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From: Peter C. <p.j...@go...> - 2025-01-20 20:12:18
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The ad...@li... address may not be working. I am trying another address for Michael. Also the Sea Lice Research Centre (SLRC) URL http://www.slrc.no/ does not work (nor as https://www.slrc.no/ rather than http). Peter On Sun, Jan 19, 2025 at 7:10 PM Peter Cock <p.j...@go...> wrote: > Hello Albert, > > Your email went to the mailing list for the software GBrowse, which is > running on https://licebase.org/ > > See https://licebase.org/about.html - LiceBase is developed at the Sea > Lice Research Centre (SLRC), hosted by University of Bergen.Try Michael > Dondrup (ad...@li...), CC'd. > > (I have used GBrowse myself in the past, but have no other connection here) > > Peter > > On Sat, Jan 4, 2025 at 7:46 AM Albert Liu <al...@ne...> wrote: > >> (If you are NOT CEO, please kindly forward this to your CEO, because this >> is urgent. If you believe this has been sent to you in error, please ignore >> it. Thanks) >> Dear CEO, >> This email is from China domain name registration center. On January 4, >> 2025, we received an application from Hongfei Ltd requested "licebase" >> as their internet keyword and China (CN) domain names (licebase.cn, >> licebase.com.cn, licebase.net.cn, licebase.org.cn). But after checking >> it, we find this name conflict with your company name or trademark. In >> order to deal with this matter better, it's necessary to send email to you >> and confirm whether this company is your business partner in China? >> >> Best regards >> ------------------------------ >> *Albert Liu* >> >> General Manager >> >> *Name Registry* >> >> Tel: +86-2161918696 | Fax: +86-2161918697 | Mob: +86-13816428671 >> >> 12F Kaike Building, No. 1801 Hongmei Road, Shanghai 200233, China >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > |
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From: Peter C. <p.j...@go...> - 2025-01-19 19:10:40
|
Hello Albert, Your email went to the mailing list for the software GBrowse, which is running on https://licebase.org/ See https://licebase.org/about.html - LiceBase is developed at the Sea Lice Research Centre (SLRC), hosted by University of Bergen.Try Michael Dondrup (ad...@li...), CC'd. (I have used GBrowse myself in the past, but have no other connection here) Peter On Sat, Jan 4, 2025 at 7:46 AM Albert Liu <al...@ne...> wrote: > (If you are NOT CEO, please kindly forward this to your CEO, because this > is urgent. If you believe this has been sent to you in error, please ignore > it. Thanks) > Dear CEO, > This email is from China domain name registration center. On January 4, > 2025, we received an application from Hongfei Ltd requested "licebase" as > their internet keyword and China (CN) domain names (licebase.cn, > licebase.com.cn, licebase.net.cn, licebase.org.cn). But after checking > it, we find this name conflict with your company name or trademark. In > order to deal with this matter better, it's necessary to send email to you > and confirm whether this company is your business partner in China? > > Best regards > ------------------------------ > *Albert Liu* > > General Manager > > *Name Registry* > > Tel: +86-2161918696 | Fax: +86-2161918697 | Mob: +86-13816428671 > > 12F Kaike Building, No. 1801 Hongmei Road, Shanghai 200233, China > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > |
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From: Albert L. <al...@ne...> - 2025-01-04 07:26:23
|
(If you are NOT CEO, please kindly forward this to your CEO, because this is urgent. If you believe this has been sent to you in error, please ignore it. Thanks)Dear CEO,This email is from China domain name registration center. On January 4, 2025, we received an application from Hongfei Ltd requested "licebase" as their internet keyword and China (CN) domain names (licebase.cn, licebase.com.cn, licebase.net.cn, licebase.org.cn). But after checking it, we find this name conflict with your company name or trademark. In order to deal with this matter better, it's necessary to send email to you and confirm whether this company is your business partner in China? Best regardsAlbert Liu General Manager Name Registry Tel: +86-2161918696 Fax: +86-2161918697 Mob: +86-13816428671 12F Kaike Building, No. 1801 Hongmei Road, Shanghai 200233, China |
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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$> > repo and merging the changes into the main branch. > > > > AND NOW THE ANNOUNCEMENT > > > > At the end of July, I will be stepping away from my role as GMOD project > coordinator, which on one hand, makes me very sad, but on the other, fills > me with immense pride in what we as the GMOD community have achieved over > the last 22 years. We have truly democratized organism genomics, allowing a > small lab to distribute data on whatever organisms are of interest to them > with (relatively) little effort. We can compare that to the MODs that > existed in the early aughts, that had staffs of many software developers to > make the same thing happen. We all did that, and I think the world is a > better place for it. > > > > I can't say yet where I'm going, as I have a few opportunities on the > table that haven't been finalized, but I hope to be fulfilling a similar > role in another community. If you're really interested, you can follow me > on Mastodon at @sco...@ge.... > > > > Thank you to all of you--I have really enjoyed working with and growing > this community, > > Scott > > > > > -- > > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > > GMOD Project Manager (http://gmod.org/ > <https://urldefense.com/v3/__http:/gmod.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLt_a75Ac4$>) > 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 > |
