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From: Colin <col...@gm...> - 2025-06-27 19:08:58
|
(note that you can also change the entire "session title" in the same way by clicking where it says "New session ..." on the top level blue navigation bar) -Colin On Fri, Jun 27, 2025 at 3:07 PM Colin <col...@gm...> wrote: > I don't believe this is currently possible. However, if this is just for > screenshot purposes or just to remember what was searched, note that you > can manually edit the "View title" in the purple bar view header. > > For example, see the screenshot below: It says "My custom text here" in > the view header, just due to me clicking the view header text and typing to > make my own custom title > > [image: image.png] > > Hope that helps > > -Colin > > On Fri, Jun 27, 2025 at 11:58 AM Vaneet Lotay <van...@uc...> > wrote: > >> Hi, >> >> >> >> My PI was curious about something in JBrowse2. When you enter a search >> result in the location box and visit the location where the gene is in the >> genome, is it possible to allow the search results to remain in the search >> box instead of it switching automatically to the genome coordinates? Or >> perhaps can the gene search result remain anywhere in that top panel after >> you've visited your gene of interest. I assume this isn't possible but >> just thought I'd ask if there's a plugin for it perhaps. >> >> Thanks, >> >> Vaneet >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > |
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From: Colin <col...@gm...> - 2025-06-27 19:07:51
|
I don't believe this is currently possible. However, if this is just for screenshot purposes or just to remember what was searched, note that you can manually edit the "View title" in the purple bar view header. For example, see the screenshot below: It says "My custom text here" in the view header, just due to me clicking the view header text and typing to make my own custom title [image: image.png] Hope that helps -Colin On Fri, Jun 27, 2025 at 11:58 AM Vaneet Lotay <van...@uc...> wrote: > Hi, > > > > My PI was curious about something in JBrowse2. When you enter a search > result in the location box and visit the location where the gene is in the > genome, is it possible to allow the search results to remain in the search > box instead of it switching automatically to the genome coordinates? Or > perhaps can the gene search result remain anywhere in that top panel after > you've visited your gene of interest. I assume this isn't possible but > just thought I'd ask if there's a plugin for it perhaps. > > Thanks, > > Vaneet > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Vaneet L. <van...@uc...> - 2025-06-27 15:58:06
|
Hi, My PI was curious about something in JBrowse2. When you enter a search result in the location box and visit the location where the gene is in the genome, is it possible to allow the search results to remain in the search box instead of it switching automatically to the genome coordinates? Or perhaps can the gene search result remain anywhere in that top panel after you've visited your gene of interest. I assume this isn't possible but just thought I'd ask if there's a plugin for it perhaps. Thanks, Vaneet |
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From: Colin <col...@gm...> - 2025-05-29 19:32:54
|
Currently there is no option for this. Potential could add it though! If you can make a github issue for it that would be great -Colin On Thu, May 29, 2025 at 2:54 PM Ke Jiang <bio...@gm...> wrote: > Hi, > > I'd like to know whether it is possible to turn off the rendering of the > "genotype" column for a VCF track in the feature details in the track > configuration. Looks like as a user viewing the track, we can click the > "columns" button to select the columns to show. But is there a way to > selectively hide columns in the backend of track configuration, so by > default users would only see certain columns of VCF INFO fields? > > For an example, see attached screenshot. We'd like to show only "sample" > and "GT" by default, no "genotype" column. > > Thanks! > > Ke > [image: Screenshot 2025-05-29 at 1.48.16 PM.png] > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Ke J. <bio...@gm...> - 2025-05-29 18:53:44
|
Hi, I'd like to know whether it is possible to turn off the rendering of the "genotype" column for a VCF track in the feature details in the track configuration. Looks like as a user viewing the track, we can click the "columns" button to select the columns to show. But is there a way to selectively hide columns in the backend of track configuration, so by default users would only see certain columns of VCF INFO fields? For an example, see attached screenshot. We'd like to show only "sample" and "GT" by default, no "genotype" column. Thanks! Ke [image: Screenshot 2025-05-29 at 1.48.16 PM.png] |
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From: Vaneet L. <van...@uc...> - 2025-05-13 17:26:42
|
