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From: Peter C. <p.j...@go...> - 2024-07-24 15:43:09
|
Well done Scott - I was following some of this effort on Mastodon, having made similar efforts although not on quite the same scale with various OBF MediaWiki sites. And best wishes for your new role; you can be very proud of what you have helped GMOD to achieve! Peter On Tue, Jul 23, 2024 at 9:42 PM Fields, Christopher J <cjf...@il...> wrote: > Hi Scott, I just wanted to say a tremendous ‘thank you’ for essentially > leading GMOD efforts over the last 20+ years. Wow, has it been that > long!?! (I’m getting old). You should be incredibly proud of the work you > and all GMOD projects and developers have accomplished; it’s a tremendous > accomplishment. > > > > Hope to see you still out there somewhere in the open-bio world, and best > of luck on your next steps in your career! > > > > Best, > > > > Chris > > > > > > *From: *Scott Cain <sc...@sc...> > *Date: *Tuesday, July 23, 2024 at 1:19 PM > *To: *gmod-announce <gmo...@li...>, gmod-devel < > gmo...@li...>, gmod-ajax < > gmo...@li...>, GMOD Tripal < > gmo...@li...>, Gbrowse (E-mail) < > gmo...@li...>, GMOD Schema/Chado List < > gmo...@li...> > *Subject: *[Gmod-gbrowse] Server change for gmod.org and an announcement > > Hello all, > > > > For several years, I've wanted to port the gmod.org > <https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> > MediaWiki instance to something else but was daunted by the task. Events > have finally conspired to force me to do it, so I've spent the last month > porting the content at gmod.org > <https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> > to a github.io > <https://urldefense.com/v3/__http:/github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtQUw79P0$> > hosted page. It was a real slog, but thank goodness for recursive wget, > Pandoc and command line Perl to allow me to change thousands of markdown > files at a time. > > > > Since gmod.org > <https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> > is now hosted at github.io > <https://urldefense.com/v3/__http:/github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtQUw79P0$>, > changes to this page can now be made with commits to the > https://github.com/GMOD/gmod.github.io > <https://urldefense.com/v3/__https:/github.com/GMOD/gmod.github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtU5TvTYs$> > repo. That means that fixes and additions can be made by creating and > editing markdown files in the gmod.github.io > <https://urldefense.com/v3/__http:/gmod.github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtViLqSVk$> > repo and merging the changes into the main branch. > > > > AND NOW THE ANNOUNCEMENT > > > > At the end of July, I will be stepping away from my role as GMOD project > coordinator, which on one hand, makes me very sad, but on the other, fills > me with immense pride in what we as the GMOD community have achieved over > the last 22 years. We have truly democratized organism genomics, allowing a > small lab to distribute data on whatever organisms are of interest to them > with (relatively) little effort. We can compare that to the MODs that > existed in the early aughts, that had staffs of many software developers to > make the same thing happen. We all did that, and I think the world is a > better place for it. > > > > I can't say yet where I'm going, as I have a few opportunities on the > table that haven't been finalized, but I hope to be fulfilling a similar > role in another community. If you're really interested, you can follow me > on Mastodon at @sco...@ge...cial. > > > > Thank you to all of you--I have really enjoyed working with and growing > this community, > > Scott > > > > > -- > > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > > GMOD Project Manager (http://gmod.org/ > <https://urldefense.com/v3/__http:/gmod.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLt_a75Ac4$>) > 216-392-3087 > > WormBase Developer (http://wormbase.org/ > <https://urldefense.com/v3/__http:/wormbase.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtqyOTGjk$> > ) > > Alliance of Genome Resources Group Leader (http://alliancegenome.org/ > <https://urldefense.com/v3/__http:/alliancegenome.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtfgzLlII$> > ) > > VirusSeq Project Manager (https://virusseq-dataportal.ca/ > <https://urldefense.com/v3/__https:/virusseq-dataportal.ca/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLt7Qo4Y2Y$> > ) > > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/ > <https://urldefense.com/v3/__https:/hcmi-searchable-catalog.nci.nih.gov/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtmGSQ6iE$> > ) > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > |
From: Fields, C. J <cjf...@il...> - 2024-07-23 20:42:03
|
Hi Scott, I just wanted to say a tremendous ‘thank you’ for essentially leading GMOD efforts over the last 20+ years. Wow, has it been that long!?! (I’m getting old). You should be incredibly proud of the work you and all GMOD projects and developers have accomplished; it’s a tremendous accomplishment. Hope to see you still out there somewhere in the open-bio world, and best of luck on your next steps in your career! Best, Chris From: Scott Cain <sc...@sc...> Date: Tuesday, July 23, 2024 at 1:19 PM To: gmod-announce <gmo...@li...>, gmod-devel <gmo...@li...>, gmod-ajax <gmo...@li...>, GMOD Tripal <gmo...@li...>, Gbrowse (E-mail) <gmo...@li...>, GMOD Schema/Chado List <gmo...@li...