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From: Евгесш Ж. <jor...@gm...> - 2020-07-10 18:50:41
|
Get Outlook for Android<https://aka.ms/ghei36> |
From: Scott C. <sc...@sc...> - 2020-07-08 17:19:52
|
Hi Jessica, This is the mailing list for people who install and maintain GBrowse instances, and so we generally don't know anything about the individual instances. The best I can suggest is that you try email in the contact email on that page, ga...@mp.... Good luck, Scott On Wed, Jul 8, 2020 at 9:42 AM Jessica Pietsch <jes...@un...> wrote: > Dear Sir or Madam, > > using the * Cardamine hirsuta* GBrowse website ( > https://gbrowse.mpipz.mpg.de/cgi-bin/gbrowse/chi1_public/) I faced the > problem that none of the gene identifier I have tried out was found. I > tried various genes and landmarks but nothing worked out. Could you advice > me what to do, e.g for CARHR242510 (*TIP41*)? > > Many thanks in advance and kind regards, > Jessica Pietsch > > > Ph.D. candidate > AG Hülskamp > Biocenter - University of Cologne > Zülpicher Straße 47b > 50674 Cologne > Germany > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Jessica P. <jes...@un...> - 2020-07-06 11:55:49
|
Dear Sir or Madam, using the /Cardamine hirsuta/ GBrowse website (https://gbrowse.mpipz.mpg.de/cgi-bin/gbrowse/chi1_public/) I faced the problem that none of the gene identifier I have tried out was found. I tried various genes and landmarks but nothing worked out. Could you advice me what to do, e.g for CARHR242510 (/TIP41/)? Many thanks in advance and kind regards, Jessica Pietsch Ph.D. candidate AG Hülskamp Biocenter - University of Cologne Zülpicher Straße 47b 50674 Cologne Germany |
From: Tapia, A. C. <and...@uk...> - 2020-05-22 09:29:05
|
Hello Scott, I tried out the 2005 feat_remapping function a few weeks ago, and, with a few minor changes, it seemed to be working. However, up until about a week ago, I was still getting the same error I saw with my own feat_remapping function when searching for features—e.g. 'Can't locate object method "method" via package "gene" (perhaps you forgot to load "gene"?)' at Feature.pm:702 (https://metacpan.org/source/SCAIN/Bio-DB-Das-Chado-0.35a/lib/Bio/DB/Das/Chado/Segment/Feature.pm#L702). I eventually found that an instance of Bio::DB::Das::Chado::Segment::Feature was being constructed with a string as its type at Chado.pm:1674 (https://metacpan.org/source/SCAIN/Bio-DB-Das-Chado-0.35a/lib/Bio/DB/Das/Chado.pm#L1674); it seems that an instance of Bio::DB::GFF::Typename is expected instead. I changed Chado.pm to use $type_obj, which is created immediately before the Feature is constructed on line 1674, as the type instead, and this seemed to fix the problem. I am guessing that this is a bug since this $type_obj is not used elsewhere in the code—should I submit this as an issue on GitHub? This change to Chado.pm seemed to resolve the remaining issues I was having with the Chado adaptor. GBrowse seems to be finding all the features in Chado, and it seems to be rendering them correctly. However, I am now struggling with another (presumably unrelated) issue; navigation is very slow in GBrowse. For example, when searching for a feature in the "Landmark or Region" search box, it takes roughly five minutes to display the results. Interestingly, I've found that I can get the response text from the HTTP request made when navigating almost immediately. It seems that the connection remains open unnecessarily for about five minutes after the data is sent. >From what I can tell, it seems that one of the processes spawned when handling navigation times out because the sleep on line 1647 of RenderPanels.pm (https://github.com/GMOD/GBrowse/blob/release-2.56/lib/Bio/Graphics/Browser2/RenderPanels.pm#L1647) is never interrupted. It looks like Apache is responsible for the timeout. Changing the Timeout in the server config changes the amount of time that GBrowse takes to navigate. My understanding of the code on line 1647 of RenderPanels.pm is that the parent process should sleep until it has received SIGALRM signals from each of its child rendering processes. However, it seems that the sleeps are never interrupted, despite the fact that the child processes call alarm(0) on line 1628. It also seems as though SIGCHLD signals are not being handled by the parent process. I know the child processes are exiting successfully, but I can't see "reaped render child" anywhere in the logs. I don't know if it will be relevant, but I'm running GBrowse 2.56 on Ubuntu 18.04 with Perl 5.26 and Apache 2.4.29. I'm not sure what else I can try to determine the cause of this issue and resolve it. Do you have any suggestions? Thanks, Andrew Tapia ________________________________ From: Scott Cain <sc...@sc...> Sent: Friday, April 24, 2020 6:58 PM To: Tapia, Andrew C. <and...@uk...> Cc: gmo...@li... <gmo...@li...