Hey Colin, Here’s an example for the hhat gene: https://jbrowse.xenbase.org/XenJBrowse/?data=data%2Fxt10_0&loc=Chr5%3A15519428..15720936&tracks=DNA%2CXT10_0_Xenbase%2CgRNAs&highlight= If you click on the gene models and then ‘show subfeatures’, you can see the UTR being repeated several times, which isn’t present in the GFF3 file itself. Most models with UTRs show this repeated issue. Thanks, Vaneet From: Colin <col...@gm...> Sent: May 12, 2025 1:35 PM To: Vaneet Lotay <van...@uc...> Cc: gmo...@li... Subject: Re: JBrowse subfeatures repeating bug? [△EXTERNAL] If you can send a link it may help -Colin On Mon, May 12, 2025 at 2:42 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote: Hi Colin, Have you ever encountered this bug below in JBrowse when using ‘NCBI’ style GFF3s with implied UTRs to be drawn in the JBrowse tracks? Anyone else ever run into this issue? I’m just wondering if there’s something that can be done to prevent it from repeating like that. I can give a direct link to someone if they want to see the issue live and recreate it. Thanks, Vaneet From: Vaneet Lotay Sent: April 9, 2025 10:51 AM To: gmo...@li...<mailto:gmo...@li...> Subject: JBrowse subfeatures repeating bug? Hi, I’m not sure if anyone’s already run into this bug before, at least it certainly seems like a bug. When I click on my gene model in JBrowse, and then click on subfeatures under a given mRNA, the same 3’UTR or 5’UTR segment gets displayed multiple times as duplicates with the same coordinates (screenshot attached). It doesn’t matter which model I select or even under which species or genome for that matter that it’s under, it always appears repeated like that in the details window. Here’s a trimmed down version of the hhex.S gene that’s in the screenshot from my GFF3 (column 9 attributes trimmed off) just so it can fit here: Chr7S Gnomon gene 15890549 15902647 . - . ID=XBXL10_1g32594;Name=hhex.S Chr7S Gnomon mRNA 15890549 15902647 . - . ID=XBmRNA61523;Parent=XBXL10_1g32594 Chr7S Gnomon exon 15902179 15902647 . - . ID=XBexon785823;Parent=XBmRNA61523 Chr7S Gnomon exon 15896206 15896384 . - . ID=XBexon785824;Parent=XBmRNA61523 Chr7S Gnomon exon 15894761 15894811 . - . ID=XBexon785825;Parent=XBmRNA61523 Chr7S Gnomon exon 15890549 15891175 . - . ID=XBexon785826;Parent=XBmRNA61523 Chr7S Gnomon CDS 15902179 15902551 . - 0 ID=XBcds718348;Parent=XBmRNA61523 Chr7S Gnomon CDS 15896206 15896384 . - 2 ID=XBcds718348;Parent=XBmRNA61523 Chr7S Gnomon CDS 15894761 15894811 . - 0 ID=XBcds718348;Parent=XBmRNA61523 Chr7S Gnomon CDS 15890948 15891175 . - 0 ID=XBcds718348;Parent=XBmRNA61523 I have this setting enabled in my track to draw out the ‘implied’ UTRs which aren’t directly supplied in the GFF3 file: "impliedUTRs" : true, Has anyone run into this before? Is it a technical bug? Why is it happening? Thanks, Vaneet |
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From: Colin <col...@gm...> - 2025-05-12 19:35:34
|
If you can send a link it may help -Colin On Mon, May 12, 2025 at 2:42 PM Vaneet Lotay <van...@uc...> wrote: > Hi Colin, > > > > Have you ever encountered this bug below in JBrowse when using ‘NCBI’ > style GFF3s with implied UTRs to be drawn in the JBrowse tracks? > > > > Anyone else ever run into this issue? I’m just wondering if there’s > something that can be done to prevent it from repeating like that. I can > give a direct link to someone if they want to see the issue live and > recreate it. > > > > Thanks, > > > Vaneet > > > > *From:* Vaneet Lotay > *Sent:* April 9, 2025 10:51 AM > *To:* gmo...@li... > *Subject:* JBrowse subfeatures repeating bug? > > > > Hi, > > > > I’m not sure if anyone’s already run into this bug before, at least it > certainly seems like a bug. When I click on my gene model in JBrowse, and > then click on subfeatures under a given mRNA, the same 3’UTR or 5’UTR > segment gets displayed multiple times as duplicates with the same > coordinates (screenshot attached). It doesn’t matter which model I select > or even under which species or genome for that matter that it’s under, it > always appears repeated like that in the details window. Here’s a trimmed > down version of the hhex.S gene that’s in the screenshot from my GFF3 > (column 9 attributes trimmed off) just so it can fit here: > > > > Chr7S Gnomon gene 15890549 15902647 . - > . ID=XBXL10_1g32594;Name=hhex.S > > Chr7S Gnomon mRNA 15890549 15902647 . - > . ID=XBmRNA61523;Parent=XBXL10_1g32594 > > Chr7S Gnomon exon 15902179 15902647 . - > . ID=XBexon785823;Parent=XBmRNA61523 > > Chr7S Gnomon exon 15896206 15896384 . - > . ID=XBexon785824;Parent=XBmRNA61523 > > Chr7S Gnomon exon 15894761 15894811 . - > . ID=XBexon785825;Parent=XBmRNA61523 > > Chr7S Gnomon exon 15890549 15891175 . - > . ID=XBexon785826;Parent=XBmRNA61523 > > Chr7S Gnomon CDS 15902179 15902551 . - > 0 ID=XBcds718348;Parent=XBmRNA61523 > > Chr7S Gnomon CDS 15896206 15896384 . - > 2 ID=XBcds718348;Parent=XBmRNA61523 > > Chr7S Gnomon CDS 15894761 15894811 . - > 0 ID=XBcds718348;Parent=XBmRNA61523 > > Chr7S Gnomon CDS 15890948 15891175 . - > 0 ID=XBcds718348;Parent=XBmRNA61523 > > > > I have this setting enabled in my track to draw out the ‘implied’ UTRs > which aren’t directly supplied in the GFF3 file: > > > > "impliedUTRs" : true, > > > > Has anyone run into this before? Is it a technical bug? Why is it > happening? > > > > Thanks, > > > Vaneet > |
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From: Vaneet L. <van...@uc...> - 2025-05-12 18:42:14
|
Hi Colin,
Have you ever encountered this bug below in JBrowse when using 'NCBI' style GFF3s with implied UTRs to be drawn in the JBrowse tracks?