> Subject: [Gmod-gbrowse] Server change for gmod.org and an announcement Hello all, For several years, I've wanted to port the gmod.org<https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> MediaWiki instance to something else but was daunted by the task. Events have finally conspired to force me to do it, so I've spent the last month porting the content at gmod.org<https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> to a github.io<https://urldefense.com/v3/__http:/github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtQUw79P0$> hosted page. It was a real slog, but thank goodness for recursive wget, Pandoc and command line Perl to allow me to change thousands of markdown files at a time. Since gmod.org<https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> is now hosted at github.io<https://urldefense.com/v3/__http:/github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtQUw79P0$>, changes to this page can now be made with commits to the https://github.com/GMOD/gmod.github.io<https://urldefense.com/v3/__https:/github.com/GMOD/gmod.github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtU5TvTYs$> repo. That means that fixes and additions can be made by creating and editing markdown files in the gmod.github.io<https://urldefense.com/v3/__http:/gmod.github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtViLqSVk$> repo and merging the changes into the main branch. AND NOW THE ANNOUNCEMENT At the end of July, I will be stepping away from my role as GMOD project coordinator, which on one hand, makes me very sad, but on the other, fills me with immense pride in what we as the GMOD community have achieved over the last 22 years. We have truly democratized organism genomics, allowing a small lab to distribute data on whatever organisms are of interest to them with (relatively) little effort. We can compare that to the MODs that existed in the early aughts, that had staffs of many software developers to make the same thing happen. We all did that, and I think the world is a better place for it. I can't say yet where I'm going, as I have a few opportunities on the table that haven't been finalized, but I hope to be fulfilling a similar role in another community. If you're really interested, you can follow me on Mastodon at @sco...@ge...cial. Thank you to all of you--I have really enjoyed working with and growing this community, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/<https://urldefense.com/v3/__http:/gmod.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLt_a75Ac4$>) 216-392-3087 WormBase Developer (http://wormbase.org/<https://urldefense.com/v3/__http:/wormbase.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtqyOTGjk$>) Alliance of Genome Resources Group Leader (http://alliancegenome.org/<https://urldefense.com/v3/__http:/alliancegenome.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtfgzLlII$>) VirusSeq Project Manager (https://virusseq-dataportal.ca/<https://urldefense.com/v3/__https:/virusseq-dataportal.ca/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLt7Qo4Y2Y$>) Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/<https://urldefense.com/v3/__https:/hcmi-searchable-catalog.nci.nih.gov/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtmGSQ6iE$>) |
From: Scott C. <sc...@sc...> - 2024-07-23 18:18:44
|
Hello all, For several years, I've wanted to port the gmod.org MediaWiki instance to something else but was daunted by the task. Events have finally conspired to force me to do it, so I've spent the last month porting the content at gmod.org to a github.io hosted page. It was a real slog, but thank goodness for recursive wget, Pandoc and command line Perl to allow me to change thousands of markdown files at a time. Since gmod.org is now hosted at github.io, changes to this page can now be made with commits to the https://github.com/GMOD/gmod.github.io repo. That means that fixes and additions can be made by creating and editing markdown files in the gmod.github.io repo and merging the changes into the main branch. AND NOW THE ANNOUNCEMENT At the end of July, I will be stepping away from my role as GMOD project coordinator, which on one hand, makes me very sad, but on the other, fills me with immense pride in what we as the GMOD community have achieved over the last 22 years. We have truly democratized organism genomics, allowing a small lab to distribute data on whatever organisms are of interest to them with (relatively) little effort. We can compare that to the MODs that existed in the early aughts, that had staffs of many software developers to make the same thing happen. We all did that, and I think the world is a better place for it. I can't say yet where I'm going, as I have a few opportunities on the table that haven't been finalized, but I hope to be fulfilling a similar role in another community. If you're really interested, you can follow me on Mastodon at @sco...@ge...cial. Thank you to all of you--I have really enjoyed working with and growing this community, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
From: Scott C. <sc...@sc...> - 2023-11-06 21:32:30
|
Hello Hafiza, You've emailed the mailing list for people who maintain GBrowse genome browsers, which you were probably using somewhere to look at rice genomic data. Unfortunately, I can't tell where you were browsing. If I knew, I might be able to help you find the right person to ask. I suggest you go back to the website that was hosting this GBrowse instance and look for contact information. Good luck! Scott On Mon, Nov 6, 2023 at 1:29 PM Hafiza Madeeha Khan via Gmod-gbrowse < gmo...@li...> wrote: > I am writing to inquire about the availability of rice mutants and to > express my interest placing an order for these mutants. > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows > > > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
From: Hafiza M. K. <221...@lu...> - 2023-11-02 07:15:13
|
I am writing to inquire about the availability of rice mutants and to express my interest placing an order for these mutants. Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows |
From: Carolina A. <car...@st...> - 2023-06-27 09:46:30
|
Dear Dr. Naruse, Thank you very much for your prompt response. Please also thank Dr. Toyoda for his help. I understand that I cannot download the target sequence from the browser and I will speak with my supervisor about mapping the reads myself. Anyway, thank you both for all your suggestions. I wish you all a nice week ahead. With kind regards, Carolina Il giorno mar 27 giu 2023 alle ore 01:34 Kiyoshi Naruse <na...@ni...> ha scritto: > Dear Carolina and Scott, > > I asked Dr. Toyoda to download the target sequence from our browser. This > feature is not implemented. > > 1. Reference sequence is the previous version (based on Sanger sequence) > but not the current version (based on PacBio sequence and it will be more > accurate). It is better to update the reference sequence for your analysis. > 2. Illumina short read data are public domain. You can use these data > without our permission for your research, so I suggest you map these > Illumina reads by yourself. This is an uncomplicated process using Bowtie > or other mapping software. You can make consensus sequence using these > data too. > Our Illumina reads data are as follows. Simple blast search using the consensus > sequence will be work for your purpose. > https://ddbj.nig.ac.jp/resource/sra-study/DRP000619 > Project name is "Whole genome sequencing of 5 medaka strains". > > Best wishes > Kiyoshi > > > 2023年6月27日(火) 1:05 Scott Cain <sc...