> Subject: Re: [Gmod-gbrowse] Issues using -recursivMapping with Bio::DB::Das::Chado adaptor CAUTION: External Sender Hi Andrew, Usually when people send an email to this mailing list, my first response is "are you sure you want to use GBrowse for this?" because generally, JBrowse is better because it's newer and shinier, but in this case, GBrowse is the only tool that I know of that can do this sort of recursive remapping that I'm aware of. Anyway, the functions you need seem to have not made it into Chado releases, but I did manage to find them in an email thread between Cyril Pommier and me from 2005(!). Cyril wrote these functions, and I think it is likely that they work, but it's possible they'll need some massaging. Please let me know if these work for you--I can make sure these functions make it into the next release of Chado. Thanks, Scott CREATE OR REPLACE FUNCTION recurs_featureslice (int, int) RETURNS setof featureloc AS 'SELECT -1, secondSeq.feature_id as feature_id, ref_seq.srcfeature_id as srcfeature_id, (secondSeq.fmin + ref_seq.fmin ) as fmin, secondSeq.is_fmin_partial as is_fmin_partial, (secondSeq.fmax + ref_seq.fmin )as fmax, secondSeq.is_fmax_partial as is_fmax_partial, (secondSeq.strand * ref_seq.strand) as strand, secondSeq.phase as phase, secondSeq.residue_info as residue_info, secondSeq.locgroup as locgroup, secondSeq.rank as rank FROM featureloc ref_seq, featureloc secondSeq WHERE ref_seq.feature_id=secondSeq.srcfeature_id AND boxquery($1, $2) @ boxrange(ref_seq.fmin,ref_seq.fmax) AND boxquery($1-ref_seq.fmin +1, $2-ref_seq.fmin +1) @ boxrange(secondSeq.fmin,secondSeq.fmax)' LANGUAGE 'sql'; and CREATE OR REPLACE FUNCTION feat_remapping (int) RETURNS setof featureloc AS 'SELECT -1, secondSeq.feature_id as feature_id, ref_seq.srcfeature_id as srcfeature_id, (secondSeq.fmin + ref_seq.fmin ) as fmin, secondSeq.is_fmin_partial as is_fmin_partial, (secondSeq.fmax + ref_seq.fmin )as fmax, secondSeq.is_fmax_partial as is_fmax_partial, (secondSeq.strand * ref_seq.strand) as strand, secondSeq.phase as phase, secondSeq.residue_info as residue_info, secondSeq.locgroup as locgroup, secondSeq.rank as rank FROM featureloc ref_seq, featureloc secondSeq WHERE ref_seq.feature_id=secondSeq.srcfeature_id AND secondSeq.feature_id=$1 AND ref_seq.feature_id=(select distinct srcfeature_id from featureloc where feature_id=$1 and rank=0)' LANGUAGE 'sql'; On Fri, Apr 24, 2020 at 1:47 PM Tapia, Andrew C. <and...@uk...<mailto:and...@uk...>> wrote: Hello, I recently migrated part of an old database to Chado, and I have been having some difficulty getting the Bio::DB::Das::Chado adaptor to work. Right now, in my featureloc table, I have contigs located relative to supercontigs (my lowest refseqs), and all other features located relative to the contigs. When I first configured GBrowse to work with Chado, I found that only the contigs were showing up in GBrowse. I eventually realized that, by default, the Bio::DB::Das::Chado adaptor expects that all features are located relative to the reference class--i.e., the supercontigs. This finally led me to the -recursivMapping argument to the adaptor, which I believed would fix the problem. However, when I enabled this option, I found that the adaptor was seemingly no longer able to find features located on the relative to the contigs; searching with the name of such a feature would produce a "Not Found" error. I believed this was caused by a missing SQL function, "feat_remapping," which is evidently used by the adaptor when the -recursivMapping argument is provided. From looking at the code for the adaptor, I also found that -recursivMapping should enable using a missing function "recurs_featureslice" in place of featureslice, though this doesn't seem to matter since the adaptor is apparently using featureloc_slice instead of featureslice. I eventually tried writing my own feat_remapping function and a "recurs_featureloc_slice" function, and although I no longer see the "Not Found" error, I am now getting some other errors that I haven't had the chance to investigate yet. I am wondering, however, if I am going about this the right way. Should I be using -recursivMapping, or should I try something else? Thanks, Andrew Tapia _______________________________________________ Gmod-gbrowse mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-gbrowse&data=02%7C01%7Candrew.tapia%40uky.edu%7Cbcdddb3248354676242108d7e8a31a40%7C2b30530b69b64457b818481cb53d42ae%7C0%7C0%7C637233659538674903&sdata=onNbkQj3Ype0rTwgYlleCuw91uUCvt6dMv%2BZE4SJ1Lg%3D&reserved=0> -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=02%7C01%7Candrew.tapia%40uky.edu%7Cbcdddb3248354676242108d7e8a31a40%7C2b30530b69b64457b818481cb53d42ae%7C0%7C0%7C637233659538674903&sdata=9tX4SRt4nrshe4RIbPi0rMfF2KItC2UieSKvrN6vJEk%3D&reserved=0>) 216-392-3087 Ontario Institute for Cancer Research |
From: Erick A. <eri...@gm...> - 2020-05-07 15:33:12
|
(apologies for cross-posting) Dear colleague, I am looking for a postdoc with the following profile: * PhD in computer sciences, bioinformatics, computational biology or similar * Experience in semantic web technologies and standards, e.g. RDF, SPARQL, SKOS (a must) * Experience in developing visualisation interfaces for RDF graphs/repositories (a must) * Exposure to bio-ontologies (desired) * Strong ability to understand user requirements and to structure and simplify complex tasks and ability to contribute in an international and dynamic research and development team * Fluent in English, both written and spoken Contract: from 1st of July till end 2020 – with a possibility for extension Location: Bayer CropScience, Monheim (Germany) + remote (due to COVID-19) Salary: competitive If you are interested, don't hesitate in contacting me. Best regards, Erick Antezana |
From: Scott C. <sc...@sc...> - 2020-04-24 22:59:23
|