Anyone else ever run into this issue? I'm just wondering if there's something that can be done to prevent it from repeating like that. I can give a direct link to someone if they want to see the issue live and recreate it.
Thanks,
Vaneet
From: Vaneet Lotay
Sent: April 9, 2025 10:51 AM
To: gmo...@li...
Subject: JBrowse subfeatures repeating bug?
Hi,
I'm not sure if anyone's already run into this bug before, at least it certainly seems like a bug. When I click on my gene model in JBrowse, and then click on subfeatures under a given mRNA, the same 3'UTR or 5'UTR segment gets displayed multiple times as duplicates with the same coordinates (screenshot attached). It doesn't matter which model I select or even under which species or genome for that matter that it's under, it always appears repeated like that in the details window. Here's a trimmed down version of the hhex.S gene that's in the screenshot from my GFF3 (column 9 attributes trimmed off) just so it can fit here:
Chr7S Gnomon gene 15890549 15902647 . - . ID=XBXL10_1g32594;Name=hhex.S
Chr7S Gnomon mRNA 15890549 15902647 . - . ID=XBmRNA61523;Parent=XBXL10_1g32594
Chr7S Gnomon exon 15902179 15902647 . - . ID=XBexon785823;Parent=XBmRNA61523
Chr7S Gnomon exon 15896206 15896384 . - . ID=XBexon785824;Parent=XBmRNA61523
Chr7S Gnomon exon 15894761 15894811 . - . ID=XBexon785825;Parent=XBmRNA61523
Chr7S Gnomon exon 15890549 15891175 . - . ID=XBexon785826;Parent=XBmRNA61523
Chr7S Gnomon CDS 15902179 15902551 . - 0 ID=XBcds718348;Parent=XBmRNA61523
Chr7S Gnomon CDS 15896206 15896384 . - 2 ID=XBcds718348;Parent=XBmRNA61523
Chr7S Gnomon CDS 15894761 15894811 . - 0 ID=XBcds718348;Parent=XBmRNA61523
Chr7S Gnomon CDS 15890948 15891175 . - 0 ID=XBcds718348;Parent=XBmRNA61523
I have this setting enabled in my track to draw out the 'implied' UTRs which aren't directly supplied in the GFF3 file:
"impliedUTRs" : true,
Has anyone run into this before? Is it a technical bug? Why is it happening?
Thanks,
Vaneet
|
|
From: Garrett S. <ste...@gm...> - 2025-04-30 23:09:04
|
Apollo 2.8.1 has been released: https://github.com/GMOD/Apollo/releases/tag/2.8.1 *Bug Fixes* - Fix not being able to see or add users in the UI when no organisms have been added yet. 2666 <https://github.com/GMOD/Apollo/pull/2666>. - Fix blat search not working in Docker image. 2670 <https://github.com/GMOD/Apollo/pull/2670>. Full change long for all versions can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md Docker builds are on docker hub: https://hub.docker.com/r/gmod/apollo Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/ Note: You can find a guide to upgrading existing Apollo installations here: https://genomearchitect.readthedocs.io/en/latest/Migration.html Report issues if found. Active mailing list (ap...@lb...) and google group <https://groups.google.com/a/lbl.gov/g/apollo>. |
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From: Ke J. <bio...@gm...> - 2025-04-09 21:17:32
|
We’ve had the same problem of one single config.json getting too many tracks and becoming too big to manage. We ended up establishing multiple instances of JBrowse2 for different user groups. I think that is an option to have multiple more manageable config.json files. Ke On Tue, Apr 8, 2025 at 11:59 AM Vaneet Lotay <van...@uc...> wrote: > Hello, > > > > I was curious when working with JBrowse2, is it very easy or user-friendly > to setup multiple config.json files for the different genomes that may be > hosted in the browser, similar to the original JBrowse? If so, then please > explain what the best way to do that is. Or is JBrowse2 basically built to > work best with one central config.json file as it is by default? > > > > Thanks, > > <https://www.google.com/maps/search/2500+University+Drive+NW+%0D%0A+Calgary,+AB+T2N+1N4+%0D%0A+CANADA?entry=gmail&source=g> > > > > <https://www.google.com/maps/search/2500+University+Drive+NW+%0D%0A+Calgary,+AB+T2N+1N4+%0D%0A+CANADA?entry=gmail&source=g> > > Vaneet > > > > *Vaneet Lotay* > > *Xenbase Bioinformatician* > > *University of Calgary* > > *2500 University Drive NW > <https://www.google.com/maps/search/2500+University+Drive+NW+%0D%0A+Calgary,+AB+T2N+1N4+%0D%0A+CANADA?entry=gmail&source=g>* > > *Calgary, AB T2N 1N4 > <https://www.google.com/maps/search/2500+University+Drive+NW+%0D%0A+Calgary,+AB+T2N+1N4+%0D%0A+CANADA?entry=gmail&source=g>* > > *CANADA > <https://www.google.com/maps/search/2500+University+Drive+NW+%0D%0A+Calgary,+AB+T2N+1N4+%0D%0A+CANADA?entry=gmail&source=g>* > > > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Vaneet L. <van...@uc...> - 2025-04-09 17:06:24
|
Hi,
I'm not sure if anyone's already run into this bug before, at least it certainly seems like a bug. When I click on my gene model in JBrowse, and then click on subfeatures under a given mRNA, the same 3'UTR or 5'UTR segment gets displayed multiple times as duplicates with the same coordinates (screenshot attached). It doesn't matter which model I select or even under which species or genome for that matter that it's under, it always appears repeated like that in the details window. Here's a trimmed down version of the hhex.S gene that's in the screenshot from my GFF3 (column 9 attributes trimmed off) just so it can fit here:
Chr7S Gnomon gene 15890549 15902647 . - . ID=XBXL10_1g32594;Name=hhex.S
Chr7S Gnomon mRNA 15890549 15902647 . - . ID=XBmRNA61523;Parent=XBXL10_1g32594