@sc...>: > >> Hi Carolina, >> >> You've emailed the mailing list that supports people who install and >> maintain GBrowse, the genome browser that medaka people are using. >> Unfortunately, I don't know anything about the data in that GBrowse >> instance, so I can't answer your questions. Did you try using their >> "contact us" page at https://shigen.nig.ac.jp/medaka/strain/contactUs.jsp >> ? I also found this email address that you might try: >> nbr...@bi.... >> >> Good luck! >> Scott >> >> >> On Mon, Jun 26, 2023 at 8:55 AM Carolina Agostini < >> car...@st...> wrote: >> >>> Good morning, >>> >>> My name is Carolina Agostini and currently I am a master student at >>> University of Trento (Italy). I have been working with medakafish for some >>> years now and I had the chance to discover this very interesting website ( >>> http://medaka.nig.ac.jp/service/menu), in which we can look at >>> different medaka strains genomes, or blast genes' sequences of interest. >>> >>> The problem is that I am having issues in understanding how the browser >>> works. Therefore I would like to ask you some specific information. >>> >>> >>> 1. For example, there is the chance to download the sequence of a >>> specific chromosome, but to which stain does it belong? There is no >>> information about that. Is it possible to download the sequences of a >>> chromosome only of the Kaga strain? >>> 2. When I try to blast a gene sequence in the BLAST search I obtain >>> a list, clicking on the list I can reach the browser main page and decide >>> what to look at. On select tracks I can for example focus my research on >>> Kaga and HdrR strains alignments, obtaining the coverage of the gene. The >>> problem is that when I try to reduce the base pairs shown on the browser, I >>> am actually able to see nucleotide sequences, but I am not able to >>> understand if the gene sequence present in HdrR genome, is also present in >>> Kaga genome and if the sequence is actually the same of whether there are >>> differences (i.e. SNPs...). >>> >>> >>> I really hope that I was able to correctly express myself, unluckily I >>> am not a bioinformatician. >>> >>> >>> I am looking forward to hear from you soon, >>> >>> Thank you in advance for your attention. >>> >>> >>> Best regards, >>> >>> Carolina >>> >>> -- >>> >>> Carolina Agostini, Master student >>> Laboratory of Translational Neurogenetics >>> >>> Department of Cellular, Computational and Integrative Biology, CIBIO >>> >>> Università degli Studi di Trento >>> <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> >>> >>> Via Sommarive 9 >>> <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> >>> >>> 38123 Trento-Povo >>> <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> >>> >>> Italy >>> <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> >>> >>> >>> >>> Tel.: (0039) 0461 283763 >>> >>> Web >>> >>> www.cibio.unitn.it/744/laboratory-of-translational-neurogenetics >>> >>> https://mcarl255.wixsite.com/mysite >>> >>> >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott >> at scottcain dot net >> GMOD Project Manager (http://gmod.org/) >> 216-392-3087 >> WormBase Developer (http://wormbase.org/) >> Alliance of Genome Resources Group Leader (http://alliancegenome.org/) >> VirusSeq Project Manager (https://virusseq-dataportal.ca/) >> Human Cancer Models Initiative Project Manager ( >> https://hcmi-searchable-catalog.nci.nih.gov/) >> >> -- >> このグループから退会し、グループからのメールの配信を停止するには nbr...@bi... >> にメールを送信してください。 >> > > > -- > > > 〒444-8585 愛知県岡崎市明大寺町字西郷中38番地 > 基礎生物学研究所 > > バイオリソース研究室 > > (併任)総合研究大学院大学 > > 生命科学研究科・基礎生物学専攻 > 成瀬 清 > 電話/ファクス: 0564-55-7580 (B15室) 0564-55-7554(301室) > email: na...@ni... > Kiyoshi NARUSE, PhD > National Institute for Basic Biology, > Laboratory of Bioresources, > Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan > TEL/FAX: 0564-55-7580 (B15) 0564-55-7554 (301) > email: na...@ni... > > NBRP Medaka(https://shigen.nig.ac.jp/medaka/) > > NBRP medaka on Facebook(https://www.facebook.com/nbrpmedaka/) > > -------------------------------------------------------------- > 大学連携バイオバックアッププロジェクト > 〒444-8787 愛知県岡崎市明大寺町字東山5-1 > 基礎生物学研究所IBBPセンター > 電話:0564-59-5930 ファクス:0564-59-5933 email:ib...@ni... (プロジェクト共通アドレス) > NIBB Center of the Interuniversity Bio-Backup Project > TEL:0564-59-5930 FAX:0564-59-5933 > > -- Carolina Agostini, Master student Laboratory of Translational Neurogenetics Department of Cellular, Computational and Integrative Biology, CIBIO Università degli Studi di Trento <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> Via Sommarive 9 <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> 38123 Trento-Povo <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> Italy <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> Tel.: (0039) 0461 283763 Web www.cibio.unitn.it/744/laboratory-of-translational-neurogenetics https://mcarl255.wixsite.com/mysite |
From: Kiyoshi N. <na...@ni...> - 2023-06-27 00:38:04
|
Dear Carolina and Scott, I asked Dr. Toyoda to download the target sequence from our browser. This feature is not implemented. 1. Reference sequence is the previous version (based on Sanger sequence) but not the current version (based on PacBio sequence and it will be more accurate). It is better to update the reference sequence for your analysis. 2. Illumina short read data are public domain. You can use these data without our permission for your research, so I suggest you map these Illumina reads by yourself. This is an uncomplicated process using Bowtie or other mapping software. You can make consensus sequence using these data too. Our Illumina reads data are as follows. Simple blast search using the consensus sequence will be work for your purpose. https://ddbj.nig.ac.jp/resource/sra-study/DRP000619 Project name is "Whole genome sequencing of 5 medaka strains". Best wishes Kiyoshi 2023年6月27日(火) 1:05 Scott Cain <sc...@sc...>: > Hi Carolina, > > You've emailed the mailing list that supports people who install and > maintain GBrowse, the genome browser that medaka people are using. > Unfortunately, I don't know anything about the data in that GBrowse > instance, so I can't answer your questions. Did you try using their > "contact us" page at https://shigen.nig.ac.jp/medaka/strain/contactUs.jsp > ? I also found this email address that you might try: > nbr...