histogram Stylesheet Message-ID: Dear DAS masters, I need to create a histogram stylesheet but I don?t know how to that. I have looked at: http://www.dasregistry.org/extension_stylesheet_histogram.jsp But there is only an output example of a histogram. I don?t see any documentation about how to do that or any template. I will really appreciate any help. Thanks Hashem -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From thomas.a.down at gmail.com Wed Jan 19 11:26:04 2011 From: thomas.a.down at gmail.com (Thomas Down) Date: Wed, 19 Jan 2011 11:26:04 +0000 Subject: [DAS] Histogram Stylesheet In-Reply-To: References: Message-ID: Hi Hashem, There are some examples in the new DAS/1.6 spec: http://www.biodas.org/documents/spec-1.6.html#glyphid Typical use is something like: 0 3 60 white black 2 Thomas. On Wed, Jan 19, 2011 at 10:45 AM, Hashem Koohy wrote: > Dear DAS masters, > I need to create a histogram stylesheet but I don?t know how to that. I > have > looked at: > http://www.dasregistry.org/extension_stylesheet_histogram.jsp > But there is only an output example of a histogram. I don?t see any > documentation about how to do that or any template. > I will really appreciate any help. > Thanks > Hashem > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > > > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das > From andy.jenkinson at ebi.ac.uk Wed Jan 19 11:26:11 2011 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Wed, 19 Jan 2011 11:26:11 +0000 Subject: [DAS] Histogram Stylesheet In-Reply-To: References: Message-ID: Hi Hashem, What kind of information are you looking for? The DAS 1.6 specification explains in more detail what the various stylesheet fields mean (type, category, glyphs etc), and has details of histograms: http://www.biodas.org/documents/spec-1.6.html#stylesheet http://www.biodas.org/documents/spec-1.6.html#glyphid Which server are you using? Since the stylesheet is a static document, for most servers you just construct it manually and tell the server where to find it. Cheers, Andy On 19 Jan 2011, at 10:45, Hashem Koohy wrote: > Dear DAS masters, > I need to create a histogram stylesheet but I don?t know how to that. I have > looked at: > http://www.dasregistry.org/extension_stylesheet_histogram.jsp > But there is only an output example of a histogram. I don?t see any > documentation about how to do that or any template. > I will really appreciate any help. > Thanks > Hashem > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > > > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das From thomas.a.down at gmail.com Thu Jan 20 10:02:05 2011 From: thomas.a.down at gmail.com (Thomas Down) Date: Thu, 20 Jan 2011 10:02:05 +0000 Subject: [DAS] New DAS client paper Message-ID: Bioinformatics has just published a new Application Note about DAS and the Dalliance genomic client: http://bioinformatics.oxfordjournals.org/content/early/2011/01/19/bioinformatics.btr020.abstract If you haven't tried Dalliance in the last month or two, major enhancements include better DAS/1.6 support and direct export of browser graphics (in SVG or PDF formats). We're also gearing up for a major new release, hopefully in the next month or so, with substantial performance and navigation improvements. If you've got any requests or suggestions, please drop me a line, or open a ticket on our Github page: https://github.com/dasmoth/dalliance Thomas Down. From andy.jenkinson at ebi.ac.uk Thu Jan 20 10:23:18 2011 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Thu, 20 Jan 2011 10:23:18 +0000 Subject: [DAS] New DAS client paper In-Reply-To: References: Message-ID: <37CE1614-54D0-4935-8D89-2603E03A4CA2@ebi.ac.uk> Good stuff Thomas! On 20 Jan 2011, at 10:02, Thomas Down wrote: > Bioinformatics has just published a new Application Note about DAS and the > Dalliance genomic client: > > > http://bioinformatics.oxfordjournals.org/content/early/2011/01/19/bioinformatics.btr020.abstract > > If you haven't tried Dalliance in the last month or two, major enhancements > include better DAS/1.6 support and direct export of browser graphics (in SVG > or PDF formats). We're also gearing up for a major new release, hopefully > in the next month or so, with substantial performance and navigation > improvements. If you've got any requests or suggestions, please drop me a > line, or open a ticket on our Github page: > > https://github.com/dasmoth/dalliance > > Thomas Down. > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das From jw12 at sanger.ac.uk Mon Jan 31 16:18:34 2011 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 31 Jan 2011 16:18:34 +0000 Subject: [DAS] Workshop Discussions Message-ID: <524D5A98-7356-443D-97A7-0EDF3A963542@sanger.ac.uk> Hi All This years DAS workshop is not far away now (less than 5 weeks away, deadline for registrations 18th Feb). If you haven't registered and would like to come - please do so here: http://www.ebi.ac.uk//training/onsite/110302DAS.html There is also a preliminary schedule up here: http://www.biodas.org/wiki/DASWorkshop2011 For Day 2 presentations we now have at least half of a days talks. Thanks to those who have volunteered already. If you have new software or made updates to software that uses DAS extensively, please volunteer to give a short talk? Whether you are attending or not, it would be good to get suggestions from the community as to what should be discussed on Day 3. There is a place on the wiki for suggestions: http://www.biodas.org/wiki/DASWorkshop2011#Suggested_Topics please add any suggestions you have and if you feel comfortable add your name next to your suggestion. My guess is that topics will arise during the workshop, but it is helpful to get an idea of peoples hopes/ joys/concerns about the DAS project beforehand. Thanks in advance, looking forward to seeing many of you in a few weeks. Jonathan. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.