Chr7S Gnomon exon 15902179 15902647 . - . ID=XBexon785823;Parent=XBmRNA61523
Chr7S Gnomon exon 15896206 15896384 . - . ID=XBexon785824;Parent=XBmRNA61523
Chr7S Gnomon exon 15894761 15894811 . - . ID=XBexon785825;Parent=XBmRNA61523
Chr7S Gnomon exon 15890549 15891175 . - . ID=XBexon785826;Parent=XBmRNA61523
Chr7S Gnomon CDS 15902179 15902551 . - 0 ID=XBcds718348;Parent=XBmRNA61523
Chr7S Gnomon CDS 15896206 15896384 . - 2 ID=XBcds718348;Parent=XBmRNA61523
Chr7S Gnomon CDS 15894761 15894811 . - 0 ID=XBcds718348;Parent=XBmRNA61523
Chr7S Gnomon CDS 15890948 15891175 . - 0 ID=XBcds718348;Parent=XBmRNA61523
I have this setting enabled in my track to draw out the 'implied' UTRs which aren't directly supplied in the GFF3 file:
"impliedUTRs" : true,
Has anyone run into this before? Is it a technical bug? Why is it happening?
Thanks,
Vaneet
|
|
From: Vaneet L. <van...@uc...> - 2025-04-08 21:52:10
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Thanks for that great info! I find it cleaner having different config files but if it loses the ability to compare multiple genomes at once, I don’t think it’s worth it. I’ll probably stick to one main config.json file. Vaneet From: Colin <col...@gm...> Sent: April 8, 2025 1:00 PM To: Vaneet Lotay <van...@uc...> Cc: gmo...@li... Subject: Re: [Gmod-ajax] JBrowse2 config file [△EXTERNAL] Hi Vaneet It will depend on your particular setup. JBrowse 2 "likes" a single config.json, particularly because it enables comparing multiple genomes. However, for either technical or administrative reasons, some people get overwhelmed by having a single config, and they make multiple configs You can navigate to specific configs using yoursite.com/jbrowse/?config=genomeA_config.json<http://yoursite.com/jbrowse/?config=genomeA_config.json> You can also use the command line to write to specific configs using e.g. jbrowse add-track --out genomeA_config.json Finally, you can also optionally write scripts to merge configs. A script to merge configs tends to be pretty simple, you can simply concatenate the list of assemblies and tracks from different configs. -Colin PS We have had a couple great meetings with your XenBase colleagues! On Tue, Apr 8, 2025 at 11:59 AM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote: Hello, I was curious when working with JBrowse2, is it very easy or user-friendly to setup multiple config.json files for the different genomes that may be hosted in the browser, similar to the original JBrowse? If so, then please explain what the best way to do that is. Or is JBrowse2 basically built to work best with one central config.json file as it is by default? Thanks, Vaneet Vaneet Lotay Xenbase Bioinformatician University of Calgary 2500 University Drive NW Calgary, AB T2N 1N4 CANADA _______________________________________________ Gmod-ajax mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Colin <col...@gm...> - 2025-04-08 19:00:41
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Hi Vaneet It will depend on your particular setup. JBrowse 2 "likes" a single config.json, particularly because it enables comparing multiple genomes. However, for either technical or administrative reasons, some people get overwhelmed by having a single config, and they make multiple configs You can navigate to specific configs using yoursite.com/jbrowse/?config=genomeA_config.json You can also use the command line to write to specific configs using e.g. jbrowse add-track --out genomeA_config.json Finally, you can also optionally write scripts to merge configs. A script to merge configs tends to be pretty simple, you can simply concatenate the list of assemblies and tracks from different configs. -Colin PS We have had a couple great meetings with your XenBase colleagues! On Tue, Apr 8, 2025 at 11:59 AM Vaneet Lotay <van...@uc...> wrote: > Hello, > > > > I was curious when working with JBrowse2, is it very easy or user-friendly > to setup multiple config.json files for the different genomes that may be > hosted in the browser, similar to the original JBrowse? If so, then please > explain what the best way to do that is. Or is JBrowse2 basically built to > work best with one central config.json file as it is by default? > > > > Thanks, > > > > Vaneet > > > > *Vaneet Lotay* > > *Xenbase Bioinformatician* > > *University of Calgary* > > *2500 University Drive NW* > > *Calgary, AB T2N 1N4* > > *CANADA* > > > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Vaneet L. <van...@uc...> - 2025-04-08 16:59:09
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Hello, I was curious when working with JBrowse2, is it very easy or user-friendly to setup multiple config.json files for the different genomes that may be hosted in the browser, similar to the original JBrowse? If so, then please explain what the best way to do that is. Or is JBrowse2 basically built to work best with one central config.json file as it is by default? Thanks, Vaneet Vaneet Lotay Xenbase Bioinformatician University of Calgary 2500 University Drive NW Calgary, AB T2N 1N4 CANADA |
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From: Scott C. <sc...@sc...> - 2025-04-07 20:40:47