@bi.... > > Good luck! > Scott > > > On Mon, Jun 26, 2023 at 8:55 AM Carolina Agostini < > car...@st...> wrote: > >> Good morning, >> >> My name is Carolina Agostini and currently I am a master student at >> University of Trento (Italy). I have been working with medakafish for some >> years now and I had the chance to discover this very interesting website ( >> http://medaka.nig.ac.jp/service/menu), in which we can look at different >> medaka strains genomes, or blast genes' sequences of interest. >> >> The problem is that I am having issues in understanding how the browser >> works. Therefore I would like to ask you some specific information. >> >> >> 1. For example, there is the chance to download the sequence of a >> specific chromosome, but to which stain does it belong? There is no >> information about that. Is it possible to download the sequences of a >> chromosome only of the Kaga strain? >> 2. When I try to blast a gene sequence in the BLAST search I obtain a >> list, clicking on the list I can reach the browser main page and decide >> what to look at. On select tracks I can for example focus my research on >> Kaga and HdrR strains alignments, obtaining the coverage of the gene. The >> problem is that when I try to reduce the base pairs shown on the browser, I >> am actually able to see nucleotide sequences, but I am not able to >> understand if the gene sequence present in HdrR genome, is also present in >> Kaga genome and if the sequence is actually the same of whether there are >> differences (i.e. SNPs...). >> >> >> I really hope that I was able to correctly express myself, unluckily I am >> not a bioinformatician. >> >> >> I am looking forward to hear from you soon, >> >> Thank you in advance for your attention. >> >> >> Best regards, >> >> Carolina >> >> -- >> >> Carolina Agostini, Master student >> Laboratory of Translational Neurogenetics >> >> Department of Cellular, Computational and Integrative Biology, CIBIO >> >> Università degli Studi di Trento >> <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> >> >> Via Sommarive 9 >> <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> >> >> 38123 Trento-Povo >> <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> >> >> Italy >> <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> >> >> >> >> Tel.: (0039) 0461 283763 >> >> Web >> >> www.cibio.unitn.it/744/laboratory-of-translational-neurogenetics >> >> https://mcarl255.wixsite.com/mysite >> >> >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > GMOD Project Manager (http://gmod.org/) > 216-392-3087 > WormBase Developer (http://wormbase.org/) > Alliance of Genome Resources Group Leader (http://alliancegenome.org/) > VirusSeq Project Manager (https://virusseq-dataportal.ca/) > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/) > > -- > このグループから退会し、グループからのメールの配信を停止するには nbr...@bi... > にメールを送信してください。 > -- 〒444-8585 愛知県岡崎市明大寺町字西郷中38番地 基礎生物学研究所 バイオリソース研究室 (併任)総合研究大学院大学 生命科学研究科・基礎生物学専攻 成瀬 清 電話/ファクス: 0564-55-7580 (B15室) 0564-55-7554(301室) email: na...@ni... Kiyoshi NARUSE, PhD National Institute for Basic Biology, Laboratory of Bioresources, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan TEL/FAX: 0564-55-7580 (B15) 0564-55-7554 (301) email: na...@ni... NBRP Medaka(https://shigen.nig.ac.jp/medaka/) NBRP medaka on Facebook(https://www.facebook.com/nbrpmedaka/) -------------------------------------------------------------- 大学連携バイオバックアッププロジェクト 〒444-8787 愛知県岡崎市明大寺町字東山5-1 基礎生物学研究所IBBPセンター 電話:0564-59-5930 ファクス:0564-59-5933 email:ib...@ni... (プロジェクト共通アドレス) NIBB Center of the Interuniversity Bio-Backup Project TEL:0564-59-5930 FAX:0564-59-5933 |
From: Scott C. <sc...@sc...> - 2023-06-26 16:28:18
|
Hi Carolina, You've emailed the mailing list that supports people who install and maintain GBrowse, the genome browser that medaka people are using. Unfortunately, I don't know anything about the data in that GBrowse instance, so I can't answer your questions. Did you try using their "contact us" page at https://shigen.nig.ac.jp/medaka/strain/contactUs.jsp ? I also found this email address that you might try: nbr...@bi.... Good luck! Scott On Mon, Jun 26, 2023 at 8:55 AM Carolina Agostini < car...@st...> wrote: > Good morning, > > My name is Carolina Agostini and currently I am a master student at > University of Trento (Italy). I have been working with medakafish for some > years now and I had the chance to discover this very interesting website ( > http://medaka.nig.ac.jp/service/menu), in which we can look at different > medaka strains genomes, or blast genes' sequences of interest. > > The problem is that I am having issues in understanding how the browser > works. Therefore I would like to ask you some specific information. > > > 1. For example, there is the chance to download the sequence of a > specific chromosome, but to which stain does it belong? There is no > information about that. Is it possible to download the sequences of a > chromosome only of the Kaga strain? > 2. When I try to blast a gene sequence in the BLAST search I obtain a > list, clicking on the list I can reach the browser main page and decide > what to look at. On select tracks I can for example focus my research on > Kaga and HdrR strains alignments, obtaining the coverage of the gene. The > problem is that when I try to reduce the base pairs shown on the browser, I > am actually able to see nucleotide sequences, but I am not able to > understand if the gene sequence present in HdrR genome, is also present in > Kaga genome and if the sequence is actually the same of whether there are > differences (i.e. SNPs...). > > > I really hope that I was able to correctly express myself, unluckily I am > not a bioinformatician. > > > I am looking forward to hear from you soon, > > Thank you in advance for your attention. > > > Best regards, > > Carolina > > -- > > Carolina Agostini, Master student > Laboratory of Translational Neurogenetics > > Department of Cellular, Computational and Integrative Biology, CIBIO > > Università degli Studi di Trento > <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> > > Via Sommarive 9 > <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> > > 38123 Trento-Povo > <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> > > Italy > <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> > > > > Tel.: (0039) 0461 283763 > > Web > > www.cibio.unitn.it/744/laboratory-of-translational-neurogenetics > > https://mcarl255.wixsite.com/mysite > > > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