Hi Andrew, Usually when people send an email to this mailing list, my first response is "are you sure you want to use GBrowse for this?" because generally, JBrowse is better because it's newer and shinier, but in this case, GBrowse is the only tool that I know of that can do this sort of recursive remapping that I'm aware of. Anyway, the functions you need seem to have not made it into Chado releases, but I did manage to find them in an email thread between Cyril Pommier and me from 2005(!). Cyril wrote these functions, and I think it is likely that they work, but it's possible they'll need some massaging. Please let me know if these work for you--I can make sure these functions make it into the next release of Chado. Thanks, Scott CREATE OR REPLACE FUNCTION recurs_featureslice (int, int) RETURNS setof featureloc AS 'SELECT -1, secondSeq.feature_id as feature_id, ref_seq.srcfeature_id as srcfeature_id, (secondSeq.fmin + ref_seq.fmin ) as fmin, secondSeq.is_fmin_partial as is_fmin_partial, (secondSeq.fmax + ref_seq.fmin )as fmax, secondSeq.is_fmax_partial as is_fmax_partial, (secondSeq.strand * ref_seq.strand) as strand, secondSeq.phase as phase, secondSeq.residue_info as residue_info, secondSeq.locgroup as locgroup, secondSeq.rank as rank FROM featureloc ref_seq, featureloc secondSeq WHERE ref_seq.feature_id=secondSeq.srcfeature_id AND boxquery($1, $2) @ boxrange(ref_seq.fmin,ref_seq.fmax) AND boxquery($1-ref_seq.fmin +1, $2-ref_seq.fmin +1) @ boxrange(secondSeq.fmin,secondSeq.fmax)' LANGUAGE 'sql'; and CREATE OR REPLACE FUNCTION feat_remapping (int) RETURNS setof featureloc AS 'SELECT -1, secondSeq.feature_id as feature_id, ref_seq.srcfeature_id as srcfeature_id, (secondSeq.fmin + ref_seq.fmin ) as fmin, secondSeq.is_fmin_partial as is_fmin_partial, (secondSeq.fmax + ref_seq.fmin )as fmax, secondSeq.is_fmax_partial as is_fmax_partial, (secondSeq.strand * ref_seq.strand) as strand, secondSeq.phase as phase, secondSeq.residue_info as residue_info, secondSeq.locgroup as locgroup, secondSeq.rank as rank FROM featureloc ref_seq, featureloc secondSeq WHERE ref_seq.feature_id=secondSeq.srcfeature_id AND secondSeq.feature_id=$1 AND ref_seq.feature_id=(select distinct srcfeature_id from featureloc where feature_id=$1 and rank=0)' LANGUAGE 'sql'; On Fri, Apr 24, 2020 at 1:47 PM Tapia, Andrew C. <and...@uk...> wrote: > Hello, > > I recently migrated part of an old database to Chado, and I have been > having some difficulty getting the Bio::DB::Das::Chado adaptor to work. > > Right now, in my featureloc table, I have contigs located relative to > supercontigs (my lowest refseqs), and all other features located relative > to the contigs. When I first configured GBrowse to work with Chado, I found > that only the contigs were showing up in GBrowse. > > I eventually realized that, by default, the Bio::DB::Das::Chado adaptor > expects that all features are located relative to the reference > class--i.e., the supercontigs. This finally led me to the -recursivMapping > argument to the adaptor, which I believed would fix the problem. However, > when I enabled this option, I found that the adaptor was seemingly no > longer able to find features located on the relative to the contigs; > searching with the name of such a feature would produce a "Not Found" error. > > I believed this was caused by a missing SQL function, "feat_remapping," > which is evidently used by the adaptor when the -recursivMapping argument > is provided. From looking at the code for the adaptor, I also found that > -recursivMapping should enable using a missing function > "recurs_featureslice" in place of featureslice, though this doesn't seem to > matter since the adaptor is apparently using featureloc_slice instead of > featureslice. > > I eventually tried writing my own feat_remapping function and a > "recurs_featureloc_slice" function, and although I no longer see the "Not > Found" error, I am now getting some other errors that I haven't had the > chance to investigate yet. I am wondering, however, if I am going about > this the right way. Should I be using -recursivMapping, or should I try > something else? > > Thanks, > > Andrew Tapia > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Tapia, A. C. <and...@uk...> - 2020-04-24 20:47:50
|
Hello, I recently migrated part of an old database to Chado, and I have been having some difficulty getting the Bio::DB::Das::Chado adaptor to work. Right now, in my featureloc table, I have contigs located relative to supercontigs (my lowest refseqs), and all other features located relative to the contigs. When I first configured GBrowse to work with Chado, I found that only the contigs were showing up in GBrowse. I eventually realized that, by default, the Bio::DB::Das::Chado adaptor expects that all features are located relative to the reference class--i.e., the supercontigs. This finally led me to the -recursivMapping argument to the adaptor, which I believed would fix the problem. However, when I enabled this option, I found that the adaptor was seemingly no longer able to find features located on the relative to the contigs; searching with the name of such a feature would produce a "Not Found" error. I believed this was caused by a missing SQL function, "feat_remapping," which is evidently used by the adaptor when the -recursivMapping argument is provided. From looking at the code for the adaptor, I also found that -recursivMapping should enable using a missing function "recurs_featureslice" in place of featureslice, though this doesn't seem to matter since the adaptor is apparently using featureloc_slice instead of featureslice. I eventually tried writing my own feat_remapping function and a "recurs_featureloc_slice" function, and although I no longer see the "Not Found" error, I am now getting some other errors that I haven't had the chance to investigate yet. I am wondering, however, if I am going about this the right way. Should I be using -recursivMapping, or should I try something else? Thanks, Andrew Tapia |
From: Scott C. <sc...@sc...> - 2020-03-17 22:01:34
|