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] Location: Liverpool, UK, and virtual Dates: July 21-22, 2025 Website: https://www.open-bio.org/events/bosc/ LinkedIn: https://www.linkedin.com/groups/14344023/ Bluesky: https://bsky.app/profile/bosc.bsky.social Slack: https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew Key Dates April 17: Deadline for submitting talk/poster abstracts <https://open-bio.org/events/bosc-2025/submit/> May 13: Talk/poster acceptance notifications May 15: Deadline for submitting late poster abstracts July 20-24: ISMB/ECCB 2025 <https://www.iscb.org/ismbeccb2025/home> July 21-22: BOSC 2025 <https://www.open-bio.org/events/bosc-2025/> (the first two full days of ISMB/ECCB 2025) July 22: BOSC/BOKR joint session <https://www.open-bio.org/2025/03/17/BOSC-BOKR-2025/> July 23-24: ISMB CollaborationFest <https://www.open-bio.org/events/bosc-2025/ismb-collaborationfest-2025/> About BOSC: Since 2000, BOSC has provided a forum for sharing ideas and results in open-source bioinformatics and open science. Our annual two-day program includes keynote talks, talks chosen from submitted abstracts, posters, a panel discussion, and more! 🍐BOSC NEWS 🍐 Joint session with BOKR: BOSC 2025 will include a joint session with the newly renamed Bio-Ontologies and Knowledge Representation (BOKR) COSI <https://www.open-bio.org/2025/03/17/BOSC-BOKR-2025/>! The joint session will include talks chosen from abstracts submitted to BOSC or BOKR, plus a keynote speaker who is well known in both the ontology and open science communities (stay tuned for an announcement soon!). Panel: Our panel topic this year will be Data Sustainability. A range of experts will share their thoughts on this important and timely subject and take questions from the audience. ISMB CollaborationFest: This year, our popular collaborative work event ( CollaborationFest <https://www.open-bio.org/events/bosc-2025/ismb-collaborationfest-2025/>, aka CoFest) will be held as part of ISMB. Choose it as a free “add-on” when you register for ISMB. Submit an abstract! Abstract submission is open until April 17 (end of the day Anywhere on Earth - no extensions)! We encourage you to submit abstracts <https://www.open-bio.org/events/bosc-2025/submit/> on any topic relevant to open source bioinformatics or open science. After review, some abstracts will be selected for lightning talks, longer talks, or posters. Abstract submission is via ISMB’s EasyChair (linked from our submission page <https://www.open-bio.org/events/bosc-2025/submit/>). Note that a short (< 250 words) text-only abstract is required for all submissions (talk or poster), plus a “long abstract” (PDF, 2 pages max) if you want to be considered for a talk. BOSC topics include (but are not limited to): - Open Science and Reproducible Research - Open Biomedical Data - Citizen/Participatory Science - Standards and Interoperability - Data Science - Workflows - Translational Bioinformatics - Open Science - Developer Tools and Libraries - Outreach and Training - AI/ML: Open Approaches - Data Sustainability - Knowledge Representation and Ontologies (for joint session with BOKR) Sponsors We are thrilled to announce the first two sponsors <https://www.open-bio.org/events/sponsors/> of BOSC 2025 (with more coming soon)! Big thanks to these excellent organizations for supporting open source bioinformatics and enabling us to offer free registration to some qualified participants! 🎉 Platinum sponsor: <https://chanzuckerberg.com/> The aim of CZI <https://chanzuckerberg.com/>’s Open Science program is the universal and immediate open sharing of all scientific knowledge, processes, and outputs. Gold sponsor: <https://seqera.io/> Seqera <https://seqera.io/>, developed by the creators of Nextflow <https://www.nextflow.io/>, empowers researchers to develop and deploy scalable bioinformatics pipelines faster. If your organization is interested in sponsoring BOSC, please let us know! The more support we get, the more attendees we can offer financial assistance to. We hope to see you (in person in Liverpool or virtually) at BOSC 2025! Sincerely, BOSC 2025 Organizing Committee (Nomi Harris, Karsten Hokamp, Jessica Maia, Hervé Ménager, Monica Munoz-Torres, Tazro Ohta, Deepak Unni, Jason Williams) -- ------------------------------------------------------------------------ Scott Cain, Ph. D. Research Professor, Penn State Cite Us: * The Galaxy Community. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update, Nucleic Acids Research, 2024, https://doi.org/10.1093/nar/gkae410 How to cite specific Galaxy instances and tools: https://galaxyproject.org/citing-galaxy/ |
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From: Colin <col...@gm...> - 2025-03-28 16:14:43
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Hi there, You might want to contact flybase I was just looking around though and it looks like there are some downloads for fly regulatory features via their wiki https://wiki.flybase.org/wiki/FlyBase:JBrowse_Tracks#Genome_Level_Features -Colin On Fri, Mar 28, 2025 at 9:59 AM James Tan Sheng Yi < jam...@tu...> wrote: > To whom it may concern, > > > Hi, I'd like to obtain the information for several tracks about genomic > regulatory elements (e.g., enhancers, POL2 sites, etc.) on Flybase > JBrowse. In particular, I need the genomic location information to > answer questions of whether my set of interesting SNPs are enriched tend > to fall within a particular type of genomic regulatory element (e.g., > enriched in enhancers of any type, enhancers of a specific type, TFBS, > etc.). I have scoured the site and found no way of getting these genomic > locations of each element in a track within a single file > straightforwardly. Any help on how to do this? > > Thank you! > > > Best, > > James > > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: James T. S. Yi <jam...@tu...> - 2025-03-28 13:41:44