From: Carolina A. <car...@st...> - 2023-06-24 10:20:59
|
Good morning, My name is Carolina Agostini and currently I am a master student at University of Trento (Italy). I have been working with medakafish for some years now and I had the chance to discover this very interesting website ( http://medaka.nig.ac.jp/service/menu), in which we can look at different medaka strains genomes, or blast genes' sequences of interest. The problem is that I am having issues in understanding how the browser works. Therefore I would like to ask you some specific information. 1. For example, there is the chance to download the sequence of a specific chromosome, but to which stain does it belong? There is no information about that. Is it possible to download the sequences of a chromosome only of the Kaga strain? 2. When I try to blast a gene sequence in the BLAST search I obtain a list, clicking on the list I can reach the browser main page and decide what to look at. On select tracks I can for example focus my research on Kaga and HdrR strains alignments, obtaining the coverage of the gene. The problem is that when I try to reduce the base pairs shown on the browser, I am actually able to see nucleotide sequences, but I am not able to understand if the gene sequence present in HdrR genome, is also present in Kaga genome and if the sequence is actually the same of whether there are differences (i.e. SNPs...). I really hope that I was able to correctly express myself, unluckily I am not a bioinformatician. I am looking forward to hear from you soon, Thank you in advance for your attention. Best regards, Carolina -- Carolina Agostini, Master student Laboratory of Translational Neurogenetics Department of Cellular, Computational and Integrative Biology, CIBIO Università degli Studi di Trento <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> Via Sommarive 9 <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> 38123 Trento-Povo <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> Italy <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g> Tel.: (0039) 0461 283763 Web www.cibio.unitn.it/744/laboratory-of-translational-neurogenetics https://mcarl255.wixsite.com/mysite |
From: Tony V. <ton...@ou...> - 2023-01-02 01:35:55
|
Thomas and Scott, Thank you very much for your collective responses. I am relieved that it was anything serious, and that order in the universe has been restored.... Regards, Tony From: Thomas Krahn<mailto:th...@tk...> Sent: Saturday, 10 December 2022 8:00 PM To: Scott Cain<mailto:sc...@sc...>; Tony Vivian<mailto:ton...@ou...> Cc: gmo...@li...<mailto:gmo...@li...> Subject: Re: [Gmod-gbrowse] YBrowse prob Dear Scott, Thank you for forwarding the user request to me. Dear Tony, YBrowse goes through an update cycle every day where the new Y SNP database is being reloaded. I'm sorry that you were accessing the browser just at the moment when the update was going on. Unfortunately YBrowse is in maintenance mode during the update and the STR markers (like DYS437) is one of the last features that is added to the database. So at the time when you were accessing YBrowse the search function couldn't find it. [cid:par...@tk...] Now it should be working again. [cid:par...@tk...] Thank you for reporting! Thomas On 12/8/22 20:38, Scott Cain wrote: Hi Tony, This is the mailing list for GBrowse, the software that powers YBrowse. I don't know anything about the data or configuration of YBrowse, so I can't answer your question. I'm going to cc Thomas Krahn, who might know more. Scott On Thu, Dec 8, 2022 at 11:35 AM Tony Vivian <ton...@ou...<mailto:ton...@ou...>> wrote: Hi I was happily browsing on your YBrowse when it started throw up..Not Found messages. As you can see from the image, I used one of your suggestions under the input box, reset the page and yet no joy ☹ Can you fix and/or suggest a solution please? Thanks, Tony [cid:image002.png@01D91EA6.B3D51170] _______________________________________________ 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 Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/) |
From: Thomas K. <th...@tk...> - 2022-12-10 09:13:31
|
Dear Scott, Thank you for forwarding the user request to me. Dear Tony, YBrowse goes through an update cycle every day where the new Y SNP database is being reloaded. I'm sorry that you were accessing the browser just at the moment when the update was going on. Unfortunately YBrowse is in maintenance mode during the update and the STR markers (like DYS437) is one of the last features that is added to the database. So at the time when you were accessing YBrowse the search function couldn't find it. Now it should be working again. Thank you for reporting! Thomas On 12/8/22 20:38, Scott Cain wrote: > Hi Tony, > > This is the mailing list for GBrowse, the software that powers > YBrowse. I don't know anything about the data or configuration of > YBrowse, so I can't answer your question. I'm going to cc Thomas > Krahn, who might know more. > > Scott > > > On Thu, Dec 8, 2022 at 11:35 AM Tony Vivian <ton...@ou...> > wrote: > > Hi > > I was happily browsing on your YBrowse when it started throw > up..Not Found messages. > > As you can see from the image, I used one of your suggestions > under the input box, reset the page and yet no joy ☹ > > Can you fix and/or suggest a solution please? > > Thanks, > > Tony > > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Project Manager (http://gmod.org/) 216-392-3087 > WormBase Developer (http://wormbase.org/) > Alliance of Genome Resources Group Leader (http://alliancegenome.org/) > VirusSeq Project Manager (https://virusseq-dataportal.ca/) > Human Cancer Models Initiative Project Manager > (https://hcmi-searchable-catalog.nci.nih.gov/) |
From: Scott C. <sc...@sc...> - 2022-12-08 20:09:56
|
Hi Tony, This is the mailing list for GBrowse, the software that powers YBrowse. I don't know anything about the data or configuration of YBrowse, so I can't answer your question. I'm going to cc Thomas Krahn, who might know more. Scott On Thu, Dec 8, 2022 at 11:35 AM Tony Vivian <ton...@ou...> wrote: > Hi > > > > I was happily browsing on your YBrowse when it started throw up..Not Found > messages. > > > > As you can see from the image, I used one of your suggestions under the > input box, reset the page and yet no joy ☹ > > > > Can you fix and/or suggest a solution please? > > > > Thanks, > > Tony > > > > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