Hi Nihal, It looks to me like Augustus isn't quite getting the GFF right: the exons and CDS features should not share the same ID, which is probably causing problems in the database, and thus is causing problems when you dump out that region. To fix it, I would be inclined to just remove all of the ID entries for those features; they really only need the Parent attributes most of the time (and certainly in this case). If that doesn't fix the problem, please also send the section of the configure file for this track too. Also, I imagine this is the case, but make sure that those nine columns are tab-delimited. Scott On Tue, Mar 17, 2020 at 2:41 PM Nihal Reddy Gade <ng...@ma...> wrote: > Good afternoon Scott, > > Below is the actual part of gff3 file. > > chr_002 AUGUSTUS gene 219153 221066 1 + . > ID=g10554;Name=TTHERM_00310240;Note="MOZ/SAS family protein" > chr_002 AUGUSTUS mRNA 219153 221066 . + . ID=g10554.t1;Parent=g10554 > chr_002 AUGUSTUS CDS 219153 219336 . + 0 ID=g10554.t1.cds;Parent=g10554.t1 > chr_002 AUGUSTUS exon 219153 219336 . + 0 ID=g10554.t1.cds;Parent=g10554.t1 > chr_002 AUGUSTUS CDS 219447 219489 . + 2 ID=g10554.t1.cds;Parent=g10554.t1 > chr_002 AUGUSTUS exon 219447 219489 . + 2 ID=g10554.t1.cds;Parent=g10554.t1 > chr_002 AUGUSTUS CDS 219749 221066 . + 1 ID=g10554.t1.cds;Parent=g10554.t1 > chr_002 AUGUSTUS exon 219749 221066 . + 1 ID=g10554.t1.cds;Parent=g10554.t1 > > But when I uploaded it to gbrowse mysql database using > bp_seqfeature_load.pl script and loaded my webpage for the above stanza I > am getting the below code which I mailed you earlier as well in jpg format. > > ##sequence-region chr_002:219153..221066 > chr_002 AUGUSTUS gene 219153 221066 1 + . > Name=TTHERM_00310240;ID=1725;Note=%22MOZ%2FSAS%20family%20protein%22 > chr_002 AUGUSTUS mRNA 219153 221066 . + . Parent=1725;ID=1726 > chr_002 AUGUSTUS exon 219153 221066 . + 0 Parent=1726;ID=1728 > chr_002 AUGUSTUS exon 219153 219336 . + 0 > chr_002 AUGUSTUS CDS 219447 219489 . + 2 > chr_002 AUGUSTUS exon 219447 219489 . + 2 > chr_002 AUGUSTUS CDS 219749 221066 . + 1 > chr_002 AUGUSTUS exon 219749 221066 . + 1 > > So, Is there anything I am missing in script or config files? > > Thanks and regards > Nihal > > On Tue, Mar 17, 2020 at 4:29 PM Nihal Reddy Gade <ng...@ma...> > wrote: > >> Good afternoon Scott, >> >> Thank you for the information. I will try adding that details in gff3 and >> load it again. >> >> >> Nihal. >> >> >> On Tue, Mar 17, 2020, 4:24 PM Scott Cain <sc...@sc...> wrote: >> >>> (cc'ing the GBrowse list back in). >>> >>> Hi Nihal, >>> >>> All of the exon and CDS lines should have "Parent=1726" in them to >>> indicate what they belong to (which is the mRNA, because of the "ID=1726". >>> If you provide that, it should show the exon/intron structure. >>> >>> Scott >>> >>> >>> On Tue, Mar 17, 2020 at 10:21 AM Nihal Reddy Gade < >>> ng...@ma...> wrote: >>> >>>> Good afternoon Scott, >>>> >>>> Sure, I am attaching you the pictures of those. >>>> >>>> Do you also need the data from config file? However they are populated >>>> in track configuration section(select tracks). >>>> >>>> >>>> >>>> Thanks and regards >>>> Nihal. >>>> >>>> On Tue, Mar 17, 2020 at 12:07 PM Scott Cain <sc...@sc...> >>>> wrote: >>>> >>>>> Hi Nihal, >>>>> >>>>> Can you please send us an example of what the GFF for the track looks >>>>> like and what the track configuration looks like? >>>>> >>>>> Thanks, >>>>> Scott >>>>> >>>>> On Tue, Mar 17, 2020 at 10:04 AM Nihal Reddy Gade via Gmod-gbrowse < >>>>> gmo...@li...> wrote: >>>>> >>>>>> Good evening Team, >>>>>> >>>>>> I am working on a project where I uploaded GBrowse mysql database >>>>>> with gff3 file. >>>>>> >>>>>> My particular configuration file is done properly as of my knowledge. >>>>>> Still I am unable to see introns in my gene prediction as shown in attached >>>>>> image. >>>>>> >>>>>> Is there any issue with my configuration file or did i miss >>>>>> something? Kindly help me in this regard. >>>>>> >>>>>> Thanks in advance >>>>>> Nihal Reddy Gade. >>>>>> _______________________________________________ >>>>>> Gmod-gbrowse mailing list >>>>>> Gmo...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> ------------------------------------------------------------------------ >>>>> Scott Cain, Ph. D. scott at >>>>> scottcain dot net >>>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>>> Ontario Institute for Cancer Research >>>>> >>>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at scottcain >>> dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> >> -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Nihal R. G. <ng...@ma...> - 2020-03-17 21:41:35
|
Good afternoon Scott, Below is the actual part of gff3 file. chr_002 AUGUSTUS gene 219153 221066 1 + . ID=g10554;Name=TTHERM_00310240;Note="MOZ/SAS family protein" chr_002 AUGUSTUS mRNA 219153 221066 . + . ID=g10554.t1;Parent=g10554 chr_002 AUGUSTUS CDS 219153 219336 . + 0 ID=g10554.t1.cds;Parent=g10554.t1 chr_002 AUGUSTUS exon 219153 219336 . + 0 ID=g10554.t1.cds;Parent=g10554.t1 chr_002 AUGUSTUS CDS 219447 219489 . + 2 ID=g10554.t1.cds;Parent=g10554.t1 chr_002 AUGUSTUS exon 219447 219489 . + 2 ID=g10554.t1.cds;Parent=g10554.t1 chr_002 AUGUSTUS CDS 219749 221066 . + 1 ID=g10554.t1.cds;Parent=g10554.t1 chr_002 AUGUSTUS exon 219749 221066 . + 1 ID=g10554.t1.cds;Parent=g10554.t1 But when I uploaded it to gbrowse mysql database using bp_seqfeature_load.pl script and loaded my webpage for the above stanza I am getting the below code which I mailed you earlier as well in jpg format. ##sequence-region chr_002:219153..221066 chr_002 AUGUSTUS gene 219153 221066 1 + . Name=TTHERM_00310240;ID=1725;Note=%22MOZ%2FSAS%20family%20protein%22 chr_002 AUGUSTUS mRNA 219153 221066 . + . Parent=1725;ID=1726 chr_002 AUGUSTUS exon 219153 221066 . + 0 Parent=1726;ID=1728 chr_002 AUGUSTUS exon 219153 219336 . + 0 chr_002 AUGUSTUS CDS 219447 219489 . + 2 chr_002 AUGUSTUS exon 219447 219489 . + 2 chr_002 AUGUSTUS CDS 219749 221066 . + 1 chr_002 AUGUSTUS exon 219749 221066 . + 1 So, Is there anything I am missing in script or config files? Thanks and regards Nihal On Tue, Mar 17, 2020 at 4:29 PM Nihal Reddy Gade <ng...