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To whom it may concern, Hi, I'd like to obtain the information for several tracks about genomic regulatory elements (e.g., enhancers, POL2 sites, etc.) on Flybase JBrowse. In particular, I need the genomic location information to answer questions of whether my set of interesting SNPs are enriched tend to fall within a particular type of genomic regulatory element (e.g., enriched in enhancers of any type, enhancers of a specific type, TFBS, etc.). I have scoured the site and found no way of getting these genomic locations of each element in a track within a single file straightforwardly. Any help on how to do this? Thank you! Best, James |
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From: Garrett S. <ste...@gm...> - 2025-03-05 00:35:57
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Version 2.8.0 of Apollo has been released: https://github.com/GMOD/Apollo/releases/tag/2.8.0. This release fixes security vulnerabilities in Apollo versions 2.4.0 through 2.7.0. For a detailed report of these vulnerabilities, please see https://www.cisa.gov/news-events/ics-advisories/icsa-25-063-07. In summary, the discovered vulnerabilities include the ability of a malicious user to escalate their privileges within the Apollo app to admin levels (that is, they can become an Apollo administrator), the ability to retrieve a list of email addresses of other Apollo users, and - most seriously of all - the ability to upload arbitrary files to the file system in any directory writable by the Tomcat process that runs the Apollo server. While the Tomcat documentation recommends not running Tomcat as the root user, this advice is often ignored by Linux distributions; for example, in Ubuntu, Tomcat runs as root. Consequently it seems likely that many installations will face the worst-case scenario that a malicious user could upload system files that would allow remote access to the Apollo server. *It is critical that you update your Apollo 2.4.0 to 2.7.0 installations as soon as possible.* While we are not aware of any active exploitation of these vulnerabilities, it is only a matter of time before publicly disclosed vulnerabilities are systematically exploited by hackers. Consequently, we strongly recommend applying the update to protect your systems. We also want to make it clear that these patches only apply to the legacy 2.0 version of Apollo. Since 2018, Apollo development has been folded into the JBrowse project, and the recently released version of Apollo (v3.0) was designed with security principles built in from the start. Naturally, as maintainers of version 2.0, we take your system security extremely seriously and have made every effort to provide this security update in as timely a fashion as possible. In addition to the aforementioned Apollo vulnerabilities, the CISA researchers also discovered a reflected cross-site scripting (XSS) vulnerability in JBrowse 1, and we have included a patch for this as well. We also note that, as with the Apollo 2 flaws, these security flaws do not apply to the latest version of JBrowse (JBrowse 2), which was designed with stronger security patterns from the outset. If you are using Docker to deploy Apollo, there are two different images you can choose from. The gmod/apollo:release-2.8.0-alternate <https://hub.docker.com/repository/docker/gmod/apollo/tags/release-2.8.0-alternate/sha256-a5d65e04fc597f0f71ea2c97dd6174ea1f1cca43912be53e3733c4fad2ee30e9> image will provide a drop-in replacement for your existing Docker image. This image, however, like past images, runs as the root user. If you would like the additional security of not running as a root user, you can use the gmod/apollo:release-2.8.0 image <https://hub.docker.com/repository/docker/gmod/apollo/tags/release-2.8.0/sha256-9760d56c6ec28edc2d3793ed11e7e659da2a7ac1973f3b1cfa32517551c2ff46>, which does not run as the root user, but will require you to update any mounted directories so they are accessible by a non-root user. We understand that updates are inconvenient, but we emphasize that taking this proactive step is essential to ensuring the security of your systems. Sincerely, The Apollo Team |
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From: Ke J. <bio...@gm...> - 2025-01-03 20:33:31
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Hi, Colin, Great docs and function! They’re very helpful! Thanks for the update! Thanks! Ke On Fri, Jan 3, 2025 at 11:39 AM Colin <col...@gm...> wrote: > Hi Ke, > Thanks for asking...I have been meaning to make a detailed documentation > guide for these features. > > Here is a short writeup explaining the different ways to launch the > breakpoint split view a gist form > https://gist.github.com/cmdcolin/274040cff8a49c9e5265c4fa64265748 > > The TLDR is that you can either launch the "breakpoint split view" from > > 1) the "SV inspector" > 2) the feature details panels from clicking on reads or variant calls from > a normal "linear genome view" > > > I am going to try to polish this up and add this to our jbrowse.org docs > > > -Colin > > On Thu, Jan 2, 2025 at 7:52 AM Ke Jiang <bio...@gm...> wrote: > >> Hi, >> >> I noticed that there is a new visualization mode for breakpoint split >> view to show paired read and split read orientations added in the update >> from Sep. 2024. This could be a very useful tool for us to explore >> potential larger scale SVs. There is not much information/docs about how >> this feature is turned on, and what kind of data is needed for this >> feature. From the Blog post, it seems we need both SV calls (VCFs?) and >> alignment tracks for this? How do we turn this view on with these tracks? >> >> Thanks! >> >> Ke >> > _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > |
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From: Colin <col...@gm...> - 2025-01-03 17:39:28
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Hi Ke, Thanks for asking...I have been meaning to make a detailed documentation guide for these features. Here is a short writeup explaining the different ways to launch the breakpoint split view a gist form https://gist.github.com/cmdcolin/274040cff8a49c9e5265c4fa64265748 The TLDR is that you can either launch the "breakpoint split view" from 1) the "SV inspector" 2) the feature details panels from clicking on reads or variant calls from a normal "linear genome view" I am going to try to polish this up and add this to our jbrowse.org docs -Colin On Thu, Jan 2, 2025 at 7:52 AM Ke Jiang <bio...@gm...> wrote: > Hi, > > I noticed that there is a new visualization mode for breakpoint split view > to show paired read and split read orientations added in the update from > Sep. 2024. This could be a very useful tool for us to explore potential > larger scale SVs. There is not much information/docs about how this feature > is turned on, and what kind of data is needed for this feature. From the > Blog post, it seems we need both SV calls (VCFs?) and alignment tracks for > this? How do we turn this view on with these tracks? > > Thanks! > > Ke > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Ke J. <bio...@gm...> - 2025-01-02 14:52:06
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Hi, I noticed that there is a new visualization mode for breakpoint split view to show paired read and split read orientations added in the update from Sep. 2024. This could be a very useful tool for us to explore potential larger scale SVs. There is not much information/docs about how this feature is turned on, and what kind of data is needed for this feature. From the Blog post, it seems we need both SV calls (VCFs?) and alignment tracks for this? How do we turn this view on with these tracks? Thanks! Ke |
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From: Revanth S. K. R. P. <rpa...@un...> - 2024-11-21 21:09:38
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Hello Colin, Thank you for the response! Yes, I got it to work upgrading jbrowse version to the latest one. Yeah, I think the feature to see where the current chromosome is located in entire genome would help for the researchers. Please let me know if you need any other information. Thanks! From: Colin <col...@gm...> Sent: Thursday, November 21, 2024 3:05 PM To: Revanth Sai Kumar Reddy Patel <rpa...@un...> Cc: gmo...@li... Subject: Re: [Gmod-ajax] Jbrowse2 | Highlight parameter Issue Caution: Non-NU Email Hi there, Here is an example of using the highlight parameter, I think it works. If it is not working, can you confirm your jbrowse version you are using? https://jbrowse.org/code/jb2/main/?config=test_data/volvox/config.json&loc=ctgA:1-800&assembly=volvox&tracks=gff3tabix_genes&highlight=ctgA:100-700<https://urldefense.com/v3/__https:/jbrowse.org/code/jb2/main/?config=test_data*volvox*config.json&loc=ctgA:1-800&assembly=volvox&tracks=gff3tabix_genes&highlight=ctgA:100-700__;Ly8!!PvXuogZ4sRB2p-tU!ERa2mmwoCtuCjJJ0y-est3ou8y_QnuKyzNbELzELXeZVzz_Ew8imG9jUTmbspzPycnMtnPFRSwJseZM-p7Bogw$> >Another issue is when I load fasta assembly in jbrowse and in the search if I go to a specific gene or chromosome, I am losing the information of other genes to its sides as it only shows the gene searched for. Please let me know if there is a fix for this. currently the search makes it zoom in to the exact boundaries of the feature of interest. do you want it to be a little more zoomed out? this is not currently configurable but we could try to add that -Colin On Wed, Nov 20, 2024 at 1:25 PM Revanth Sai Kumar Reddy Patel via Gmod-ajax <gmo...@li...<mailto:gmo...@li...>> wrote: Dear Team, Hope you are doing well. I appreciate the development and contributions to open source community for Jbrowse. I am currently facing issue using highlight in URL, I am using it as suggested in the document, but I don’t see anything highlighted on the UI. Please help me what could be going wrong here, do I need to install any other plugins or change configs? Another issue is when I load fasta assembly in jbrowse and in the search if I go to a specific gene or chromosome, I am losing the information of other genes to its sides as it only shows the gene searched for. Please let me know if there is a fix for this. I appreciate your response. Best, [cid:image001.gif@01DB3C27.4AFAC0A0] Revanth Sai Kumar Reddy Patel Software/System Engineer – Dr. Yin’s Lab University of Nebraska–Lincoln _______________________________________________ Gmod-ajax mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-ajax<https://urldefense.com/v3/__https:/lists.sourceforge.net/lists/listinfo/gmod-ajax__;!!PvXuogZ4sRB2p-tU!ERa2mmwoCtuCjJJ0y-est3ou8y_QnuKyzNbELzELXeZVzz_Ew8imG9jUTmbspzPycnMtnPFRSwJseZNJCWfepg$> |