From: Tony V. <ton...@ou...> - 2022-11-17 03:43:16
|
Hi I was happily browsing on your YBrowse when it started throw up..Not Found messages. As you can see from the image, I used one of your suggestions under the input box, reset the page and yet no joy ☹ Can you fix and/or suggest a solution please? Thanks, Tony [cid:image003.png@01D8FA92.DFC6DA30] |
From: Mohd A. Ab H. <ami...@mp...> - 2022-10-31 09:35:57
|
Dear sir, I need your help on my gbrowse, all the tracks are hidden, the ballon is showing the properties of the track but the track is hidden. Please help [ http://genomsawit.mpob.gov.my/pic/GS_logo3.png ] Mohd Amin Ab Halim Bioinformatics t: 03-8769 4963 e: ami...@mp... MPOB No. 6, Jalan Institusi, Bandar Baru Bangi 43000 Kajang, Selangor [ http://mpob.gov.my/ | mpob.gov.my ] [ https://www.facebook.com/amean23 ] [ https://www.linkedin.com/company/amean23 ] [ https://www.youtube.com/user/amean23 ] |
From: Scott C. <sc...@sc...> - 2022-08-29 22:45:27
|
Hi Abigail, You've reached the email support for people who set up GBrowse instances, but as it happens, I took a quick look at ciliate.org and found this page: http://ciliate.org/index.php/home/downloads from which you should be able to get the full genome sequence of the organism you're interested in. If not, I'd suggest that you contact the curators at ciliate.org (cc'ed here). Thanks and good luck, Scott On Mon, Aug 29, 2022 at 3:32 PM Abigail Howell <aah...@as...> wrote: > Hello, > > I was wondering how to download the entire gff on > http://www.ciliate.org/gb2/gbrowse/tetrahymena2020/ rather than just a > section of it, thank you! > > Best, > Abby > > -- > *Abigail Howell* > > Arizona State University | Barrett Honors College | Class of 2017 > > Biological Sciences (Biomedical Sciences), BS > > Ph.D. Candidate, Molecular and Cellular Biology > > Arizona State University > > aah...@as... | (480) 292-2575 > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
From: Abigail H. <aah...@as...> - 2022-08-29 20:58:02
|
Hello, I was wondering how to download the entire gff on http://www.ciliate.org/gb2/gbrowse/tetrahymena2020/ rather than just a section of it, thank you! Best, Abby -- *Abigail Howell* Arizona State University | Barrett Honors College | Class of 2017 Biological Sciences (Biomedical Sciences), BS Ph.D. Candidate, Molecular and Cellular Biology Arizona State University aah...@as... | (480) 292-2575 |
From: Scott C. <sc...@sc...> - 2022-05-02 03:12:39
|
Is this the problem? If so, that should be an easy fix: couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck' Is /var/lib/gbrowse2/sessions/ writable by the webserver? On Fri, Apr 29, 2022 at 5:53 PM Ramanathan, Vivek <vra...@bc...> wrote: > Dear Scott, > > > > Please find attached the error. The error is related to database > connection. > > > > However, the following perl script is successful. > > > > use Bio::DB::SeqFeature::Store; > > > > # Open the feature database > > my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', > > -dsn => > 'dbi:mysql:database=getbac:host=10.15.12.121', > > -user => 'admin', > > -pass => '######', > > -create => 1 ); > > my $feature = $db->fetch(1); > > > > Regards, > > Vivek > > Ld. Programmer/Analyst > > Tel: (713)798-3425 > > Email: viv...@bc... > > > > *From:* Scott Cain <sc...@sc...> > *Sent:* Friday, April 29, 2022 7:17 PM > *To:* Rajaya, Kiran <ra...@bc...> > *Cc:* Gbrowse (E-mail) <gmo...@li...>; Ramanathan, > Vivek <vra...@bc...> > *Subject:* Re: gbrowse2 > > > > Are there any error messages in the apache error log? > > > > The connection bit I use in my (very old but still mostly functional) > GBrowse instance looks like this: > > > > [this_database:database] > db_args = -adaptor DBI::mysql -dsn > dbi:mysql:database=c_elegans_PRJNA13758_WS284;host=rdbms.wormbase.org > <https://urldefense.proofpoint.com/v2/url?u=http-3A__rdbms.wormbase.org&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Aw-d35oMueWL9ZC1DtA2jkstG2_G9UsPtujet09dtPs&m=O-6Tgm2jV9nwizZugYpYb_UXlL3P1i0RKBBGOSMiWTwzBZSROz3h80PTtj7xLSCj&s=LHC17xN_My2KVQONxnlYxmectFk9WVzLmlZW64VjKYQ&e=> > -user ********* -pass ********* > search options = default, +wildcard, -stem, +fulltext, +autocomplete > db_adaptor = Bio::DB::SeqFeature::Store > > > > On Fri, Apr 29, 2022 at 4:34 PM Rajaya, Kiran <ra...@bc...> wrote: > > Hi Scott, > > > > Thanks for your prompt response. The MySQL is on a different server from > where gbrowse is installed and we are able to connect to MySQL fine.. the > modules are also installed. > > > > Thanks > > Kiran > > > > Get Outlook for Android > <https://urldefense.proofpoint.com/v2/url?u=https-3A__aka.ms_AAb9ysg&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Aw-d35oMueWL9ZC1DtA2jkstG2_G9UsPtujet09dtPs&m=O-6Tgm2jV9nwizZugYpYb_UXlL3P1i0RKBBGOSMiWTwzBZSROz3h80PTtj7xLSCj&s=mw0V_shH7h63pSC23qfNsWoNmgN5VAKZ3Sc1Leuts0g&e=> > > > ------------------------------ > > *From:* Scott Cain <sc...@sc...> > *Sent:* Friday, April 29, 2022, 6:10 PM > *To:* Rajaya, Kiran <ra...@bc...>; Gbrowse (E-mail) < > gmo...@li...> > *Cc:* he...@gm... <he...@gm...> > *Subject:* Re: gbrowse2 > > > ****CAUTION:*** This email is not from a BCM Source. Only click links or > open attachments you know are safe.* > ------------------------------ > > Hi Kiran, > > > > Oh, that could be difficult to debug. I'll start with suggesting that you > move to JBrowse 1 (quite stable) or JBrowse 2 (active development with new > features getting added often). http://jbrowse.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__jbrowse.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=XIIakvN9-mX88hFwKeTtLHUhV8huao67UvIqVIjAhFw&e=> > > > > I'll start with this: is the mysql database on the same machine as the > GBrowse 2 install, and are there any useful error messages in the apache > error log? Are the DBI and DBD::mysql perl modules installed? > > > > Scott > > > > > > On Fri, Apr 29, 2022 at 3:33 PM Rajaya, Kiran <ra...@bc...> wrote: > > Hi, > > > > I have question about gbrowse2 that we have setup on a new server since we > migrated. We have setup everything however the gbrowse is not able to call > the MySQL database. How can I check what is missing to make the connection > successfully? > > > > Thanks! > > Kiran > > > > > > -- > > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > > GMOD Project Manager (http://gmod.