@ma...> wrote: > Good afternoon Scott, > > Thank you for the information. I will try adding that details in gff3 and > load it again. > > > Nihal. > > > On Tue, Mar 17, 2020, 4:24 PM Scott Cain <sc...@sc...> wrote: > >> (cc'ing the GBrowse list back in). >> >> Hi Nihal, >> >> All of the exon and CDS lines should have "Parent=1726" in them to >> indicate what they belong to (which is the mRNA, because of the "ID=1726". >> If you provide that, it should show the exon/intron structure. >> >> Scott >> >> >> On Tue, Mar 17, 2020 at 10:21 AM Nihal Reddy Gade <ng...@ma...> >> wrote: >> >>> Good afternoon Scott, >>> >>> Sure, I am attaching you the pictures of those. >>> >>> Do you also need the data from config file? However they are populated >>> in track configuration section(select tracks). >>> >>> >>> >>> Thanks and regards >>> Nihal. >>> >>> On Tue, Mar 17, 2020 at 12:07 PM Scott Cain <sc...@sc...> wrote: >>> >>>> Hi Nihal, >>>> >>>> Can you please send us an example of what the GFF for the track looks >>>> like and what the track configuration looks like? >>>> >>>> Thanks, >>>> Scott >>>> >>>> On Tue, Mar 17, 2020 at 10:04 AM Nihal Reddy Gade via Gmod-gbrowse < >>>> gmo...@li...> wrote: >>>> >>>>> Good evening Team, >>>>> >>>>> I am working on a project where I uploaded GBrowse mysql database with >>>>> gff3 file. >>>>> >>>>> My particular configuration file is done properly as of my knowledge. >>>>> Still I am unable to see introns in my gene prediction as shown in attached >>>>> image. >>>>> >>>>> Is there any issue with my configuration file or did i miss something? >>>>> Kindly help me in this regard. >>>>> >>>>> Thanks in advance >>>>> Nihal Reddy Gade. >>>>> _______________________________________________ >>>>> Gmod-gbrowse mailing list >>>>> Gmo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>> >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain >>>> dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> >>> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> > |
From: Nihal R. G. <ng...@ma...> - 2020-03-17 21:30:13
|
Good afternoon Scott, Thank you for the information. I will try adding that details in gff3 and load it again. Nihal. On Tue, Mar 17, 2020, 4:24 PM Scott Cain <sc...@sc...> wrote: > (cc'ing the GBrowse list back in). > > Hi Nihal, > > All of the exon and CDS lines should have "Parent=1726" in them to > indicate what they belong to (which is the mRNA, because of the "ID=1726". > If you provide that, it should show the exon/intron structure. > > Scott > > > On Tue, Mar 17, 2020 at 10:21 AM Nihal Reddy Gade <ng...@ma...> > wrote: > >> Good afternoon Scott, >> >> Sure, I am attaching you the pictures of those. >> >> Do you also need the data from config file? However they are populated in >> track configuration section(select tracks). >> >> >> >> Thanks and regards >> Nihal. >> >> On Tue, Mar 17, 2020 at 12:07 PM Scott Cain <sc...@sc...> wrote: >> >>> Hi Nihal, >>> >>> Can you please send us an example of what the GFF for the track looks >>> like and what the track configuration looks like? >>> >>> Thanks, >>> Scott >>> >>> On Tue, Mar 17, 2020 at 10:04 AM Nihal Reddy Gade via Gmod-gbrowse < >>> gmo...@li...> wrote: >>> >>>> Good evening Team, >>>> >>>> I am working on a project where I uploaded GBrowse mysql database with >>>> gff3 file. >>>> >>>> My particular configuration file is done properly as of my knowledge. >>>> Still I am unable to see introns in my gene prediction as shown in attached >>>> image. >>>> >>>> Is there any issue with my configuration file or did i miss something? >>>> Kindly help me in this regard. >>>> >>>> Thanks in advance >>>> Nihal Reddy Gade. >>>> _______________________________________________ >>>> Gmod-gbrowse mailing list >>>> Gmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at scottcain >>> dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> >> > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > |
From: Scott C. <sc...@sc...> - 2020-03-17 21:24:19
|
(cc'ing the GBrowse list back in). Hi Nihal, All of the exon and CDS lines should have "Parent=1726" in them to indicate what they belong to (which is the mRNA, because of the "ID=1726". If you provide that, it should show the exon/intron structure. Scott On Tue, Mar 17, 2020 at 10:21 AM Nihal Reddy Gade <ng...@ma...> wrote: > Good afternoon Scott, > > Sure, I am attaching you the pictures of those. > > Do you also need the data from config file? However they are populated in > track configuration section(select tracks). > > > > Thanks and regards > Nihal. > > On Tue, Mar 17, 2020 at 12:07 PM Scott Cain <sc...@sc...> wrote: > >> Hi Nihal, >> >> Can you please send us an example of what the GFF for the track looks >> like and what the track configuration looks like? >> >> Thanks, >> Scott >> >> On Tue, Mar 17, 2020 at 10:04 AM Nihal Reddy Gade via Gmod-gbrowse < >> gmo...@li...> wrote: >> >>> Good evening Team, >>> >>> I am working on a project where I uploaded GBrowse mysql database with >>> gff3 file. >>> >>> My particular configuration file is done properly as of my knowledge. >>> Still I am unable to see introns in my gene prediction as shown in attached >>> image. >>> >>> Is there any issue with my configuration file or did i miss something? >>> Kindly help me in this regard. >>> >>> Thanks in advance >>> Nihal Reddy Gade. >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Scott C. <sc...@sc...> - 2020-03-17 17:13:50