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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$> repo and merging the changes into the main branch. AND NOW THE ANNOUNCEMENT At the end of July, I will be stepping away from my role as GMOD project coordinator, which on one hand, makes me very sad, but on the other, fills me with immense pride in what we as the GMOD community have achieved over the last 22 years. We have truly democratized organism genomics, allowing a small lab to distribute data on whatever organisms are of interest to them with (relatively) little effort. We can compare that to the MODs that existed in the early aughts, that had staffs of many software developers to make the same thing happen. We all did that, and I think the world is a better place for it. I can't say yet where I'm going, as I have a few opportunities on the table that haven't been finalized, but I hope to be fulfilling a similar role in another community. If you're really interested, you can follow me on Mastodon at @sco...@ge.... Thank you to all of you--I have really enjoyed working with and growing this community, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/<https://urldefense.com/v3/__http:/gmod.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLt_a75Ac4$>) 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$>) Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/<https://urldefense.com/v3/__https:/hcmi-searchable-catalog.nci.nih.gov/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtmGSQ6iE$>) |
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From: Scott C. <sc...@sc...> - 2024-07-23 18:18:44
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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.... 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/) |
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From: Scott C. <sc...@sc...> - 2023-11-06 21:32:30
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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/) |
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From: Hafiza M. K. <221...@lu...> - 2023-11-02 07:15:13
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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 |
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From: Carolina A. <car...@st...> - 2023-06-27 09:46:30
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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 |
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From: Kiyoshi N. <na...@ni...> - 2023-06-27 00:38:04
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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 |
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From: Scott C. <sc...@sc...> - 2023-06-26 16:28:18
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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/) |
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From: Carolina A. <car...@st...> - 2023-06-24 10:20:59
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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 |
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From: Tony V. <ton...@ou...> - 2023-01-02 01:35:55
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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/) |
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From: Thomas K. <th...@tk...> - 2022-12-10 09:13:31
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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/) |
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From: Scott C. <sc...@sc...> - 2022-12-08 20:09:56
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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/) |
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From: Tony V. <ton...@ou...> - 2022-11-17 03:43:16
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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] |
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From: Mohd A. Ab H. <ami...@mp...> - 2022-10-31 09:35:57
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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 ] |
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From: Scott C. <sc...@sc...> - 2022-08-29 22:45:27
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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/) |
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From: Abigail H. <aah...@as...> - 2022-08-29 20:58:02
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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 |
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From: Scott C. <sc...@sc...> - 2022-05-02 03:12:39
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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/) |
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From: Scott C. <sc...@sc...> - 2022-04-30 00:17:43
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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/) |
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From: Rajaya, K. <ra...@bc...> - 2022-04-30 00:10:05
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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...<mailto: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=>) |
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From: Scott C. <sc...@sc...> - 2022-04-30 00:03:38
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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/) |
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