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=Fd7Ky6SNhoDPhG4W0EMV0GiQqIxTaqUUWyAPj3KKnWc&e=>) > 216-392-3087 > > WormBase Developer (http://wormbase.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__wormbase.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=3bxGb8tS10UMCojT16HmKRLk9ZNxLEkDS8F-lunME1M&e=> > ) > > Alliance of Genome Resources Group Leader (http://alliancegenome.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__alliancegenome.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=XEjtgIqbuOa3aOLXCCijqCTM5oWJre1NDL7EaUr7dac&e=> > ) > > VirusSeq Project Manager (https://virusseq-dataportal.ca/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__virusseq-2Ddataportal.ca_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=OFzE21Mf6PYkwslGeuMB4xVIDe6lbOf1x4NBbzPM9ac&e=> > ) > > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__hcmi-2Dsearchable-2Dcatalog.nci.nih.gov_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=1ayszIll2pyNbqyHxWAiKA0HbnrlueykEKFeA-UiPbA&e=> > ) > > > > > > -- > > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > > GMOD Project Manager (http://gmod.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Aw-d35oMueWL9ZC1DtA2jkstG2_G9UsPtujet09dtPs&m=O-6Tgm2jV9nwizZugYpYb_UXlL3P1i0RKBBGOSMiWTwzBZSROz3h80PTtj7xLSCj&s=TW7Hj8SS8mCneGx_CFTqFQivwBbGmjvIKLqwjsrL9GI&e=>) > 216-392-3087 > > WormBase Developer (http://wormbase.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__wormbase.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Aw-d35oMueWL9ZC1DtA2jkstG2_G9UsPtujet09dtPs&m=O-6Tgm2jV9nwizZugYpYb_UXlL3P1i0RKBBGOSMiWTwzBZSROz3h80PTtj7xLSCj&s=wiaQuEfR1v1uDhNJ3TPkDYecAg8jzTyIfYVgEnsJ6Gg&e=> > ) > > Alliance of Genome Resources Group Leader (http://alliancegenome.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__alliancegenome.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Aw-d35oMueWL9ZC1DtA2jkstG2_G9UsPtujet09dtPs&m=O-6Tgm2jV9nwizZugYpYb_UXlL3P1i0RKBBGOSMiWTwzBZSROz3h80PTtj7xLSCj&s=JXDGR9JmkcD1Qyoy9iP5uTVmSW9AjfutDXv53wfuSAo&e=> > ) > > VirusSeq Project Manager (https://virusseq-dataportal.ca/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__virusseq-2Ddataportal.ca_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Aw-d35oMueWL9ZC1DtA2jkstG2_G9UsPtujet09dtPs&m=O-6Tgm2jV9nwizZugYpYb_UXlL3P1i0RKBBGOSMiWTwzBZSROz3h80PTtj7xLSCj&s=Y4lebneF5AwIByya3ycP4dUOJAXY3i7j6jDCWZXNW4M&e=> > ) > > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__hcmi-2Dsearchable-2Dcatalog.nci.nih.gov_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Aw-d35oMueWL9ZC1DtA2jkstG2_G9UsPtujet09dtPs&m=O-6Tgm2jV9nwizZugYpYb_UXlL3P1i0RKBBGOSMiWTwzBZSROz3h80PTtj7xLSCj&s=OmbzSF4xyLYQEkogmVVC_ZcfV6Iy_IkadGvHiW8FNkQ&e=> > ) > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
From: Scott C. <sc...@sc...> - 2022-04-30 00:17:43
|
Are there any error messages in the apache error log? The connection bit I use in my (very old but still mostly functional) GBrowse instance looks like this: [this_database:database] db_args = -adaptor DBI::mysql -dsn dbi:mysql:database=c_elegans_PRJNA13758_WS284;host=rdbms.wormbase.org -user ********* -pass ********* search options = default, +wildcard, -stem, +fulltext, +autocomplete db_adaptor = Bio::DB::SeqFeature::Store On Fri, Apr 29, 2022 at 4:34 PM Rajaya, Kiran <ra...@bc...> wrote: > Hi Scott, > > Thanks for your prompt response. The MySQL is on a different server from > where gbrowse is installed and we are able to connect to MySQL fine.. the > modules are also installed. > > Thanks > Kiran > > Get Outlook for Android <https://aka.ms/AAb9ysg> > > ------------------------------ > *From:* Scott Cain <sc...@sc...> > *Sent:* Friday, April 29, 2022, 6:10 PM > *To:* Rajaya, Kiran <ra...@bc...>; Gbrowse (E-mail) < > gmo...@li...> > *Cc:* he...@gm... <he...@gm...> > *Subject:* Re: gbrowse2 > > ****CAUTION:*** This email is not from a BCM Source. Only click links or > open attachments you know are safe.* > ------------------------------ > Hi Kiran, > > Oh, that could be difficult to debug. I'll start with suggesting that you > move to JBrowse 1 (quite stable) or JBrowse 2 (active development with new > features getting added often). http://jbrowse.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__jbrowse.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=XIIakvN9-mX88hFwKeTtLHUhV8huao67UvIqVIjAhFw&e=> > > I'll start with this: is the mysql database on the same machine as the > GBrowse 2 install, and are there any useful error messages in the apache > error log? Are the DBI and DBD::mysql perl modules installed? > > Scott > > > On Fri, Apr 29, 2022 at 3:33 PM Rajaya, Kiran <ra...@bc...> wrote: > >> Hi, >> >> >> >> I have question about gbrowse2 that we have setup on a new server since >> we migrated. We have setup everything however the gbrowse is not able to >> call the MySQL database. How can I check what is missing to make the >> connection successfully? >> >> >> >> Thanks! >> >> Kiran >> >> >> > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > GMOD Project Manager (http://gmod.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=Fd7Ky6SNhoDPhG4W0EMV0GiQqIxTaqUUWyAPj3KKnWc&e=>) > 216-392-3087 > WormBase Developer (http://wormbase.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__wormbase.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=3bxGb8tS10UMCojT16HmKRLk9ZNxLEkDS8F-lunME1M&e=> > ) > Alliance of Genome Resources Group Leader (http://alliancegenome.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__alliancegenome.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=XEjtgIqbuOa3aOLXCCijqCTM5oWJre1NDL7EaUr7dac&e=> > ) > VirusSeq Project Manager (https://virusseq-dataportal.ca/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__virusseq-2Ddataportal.ca_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=OFzE21Mf6PYkwslGeuMB4xVIDe6lbOf1x4NBbzPM9ac&e=> > ) > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__hcmi-2Dsearchable-2Dcatalog.nci.nih.gov_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=1ayszIll2pyNbqyHxWAiKA0HbnrlueykEKFeA-UiPbA&e=> > ) > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
From: Scott C. <sc...@sc...> - 2022-04-30 00:03:38
|