|
Hi Nihal, Can you please send us an example of what the GFF for the track looks like and what the track configuration looks like? Thanks, Scott On Tue, Mar 17, 2020 at 10:04 AM Nihal Reddy Gade via Gmod-gbrowse < gmo...@li...> wrote: > Good evening Team, > > I am working on a project where I uploaded GBrowse mysql database with > gff3 file. > > My particular configuration file is done properly as of my knowledge. > Still I am unable to see introns in my gene prediction as shown in attached > image. > > Is there any issue with my configuration file or did i miss something? > Kindly help me in this regard. > > Thanks in advance > Nihal Reddy Gade. > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Nihal R. G. <ng...@ma...> - 2020-03-17 05:03:37
|
Good evening Team, I am working on a project where I uploaded GBrowse mysql database with gff3 file. My particular configuration file is done properly as of my knowledge. Still I am unable to see introns in my gene prediction as shown in attached image. Is there any issue with my configuration file or did i miss something? Kindly help me in this regard. Thanks in advance Nihal Reddy Gade. |
From: Vaneet L. <van...@uc...> - 2020-03-05 18:22:48
|
Hello, I'm diving back into GBrowse as we're still keeping it active for our Xenbase users. What I'm wondering is does GBrowse have any way to display implied UTRs as part of a special glyph perhaps? I am using the gene glyph since many of the gene models in my GFF3 have alternate transcripts attached to the same gene. I know JBrowse has a setting for implied UTRs but I just wonder if there was a way to deal with this in GBrowse. I saw an old forum post on this topic from 2001 but I'm not sure if a solution was ever proposed or found beyond actually generating UTRs in the GFF3 file from the implied ones somehow manually. Thanks, Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building - University of Calgary 2500 University Drive NW Calgary, AB T2N 1N4 CANADA |
From: Scott C. <sc...@sc...> - 2020-02-21 02:16:33
|
Hello, I am very pleased to announce that GMOD in conjunction with Reactome, Galaxy and OICR/WormBase, together forming Open Genome Informatics, has been accepted for the Google Summer of Code. If you or someone you know might be a student interested in participating in GSoC, please take a look at http://gmod.org/wiki/GSOC_Project_Ideas_2020 where there are proposed projects that cover a fair number of technologies. Official proposals from students will be due in mid March (more on that later). But WAIT! There's more: if you might be interested in being a mentor and working with a student this summer, it's not too late! You can add new project ideas to the page above (contact me if you need an account), or you can even volunteer to add yourself to one of the existing ideas as a potential mentor. Please feel free to forward this to other mailing lists or people who might be interested. We are already an eclectic, dispersed group, so everyone is welcome. Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Nihal R. G. <ng...@ma...> - 2020-01-27 22:37:20
|
Good afternoon Scott, There are few reasons, firstly our websites use both GBrowse and JBrowse. We use GBrowse because it is helping our professors to get the data they need from perticular segments. I dont know exactly which data they need but both GBrowse and JBrowse has benefits for us, thats what i can say . It is pleasure working with these GMOD projects. I started working on this for the past 3 months. I found my mistake today and now everything is working fine. Thanks for your response. Also i am glad that i joined the mailing list today. I will be working on this in future as well. Hope I will get few more doubts as its a fresh start and I will post them for help. Thanks and Regards Nihal Reddy Gade Master of Science (Computer Science) Graduate Assistant Bradley University. On Mon, Jan 27, 2020, 3:27 PM Scott Cain <sc...@sc...> wrote: > Hi Nihal, > > I will certainly do everything I can to help you with GBrowse, but first I > have to ask: is there a reason you don't want to use JBrowse ( > http://jbrowse.org/) ? GBrowse is a work horse, but it has been only > minimally maintained for the last several years, where JBrowse (also a GMOD > project) is actively maintained and has a large developer and user > community. > > Scott > > > On Mon, Jan 27, 2020 at 1:05 PM Nihalreddy Gade < > gad...@gm...> wrote: > >> Good morning Team, >> >> I have new gff3 file and fasta file with me, i have followed all the >> steps mentioned in file:///opt/gbrowse/htdocs/tutorial/tutorial.html. How >> ever the data is not very small like volvox but still i used in memory >> adaptor. i have tried it with berkeley db as well it is not giving me the >> actual result. I have added all the config files and gff3 files in exact >> locations. Could you please help me what i am missing . I am getting the >> output as the result not found as shown in the attached picture. >> >> Please do let me know what i might be missing. >> >> Thanks and regards >> Nihal >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > |
From: Scott C. <sc...@sc...> - 2020-01-27 21:47:48
|