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From: Colin <col...@gm...> - 2024-11-21 21:05:34
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Hi there, Here is an example of using the highlight parameter, I think it works. If it is not working, can you confirm your jbrowse version you are using? https://jbrowse.org/code/jb2/main/?config=test_data/volvox/config.json&loc=ctgA:1-800&assembly=volvox&tracks=gff3tabix_genes&highlight=ctgA:100-700 >Another issue is when I load fasta assembly in jbrowse and in the search if I go to a specific gene or chromosome, I am losing the information of other genes to its sides as it only shows the gene searched for. Please let me know if there is a fix for this. currently the search makes it zoom in to the exact boundaries of the feature of interest. do you want it to be a little more zoomed out? this is not currently configurable but we could try to add that -Colin On Wed, Nov 20, 2024 at 1:25 PM Revanth Sai Kumar Reddy Patel via Gmod-ajax <gmo...@li...> wrote: > Dear Team, > > Hope you are doing well. I appreciate the development and contributions to > open source community for Jbrowse. > > I am currently facing issue using highlight in URL, I am using it as > suggested in the document, but I don’t see anything highlighted on the UI. > Please help me what could be going wrong here, do I need to install any > other plugins or change configs? > > > Another issue is when I load fasta assembly in jbrowse and in the search > if I go to a specific gene or chromosome, I am losing the information of > other genes to its sides as it only shows the gene searched for. Please let > me know if there is a fix for this. > > I appreciate your response. > > Best, > > *Revanth Sai Kumar Reddy Patel* > > *Software/System Engineer – **Dr. Yin’s Lab* > > University of Nebraska–Lincoln > > > > > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Revanth S. K. R. P. <rpa...@un...> - 2024-11-20 16:21:12
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Dear Team, Hope you are doing well. I appreciate the development and contributions to open source community for Jbrowse. I am currently facing issue using highlight in URL, I am using it as suggested in the document, but I don't see anything highlighted on the UI. Please help me what could be going wrong here, do I need to install any other plugins or change configs? Another issue is when I load fasta assembly in jbrowse and in the search if I go to a specific gene or chromosome, I am losing the information of other genes to its sides as it only shows the gene searched for. Please let me know if there is a fix for this. I appreciate your response. Best, [cid:ima...@01...D69170] Revanth Sai Kumar Reddy Patel Software/System Engineer - Dr. Yin's Lab University of Nebraska-Lincoln |
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From: Colin <col...@gm...> - 2024-11-16 20:36:24
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Not sure if the attached images made it through in my previous email but I added the screenshots to github here https://github.com/GMOD/jbrowse-components/issues/4659#issuecomment-2480802412 -Colin On Fri, Nov 15, 2024 at 4:27 PM Colin <col...@gm...> wrote: > Hi there, > I think this question came through our gitter chat earlier but I'll repeat > what we said there > > The screenshot showing that "Link supplementary reads" functionality was > an older demo for a poster, but it was a bit hacky so it didn't end up > getting merged unfortunately! > > I put in a new feature request for this though as it would be a very > useful feature https://github.com/GMOD/jbrowse-components/issues/4659 > > Some alternatives to get this functionality "today" using jbrowse would be > to use the "breakpoint split view" > > It can draw connections between reads in the "single row" mode. The > screenshot below shows this > [image: image.png] > > > [image: image.png] > > There are also the "read cloud" and "read arcs" modes but these are a bit > weirder for long reads. Hope that helps, I can update this thread if we add > the "Link supplementary reads" functionality > > -Colin > > On Fri, Nov 15, 2024 at 11:18 AM Robert Månsson Welinder < > rob...@sc...> wrote: > >> Hi, >> >> Started playing around with looking at PacBio long-read data in JBrowse 2 >> (2.16.1). >> >> How do I find the option that is called "link samplementary reads" in the >> JBrowse 2 demo? >> [image: Screenshot 2024-11-15 at 13.10.28.png] >> >> [Link to demo: >> https://s3.amazonaws.com/jbrowse.org/code/jb2/beta/skbr3_demo/index.html?config=test_data%2Fconfig_demo.json&session=share-4e68d7667f204ee4dfaf01279ee488275686147d4c93c86a80fb2994ad6c43c6&password=c17703b]c1fc0d1c7508bc1af8cf42892) >> >> >> Basically looking at translocations affecting the Immunoglobulin heavy >> chain locus and then one would like the VDJ recombination events to be >> linked via "lines" as shown above for "Link supplementary reads" while the >> actual translocations are shows using the "top/bottom split-view". >> >> Thanks in advance / Robert >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > |
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