Hi Kiran, Oh, that could be difficult to debug. I'll start with suggesting that you move to JBrowse 1 (quite stable) or JBrowse 2 (active development with new features getting added often). http://jbrowse.org/ I'll start with this: is the mysql database on the same machine as the GBrowse 2 install, and are there any useful error messages in the apache error log? Are the DBI and DBD::mysql perl modules installed? Scott On Fri, Apr 29, 2022 at 3:33 PM Rajaya, Kiran <ra...@bc...> wrote: > Hi, > > > > I have question about gbrowse2 that we have setup on a new server since we > migrated. We have setup everything however the gbrowse is not able to call > the MySQL database. How can I check what is missing to make the connection > successfully? > > > > Thanks! > > Kiran > > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
From: Scott C. <sc...@sc...> - 2022-03-23 16:55:23
|
Hello Haitham, You've reached the mailing list for people who support GBrowse installations, which is the software that powers YBrowse. I've tried a few times to reach the people that are responsible for YBrowse unsuccessfully, since I occasionally get emails like this. If you have any idea who I should contact in the future, please let me know. Good luck! Scott On Wed, Mar 23, 2022 at 9:52 AM You know Who <who...@gm...> wrote: > Dears: > > When is the next YBrowse update? > > Regards, > > Haitham > > > > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) |
From: Scott C. <sc...@sc...> - 2022-03-23 04:31:26
|
BOSC 2022 dates: July 13-14, as part of ISMB 2022 Location: Madison, WI, USA, and virtual Website: <https://www.open-bio.org/wiki/BOSC_2019> https://www.open-bio.org/events/bosc/ BOSC announcements mailing list: <http://lists.open-bio.org/mailman/listinfo/bosc-announce> https://groups.google.com/forum/#!forum/bosc-announce Slack channel: https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew Twitter: @OBF_BOSC <https://twitter.com/OBF_BOSC>, #BOSC2022 Key Dates - April 21, 2022: Deadline for submitting talk/poster abstracts <https://www.open-bio.org/events/bosc-2022/submit/> - May 12: Talk/poster acceptance notifications - May 19: Late poster (and Late-Breaking Lightning Talk) submission deadline - May 26: Late poster / LBLT acceptance notifications - July 13-14: BOSC 2022 <https://www.open-bio.org/events/bosc-2022/> - July 15-16: CollaborationFest (CoFest) About BOSC The Bioinformatics Open Source Conference promotes and facilitates the open source development of bioinformatics tools and open science. Since 2000, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics and open science. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them. As usual, BOSC will include keynote talks, longer and shorter (lightning) talks from submitted abstracts, posters, Birds of a Feather, and more! New this year: Joint session with Bio-Ontologies <https://www.open-bio.org/2022/03/03/bosc-and-bio-ontologies-joint-session/> ! We are excited to announce that BOSC and Bio-Ontologies <https://www.bio-ontologies.org.uk/ismb-annual-meeting> will join forces for part of a day at ISMB 2022. The joint session will feature keynote speaker Melissa Haendel as well as talks chosen from abstracts submitted to BOSC or Bio-Ontologies. Keynote Speakers <https://open-bio.org/events/bosc-2022/bosc-2022-keynotes> Melissa Haendel is the Chief Research Informatics Officer at University of Colorado Anschutz Medical Campus, and Director of the Center for Data to Health (CD2H). With expertise in molecular genetics and developmental biology as well as translational informatics, Dr. Haendel focuses on open science and data integration to improve rare-disease diagnosis and mechanism discovery. She is a leader in ontologies and standards for data sharing. Lior Pachter is the Bren professor of computational biology at Caltech. He is a Fellow of the International Society of Computational Biology <https://www.iscb.org/iscb-fellows> and has been awarded a National Science Foundation CAREER award, a Sloan Research Fellowship His research interests span the mathematical and biological sciences, including algorithms, combinatorics, comparative genomics, algebraic statistics, molecular biology and evolution. Dr. Pachter is known as a vociferous advocate of open and accountable science. A third keynote speaker will be announced soon! Abstract submission We encourage you to submit abstracts <https://www.open-bio.org/events/bosc-2022/submit/> (due April 21 – sorry, no extensions) 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. Abstracts that are not chosen for talks will automatically be considered for posters. Abstract submission will be via ISMB’s EasyChair. Note that ISMB/ECCB requires a short (200-word) text-only abstract for all submissions (talk or poster), plus a “long abstract” (PDF, 2 pages max) if you want to be considered for a talk. A second, later round of submissions will end May 19. Abstracts submitted in the late round will be considered only for posters and a limited number of “late-breaking lightning talk” slots; they are not eligible for longer talks. Registration fee assistance We realize that the cost of ISMB may be prohibitive for some. If you are submitting an abstract to BOSC and would have difficulty covering the cost of registration, you can request a registration fee waiver right on the abstract submission form (which will not be seen by reviewers). Those who are not submitting abstracts can apply for an OBF Event Fellowship <https://www.open-bio.org/event-awards/> (deadline April 1, 2022). BOSC topics include (but are not limited to): - Ontologies: Open Source Tools and Approaches (new this year – joint session with Bio-Ontologies COSI <http://www.bio-ontologies.org.uk/>) - Open Science and Reproducible Research - Open Biomedical Data - Citizen/Participatory Science - Standards and Interoperability - Data Science - Workflows - Open Approaches to Translational Bioinformatics - Open Science for Global Health - Developer Tools and Libraries - Inclusion, Outreach and Training - Bioinformatics Open Source Project Reports (about new or existing projects) - Open and interoperable ontologies (joint session with Bio-Ontologies <https://www.open-bio.org/2022/03/03/bosc-and-bio-ontologies-joint-session/> ) We look forward to reading your abstract and seeing you (in person or virtually) at BOSC 2022! Sincerely, BOSC 2022 Organizing Committee: Nomi Harris, Karsten Hokamp, Hervé Ménager, Monica Munoz-Torres, Deepak Unni, Nicole Vasilevsky, Jason Williams -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) |
From: You k. W. <who...@gm...> - 2022-03-14 20:39:02
|
Dears: When is the next YBrowse update? Regards, Haitham |