Great, glad to hear it's working. I'm in a similar boat: I support both JBrowse and GBrowse for WormBase :-) Good luck going forward, Scott On Mon, Jan 27, 2020 at 1:38 PM Nihal Reddy Gade <ng...@ma...> wrote: > Good afternoon Scott, > > There are few reasons, firstly our websites use both GBrowse and JBrowse. > We use GBrowse because it is helping our professors to get the data they > need from perticular segments. I dont know exactly which data they need but > both GBrowse and JBrowse has benefits for us, thats what i can say . > > It is pleasure working with these GMOD projects. I started working on this > for the past 3 months. I found my mistake today and now everything is > working fine. Thanks for your response. Also i am glad that i joined the > mailing list today. I will be working on this in future as well. Hope I > will get few more doubts as its a fresh start and I will post them for help. > > > Thanks and Regards > Nihal Reddy Gade > Master of Science (Computer Science) > Graduate Assistant > Bradley University. > > > On Mon, Jan 27, 2020, 3:27 PM Scott Cain <sc...@sc...> wrote: > >> Hi Nihal, >> >> I will certainly do everything I can to help you with GBrowse, but first >> I have to ask: is there a reason you don't want to use JBrowse ( >> http://jbrowse.org/) ? GBrowse is a work horse, but it has been only >> minimally maintained for the last several years, where JBrowse (also a GMOD >> project) is actively maintained and has a large developer and user >> community. >> >> Scott >> >> >> On Mon, Jan 27, 2020 at 1:05 PM Nihalreddy Gade < >> gad...@gm...> wrote: >> >>> Good morning Team, >>> >>> I have new gff3 file and fasta file with me, i have followed all the >>> steps mentioned in file:///opt/gbrowse/htdocs/tutorial/tutorial.html. How >>> ever the data is not very small like volvox but still i used in memory >>> adaptor. i have tried it with berkeley db as well it is not giving me the >>> actual result. I have added all the config files and gff3 files in exact >>> locations. Could you please help me what i am missing . I am getting the >>> output as the result not found as shown in the attached picture. >>> >>> Please do let me know what i might be missing. >>> >>> Thanks and regards >>> Nihal >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Scott C. <sc...@sc...> - 2020-01-27 21:27:45
|
Hi Nihal, I will certainly do everything I can to help you with GBrowse, but first I have to ask: is there a reason you don't want to use JBrowse ( http://jbrowse.org/) ? GBrowse is a work horse, but it has been only minimally maintained for the last several years, where JBrowse (also a GMOD project) is actively maintained and has a large developer and user community. Scott On Mon, Jan 27, 2020 at 1:05 PM Nihalreddy Gade < gad...@gm...> wrote: > Good morning Team, > > I have new gff3 file and fasta file with me, i have followed all the steps > mentioned in file:///opt/gbrowse/htdocs/tutorial/tutorial.html. How ever > the data is not very small like volvox but still i used in memory adaptor. > i have tried it with berkeley db as well it is not giving me the actual > result. I have added all the config files and gff3 files in exact > locations. Could you please help me what i am missing . I am getting the > output as the result not found as shown in the attached picture. > > Please do let me know what i might be missing. > > Thanks and regards > Nihal > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Nihalreddy G. <gad...@gm...> - 2020-01-26 12:27:23
|
On Sun, Jan 26, 2020 at 6:26 AM Nihalreddy Gade < gad...@gm...> wrote: > Good morning Team, > > I have new gff3 file and fasta file with me, i have followed all the steps > mentioned in file:///opt/gbrowse/htdocs/tutorial/tutorial.html. How ever > the data is not very small like volvox but still i used in memory adaptor. > i have tried it with berkeley db as well it is not giving me the actual > result. I have added all the config files and gff3 files in exact > locations. Could you please help me what i am missing . I am getting the > output as the result not found as shown in the attached picture. > > Please do let me know what i might be missing. > > Thanks and regards > Nihal > |
From: Nihalreddy G. <gad...@gm...> - 2020-01-26 12:26:29
|
Good morning Team, I have new gff3 file and fasta file with me, i have followed all the steps mentioned in file:///opt/gbrowse/htdocs/tutorial/tutorial.html. How ever the data is not very small like volvox but still i used in memory adaptor. i have tried it with berkeley db as well it is not giving me the actual result. I have added all the config files and gff3 files in exact locations. Could you please help me what i am missing . I am getting the output as the result not found as shown in the attached picture. Please do let me know what i might be missing. Thanks and regards Nihal |
From: Scott C. <sc...@sc...> - 2019-12-04 19:16:11
|
Hi Chris, I think JBrowse 2 will be significantly more flexible in how it does display, though to be fair, GBrowse_syn can do more that two compared sequences (at WormBase we do 4)--it's just that they UI for doing it kind of sucks :-) We've seen the amazing work the EuPathDB folks and I'm glad they released it as a JBrowse 1 plugin. Scott On Tue, Nov 26, 2019 at 2:57 PM Fields, Christopher J <cjf...@il...> wrote: > Hi Scott, > > > > I am involved with a few projects that would benefit from this. The > tricky part for us is comparing more than 2 genomes at a time (one project > has more than ten assemblies) so setting/switching the reference and being > able to change the genomes compared against is useful (as well as layering > in trackes). I’m guessing this would be limited to 1 reference and 2 > genomes, like gbrowse_syn? > > > > chris > > > > *From: *Scott Cain <sc...@sc...> > *Date: *Tuesday, November 26, 2019 at 4:23 PM > *To: *GMOD-Gbrowse <gmo...@li...> > *Subject: *[Gmod-gbrowse] Users of gbrowse_syn? > > > > Hello (hello .... hello.....hello) (that's supposed to be an echo) > > > > I'm wondering if there are any users out there who still use gbrowse_syn > on a production website. The only one I know of off the top of my head is > the one I'm responsible for at WormBase. Are there any others? > > > > I'm asking because the developers of JBrowse are working on a new version > that will have support for synteny browsing, so we'd like to make sure > we're covering use cases. > > > > Thanks, > > Scott > > > > > -- > > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Jason S. <jas...@gm...> - 2019-11-27 02:09:30
|
You should contact EuPathDB they have an implementation already I think. Jason Stajich, PhD jas...@gm... On Nov 26, 2019, 2:57 PM -0800, Fields, Christopher J <cjf...@il...>, wrote: > Hi Scott, > > I am involved with a few projects that would benefit from this. The tricky part for us is comparing more than 2 genomes at a time (one project has more than ten assemblies) so setting/switching the reference and being able to change the genomes compared against is useful (as well as layering in trackes). I’m guessing this would be limited to 1 reference and 2 genomes, like gbrowse_syn? > > chris > > From: Scott Cain <sc...@sc...> > Date: Tuesday, November 26, 2019 at 4:23 PM > To: GMOD-Gbrowse <gmo...@li...> > Subject: [Gmod-gbrowse] Users of gbrowse_syn? > > Hello (hello .... hello.....hello) (that's supposed to be an echo) > > I'm wondering if there are any users out there who still use gbrowse_syn on a production website. The only one I know of off the top of my head is the one I'm responsible for at WormBase. Are there any others? > > I'm asking because the developers of JBrowse are working on a new version that will have support for synteny browsing, so we'd like to make sure we're covering use cases. > > Thanks, > Scott > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
From: Fields, C. J <cjf...@il...> - 2019-11-26 22:57:15
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Hi Scott, I am involved with a few projects that would benefit from this. The tricky part for us is comparing more than 2 genomes at a time (one project has more than ten assemblies) so setting/switching the reference and being able to change the genomes compared against is useful (as well as layering in trackes). I’m guessing this would be limited to 1 reference and 2 genomes, like gbrowse_syn? chris From: Scott Cain <sc...@sc...> Date: Tuesday, November 26, 2019 at 4:23 PM To: GMOD-Gbrowse <gmo...@li...> Subject: [Gmod-gbrowse] Users of gbrowse_syn? Hello (hello .... hello.....hello) (that's supposed to be an echo) I'm wondering if there are any users out there who still use gbrowse_syn on a production website. The only one I know of off the top of my head is the one I'm responsible for at WormBase. Are there any others? I'm asking because the developers of JBrowse are working on a new version that will have support for synteny browsing, so we'd like to make sure we're covering use cases. Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Scott C. <sc...@sc...> - 2019-11-26 22:23:21
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Hello (hello .... hello.....hello) (that's supposed to be an echo) I'm wondering if there are any users out there who still use gbrowse_syn on a production website. The only one I know of off the top of my head is the one I'm responsible for at WormBase. Are there any others? I'm asking because the developers of JBrowse are working on a new version that will have support for synteny browsing, so we'd like to make sure we're covering use cases. Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Jennifer J. <jj...@st...> - 2019-11-20 21:06:52
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Dear Katherine, The issue should be resolved now. Please try viewing the tracks again and let us know if you still experience any problems. Thank you for your patience, Jennifer Jou Associate Data Wrangler ENCODE DCC ________________________________ From: encode-help <enc...@li...> on behalf of Scott Cain <sc...@sc...> Sent: Monday, November 18, 2019 10:09 AM To: Luo, Katherine L. <kl...@cu...> Cc: ENCODE help desk <enc...@li...>; gmo...@li... <gmo...@li...> Subject: Re: [encode-help] [Gmod-gbrowse] GBrowse for c. elegans not working? Hi Katherine, You've reached the help desk for people who install and support GBrowse instances. As it happens, I also work for WormBase, so I can tell you that all of the data in the modENCODE GBrowse are also available at WormBase, either in the C. elegans JBrowse instance, where there is a "modENCODE data (2014)" set of tracks: https://wormbase.org/tools/genome/jbrowse-simple/?data=data%2Fc_elegans_PRJNA13758 or for modENCODE data that are mapped to an older assembly of C. elegans, see this separate JBrowse instance: https://wormbase.org/tools/genome/jbrowse-simple/?data=data%2Fold-modencode Of course, ideally, the modENCODE GBrowse instance would also be working, so I'll cc this email to the modENCODE support folks. Please let me know if you have any questions related to JBrowse at WormBase, Scott On Mon, Nov 18, 2019 at 9:58 AM Luo, Katherine L. <kl...@cu...<mailto:kl...@cu...>> wrote: Hello, I am trying to examine some tracks using the C. elegans GBrowse, but it never seems to be able to load. Here is a screenshot. I have used both Chrome and Firefox, and both are not working. Best, Katherine [cid:16e7fab5f6ecb971f161][cid:16e7fab5f6fcb971f162] _______________________________________________ Gmod-gbrowse mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |