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From: Guignon, V. (A. Bioversity-CIAT) <v.g...@cg...> - 2024-08-19 09:29:09
|
Hi Parwa, To complete Scott answer, if you consider a web user interface in your project, you definitely should use Tripal/Drupal. It will help you instantiate a Chado schema and even if you just use sub-parts of it, it’s fine! The Tripal community is quite active and holds weekly meetings on Gather Town (where you could get live support and even if the weekly meeting might be late for you, we can chat on slack - https://tripal-project.slack.com/archives/C63AQ0FQE - or you could meet earlier with European people like me on demand). Regarding your plans, you can give a try to Tripal 4 (at least to instantiate a Chado schema) but if you feel like you’re missing pieces, contact us and we could try to find solutions. I’m currently working on a parallel project also based on Drupal (and compatible with Tripal) that could fill the gaps. Valentin From: Scott Cain <sc...@sc...> Sent: Thursday, 15 August 2024 18:12 To: PARWAMUHSIN ISMAEL <par...@og...>; GMOD Schema/Chado List <gmo...@li...> Subject: Re: [Gmod-schema] Query Regarding Selective Use of Chado Modules for Custom Database Design Warning: External Sender, this email originated from outside of the organization. Do not click any links or open attachments unless you recognize the sender and know the content is safe. Hi Parwa, I'm not sure what you mean by "supported." Obviously, Chado is open source, so if there are pieces you find useful for your own project, you are welcome to use them (though citing Chado would be nice if this is something that might get published). The loading tools that are "packaged" with Chado are quite old and might not work well for a stock Chado installation. Most people who use Chado use it with Tripal (https://tripal.info/) a Drupal-based web frontend for Chado which comes with its own loading tools. Certainly, your use case would not work with Tripal out of the box either. Basically, what I'm saying, you're likely to need to write your own loading tools. Scott On Mon, Aug 12, 2024 at 3:17 PM PARWAMUHSIN ISMAEL <par...@og...<mailto:par...@og...>> wrote: Dear Chado Support Team, I hope this message finds you well. I am currently in the process of designing a database for biological data. For this project, I am considering using a subset of the Chado schema and wanted to inquire about the feasibility and potential implications of this approach. Specifically, I am interested in using only three modules from the Chado schema: cv: Limited to the cv and cvterm tables, along with cvterm_dbxref. organism: In its entirety. publication: Limited to the pub, pubprop, and pub_dbxref tables. Additionally, I plan to add some custom tables tailored to the specific needs of my project. Would this selective use of the Chado schema be supported, or could it potentially lead to any issues in terms of database integrity, compatibility with Chado tools, or future data integration? I appreciate any insights or recommendations you can provide on this matter. Thank you for your time and support. Best regards, Parwa Muhsin Ismael Istanbul University -- ------------------------------------------------------------------------ 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/) Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/) |
From: Scott C. <sc...@sc...> - 2024-08-15 16:35:04
|
Hi Parwa, I'm not sure what you mean by "supported." Obviously, Chado is open source, so if there are pieces you find useful for your own project, you are welcome to use them (though citing Chado would be nice if this is something that might get published). The loading tools that are "packaged" with Chado are quite old and might not work well for a stock Chado installation. Most people who use Chado use it with Tripal (https://tripal.info/) a Drupal-based web frontend for Chado which comes with its own loading tools. Certainly, your use case would not work with Tripal out of the box either. Basically, what I'm saying, you're likely to need to write your own loading tools. Scott On Mon, Aug 12, 2024 at 3:17 PM PARWAMUHSIN ISMAEL < par...@og...> wrote: > Dear Chado Support Team, > I hope this message finds you well. > I am currently in the process of designing a database for biological data. > For this project, I am considering using a subset of the Chado schema and > wanted to inquire about the feasibility and potential implications of this > approach. > > Specifically, I am interested in using only three modules from the Chado > schema: > > cv: Limited to the cv and cvterm tables, along with cvterm_dbxref. > organism: In its entirety. > publication: Limited to the pub, pubprop, and pub_dbxref tables. > Additionally, I plan to add some custom tables tailored to the specific > needs of my project. > > Would this selective use of the Chado schema be supported, or could it > potentially lead to any issues in terms of database integrity, > compatibility with Chado tools, or future data integration? > > I appreciate any insights or recommendations you can provide on this > matter. > > Thank you for your time and support. > > Best regards, > Parwa Muhsin Ismael > Istanbul University > > -- ------------------------------------------------------------------------ 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/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
From: Scott C. <sc...@sc...> - 2024-08-08 17:08:39
|
Hi Parwa, The database you are using is probably Chado, that database that sits under a Tripal instance (and is used in other settings too). The schema you are probably using is 1.31 which has been around for a long time. The primary keys of all of the tables are auto incrementing bigserials (bigints). The schema is defined here: https://raw.githubusercontent.com/GMOD/Chado/1.31/chado/modules/default_schema.sql And more information can be found from the gmod web site: https://gmod.org/wiki/Introduction_to_Chado Generally, PostgreSQL manages the creation of new primary keys on INSERT. Please let us know if you have any other questions, Scott On Wed, Aug 7, 2024 at 9:36 AM PARWAMUHSIN ISMAEL < par...@og...> wrote: > Dear GMOD Team, > > I hope this message finds you well. > > I am currently working with databases that utilize GMOD tools and have a > few questions regarding the primary keys used in these databases. > Specifically, I would like to understand the format and generation method > of these primary keys, including but not limited to cv_ids, cvterm_ids, and > other key types: > > Are the primary keys auto-incremented integers, UUIDs, or do they follow a > different format? > Could you provide details on how primary keys such as cv_ids, cvterm_ids, > and others are generated and managed? > If there is specific documentation or a schema that outlines these > details, I would appreciate it if you could point me to it. > Your assistance with this matter would be greatly appreciated. > > Thank you for your help! > > Best regards, > Parwa Ismael > Istanbul University > -- ------------------------------------------------------------------------ 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: 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 18:19:38
|
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: Joe C. <jwc...@lb...> - 2023-05-12 16:08:49
|
Hi Scott, For those of us in institutionalized settings, running a custom compilation of postgres might be a hurdle. They tend not to like custom builds of privileged code. I think we might want to talk about other issues where chado is showing its age. Chromosomes are getting bigger and it’s only a matter of time before fmin and fmax need to be larger than 2G. (I’m looking at a pine tree outside my window now.) We’re running a big db - the current size is 11T - and I’ve needed to promote some counters to bigints. We can call it okiichado. I’ve wondered whether it makes sense to store residues in chunks in a dimension table rather than as a column in the feature table. I realize that internally postgres breaks things up and stores it differently than the main records. But what are the access patterns that we really use? For most features (mRNAs, peptides,…) we will want to grab the whole thing. But for chromosomes don’t we normally just want a substring? Would storing things in chunks make that more efficient? We’d need a function call to be able to access a substring so that makes it more complicated. (Right now we’re a hybrid of storing residues for some things accessed often in the feature table and chunked for the bigger things in a dimension table.) > On May 11, 2023, at 9:54 PM, Scott Cain <sc...@sc...> wrote: > > I was kind of remembering that you wrote about this. I wonder if we could/should compile our own Postgres server to bump up that limit. At first blush, that sounds like a terrible idea but I could be convinced. > >> On May 11, 2023, at 4:14 PM, Joe Carlson <jwc...@lb...> wrote: >> >> Hello, >> >> I cannot be done. Even though the documentation for a TEXT type in postgresql says it is ‘variable unlimited length', there is an internal limitation of the size of an allocated buffer. It’s in the documentation for the character data type https://www.postgresql.org/docs/current/datatype-character.html: <https://www.postgresql.org/docs/current/datatype-character.html:> I really _should_ learn to proofread. I meant to say ‘It cannot be done…' Joe >> >>> In any case, the longest possible character string that can be stored is about 1 GB. >> >> >> I recently ran into this problem myself and tried various ways around the limit by storing chunks and trying to concatenate with plpgsql functions, but that did not work. (https://www.postgresql.org/message-id/80025ECD-44A6-454F-A4F9-784474B84952%40lbl.gov <https://www.postgresql.org/message-id/800...@lb...>). >> >> You need to store residues as chunked pieces in a separate table and rely on your middleware code to split pieces on injest and concatenate on output. >> >> Joe Carlson >> >>> On May 9, 2023, at 10:22 AM, Cheng, Chun-Huai via Gmod-schema <gmo...@li... <mailto:gmo...@li...>> wrote: >>> >>> Hi, >>> >>> We have a big genome with large chromosomes that each of them is greater than 1G bp. We're having trouble loading them into the 'feature' table. We've tried the Tripal FASTA loader and a custom script, but both failed with some error (in Postgres v12 log: ERROR: invalid memory alloc request size 1161290884). Is there any way we can load the sequences for the genome into Chado? >>> >>> Here's some length information about the genome: >>> >>> chr1 1853204363 >>> chr2 1709916750 >>> chr3 1527935595 >>> chr4 1588398909 >>> chr5 1297479159 >>> chr6 1379031673 >>> >>> >>> Thank you very much for your help, >>> >>> Chun-Huai Cheng >>> _______________________________________________ >>> Gmod-schema mailing list >>> Gmo...@li... <mailto:Gmo...@li...> >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema <https://lists.sourceforge.net/lists/listinfo/gmod-schema> >> _______________________________________________ >> Gmod-schema mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-schema |
From: Cheng, Chun-H. <chu...@ws...> - 2023-05-12 16:04:56
|
Thank you both for answering my questions. I don't mind using the GMOD version of Postgres if it's well maintained. Or at least should we urge the Postgres developers to bump that limit in the future release? Chun-Huai ________________________________ From: Scott Cain <sc...@sc...> Sent: Thursday, May 11, 2023 9:54 PM To: Joe Carlson <jwc...@lb...> Cc: Cheng, Chun-Huai <chu...@ws...>; gmo...@li... <gmo...@li...> Subject: Re: [Gmod-schema] Loading chromosome sequences greater than 1G bp long. [EXTERNAL EMAIL] I was kind of remembering that you wrote about this. I wonder if we could/should compile our own Postgres server to bump up that limit. At first blush, that sounds like a terrible idea but I could be convinced. On May 11, 2023, at 4:14 PM, Joe Carlson <jwc...@lb...> wrote: Hello, I cannot be done. Even though the documentation for a TEXT type in postgresql says it is ‘variable unlimited length', there is an internal limitation of the size of an allocated buffer. It’s in the documentation for the character data type https://www.postgresql.org/docs/current/datatype-character.html:<https://urldefense.com/v3/__https://www.postgresql.org/docs/current/datatype-character.html:__;!!JmPEgBY0HMszNaDT!r6EhVZuJU69Aj_RlYei7ShU_fjjwROeYApefHMo6TG3Hczdk1aP0_uYvPhCLfdMhFAMsNrqhpke6KF8kD5N0eg$> In any case, the longest possible character string that can be stored is about 1 GB. I recently ran into this problem myself and tried various ways around the limit by storing chunks and trying to concatenate with plpgsql functions, but that did not work. (https://www.postgresql.org/message-id/80025ECD-44A6-454F-A4F9-784474B84952%40lbl.gov<https://urldefense.com/v3/__https://www.postgresql.org/message-id/800...@lb...__;!!JmPEgBY0HMszNaDT!r6EhVZuJU69Aj_RlYei7ShU_fjjwROeYApefHMo6TG3Hczdk1aP0_uYvPhCLfdMhFAMsNrqhpke6KF9HEvjIzQ$>). You need to store residues as chunked pieces in a separate table and rely on your middleware code to split pieces on injest and concatenate on output. Joe Carlson On May 9, 2023, at 10:22 AM, Cheng, Chun-Huai via Gmod-schema <gmo...@li...<mailto:gmo...@li...>> wrote: Hi, We have a big genome with large chromosomes that each of them is greater than 1G bp. We're having trouble loading them into the 'feature' table. We've tried the Tripal FASTA loader and a custom script, but both failed with some error (in Postgres v12 log: ERROR: invalid memory alloc request size 1161290884). Is there any way we can load the sequences for the genome into Chado? Here's some length information about the genome: chr1 1853204363 chr2 1709916750 chr3 1527935595 chr4 1588398909 chr5 1297479159 chr6 1379031673 Thank you very much for your help, Chun-Huai Cheng _______________________________________________ Gmod-schema mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-schema<https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/gmod-schema__;!!JmPEgBY0HMszNaDT!r6EhVZuJU69Aj_RlYei7ShU_fjjwROeYApefHMo6TG3Hczdk1aP0_uYvPhCLfdMhFAMsNrqhpke6KF-P204wlg$> _______________________________________________ Gmod-schema mailing list Gmo...@li... https://lists.sourceforge.net/lists/listinfo/gmod-schema<https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/gmod-schema__;!!JmPEgBY0HMszNaDT!r6EhVZuJU69Aj_RlYei7ShU_fjjwROeYApefHMo6TG3Hczdk1aP0_uYvPhCLfdMhFAMsNrqhpke6KF-P204wlg$> |
From: Scott C. <sc...@sc...> - 2023-05-12 05:19:49
|
<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div dir="ltr"></div><div dir="ltr">I was kind of remembering that you wrote about this. I wonder if we could/should compile our own Postgres server to bump up that limit. At first blush, that sounds like a terrible idea but I could be convinced. </div><div dir="ltr"><br><blockquote type="cite">On May 11, 2023, at 4:14 PM, Joe Carlson <jwc...@lb...> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><meta http-equiv="Content-Type" content="text/html; charset=utf-8">Hello,<div class=""><br class=""></div><div class="">I cannot be done. Even though the documentation for a TEXT type in postgresql says it is ‘variable unlimited length', there is an internal limitation of the size of an allocated buffer. It’s in the documentation for the character data type <a href="https://www.postgresql.org/docs/current/datatype-character.html:" class="">https://www.postgresql.org/docs/current/datatype-character.html:</a></div><div class=""><br class=""></div><div class=""><blockquote type="cite" class=""><span style="font-family: "Open Sans", sans-serif; font-size: 14.4px; font-variant-ligatures: normal; orphans: 2; widows: 2; text-decoration-thickness: initial;" class="">In any case, the longest possible character string that can be stored is about 1 GB.</span></blockquote></div><div class=""><br class=""></div><div class="">I recently ran into this problem myself and tried various ways around the limit by storing chunks and trying to concatenate with plpgsql functions, but that did not work. (<a href="https://www.postgresql.org/message-id/800...@lb..." class="">https://www.postgresql.org/message-id/80025ECD-44A6-454F-A4F9-784474B84952%40lbl.gov</a>).</div><div class=""><br class=""></div><div class="">You need to store residues as chunked pieces in a separate table and rely on your middleware code to split pieces on injest and concatenate on output.</div><div class=""><br class=""></div><div class="">Joe Carlson<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On May 9, 2023, at 10:22 AM, Cheng, Chun-Huai via Gmod-schema <<a href="mailto:gmo...@li..." class="">gmo...@li...</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="elementToProof ContentPasted0" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Hi,<div class=""><br class="ContentPasted0"></div><div class="ContentPasted0">We have a big genome with large chromosomes that each of them is greater than 1G bp. We're having trouble loading them into the 'feature' table. We've tried the Tripal FASTA loader and a custom script, but both failed with some error (in Postgres v12 log: ERROR: invalid memory alloc request size 1161290884). Is there any way we can load the sequences for the genome into Chado?</div><div class=""><br class="ContentPasted0"></div><div class="ContentPasted0">Here's some length information about the genome:</div><div class="ContentPasted0"><br class=""></div><div class="ContentPasted0">chr1 1853204363</div><div class="ContentPasted0">chr2 1709916750</div><div class="ContentPasted0">chr3 1527935595</div><div class="ContentPasted0">chr4 1588398909</div><div class="ContentPasted0">chr5 1297479159</div><div class="ContentPasted0">chr6 1379031673</div><div class=""><br class="ContentPasted0"></div><div class=""><br class="ContentPasted0"></div><div class="ContentPasted0">Thank you very much for your help,</div><br class=""></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Chun-Huai Cheng</span><br class=""></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Gmod-schema mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="mailto:Gmo...@li..." style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Gmo...@li...</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="https://lists.sourceforge.net/lists/listinfo/gmod-schema" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://lists.sourceforge.net/lists/listinfo/gmod-schema</a></div></blockquote></div><br class=""></div><span>_______________________________________________</span><br><span>Gmod-schema mailing list</span><br><span>Gmo...@li...</span><br><span>https://lists.sourceforge.net/lists/listinfo/gmod-schema</span><br></div></blockquote></body></html> |
From: Joe C. <jwc...@lb...> - 2023-05-11 23:14:33
|
Hello, I cannot be done. Even though the documentation for a TEXT type in postgresql says it is ‘variable unlimited length', there is an internal limitation of the size of an allocated buffer. It’s in the documentation for the character data type https://www.postgresql.org/docs/current/datatype-character.html: > In any case, the longest possible character string that can be stored is about 1 GB. I recently ran into this problem myself and tried various ways around the limit by storing chunks and trying to concatenate with plpgsql functions, but that did not work. (https://www.postgresql.org/message-id/80025ECD-44A6-454F-A4F9-784474B84952%40lbl.gov <https://www.postgresql.org/message-id/800...@lb...>). You need to store residues as chunked pieces in a separate table and rely on your middleware code to split pieces on injest and concatenate on output. Joe Carlson > On May 9, 2023, at 10:22 AM, Cheng, Chun-Huai via Gmod-schema <gmo...@li...> wrote: > > Hi, > > We have a big genome with large chromosomes that each of them is greater than 1G bp. We're having trouble loading them into the 'feature' table. We've tried the Tripal FASTA loader and a custom script, but both failed with some error (in Postgres v12 log: ERROR: invalid memory alloc request size 1161290884). Is there any way we can load the sequences for the genome into Chado? > > Here's some length information about the genome: > > chr1 1853204363 > chr2 1709916750 > chr3 1527935595 > chr4 1588398909 > chr5 1297479159 > chr6 1379031673 > > > Thank you very much for your help, > > Chun-Huai Cheng > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... <mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-schema <https://lists.sourceforge.net/lists/listinfo/gmod-schema> |
From: Cheng, Chun-H. <chu...@ws...> - 2023-05-09 17:44:42
|
Hi, We have a big genome with large chromosomes that each of them is greater than 1G bp. We're having trouble loading them into the 'feature' table. We've tried the Tripal FASTA loader and a custom script, but both failed with some error (in Postgres v12 log: ERROR: invalid memory alloc request size 1161290884). Is there any way we can load the sequences for the genome into Chado? Here's some length information about the genome: chr1 1853204363 chr2 1709916750 chr3 1527935595 chr4 1588398909 chr5 1297479159 chr6 1379031673 Thank you very much for your help, Chun-Huai Cheng |
From: Scott C. <sc...@sc...> - 2023-04-14 16:41:39
|
Highlights - Submit <https://www.open-bio.org/events/bosc-2023/submit/> your 1-2 page abstract by April 20 (by the end of the day anywhere in the world). (Sorry, no extensions.) - You can request registration fee assistance right on the submission form! - We have two exciting Keynote Speakers <https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/> lined up! - We are planning a Panel Discussion about Open and Ethical Data Sharing! - BOSC and Bio-Ontologies <https://www.bio-ontologies.org.uk/ismb-annual-meeting/2023-meeting> will join forces for a joint session on July 24 or 25. - We welcome our first sponsors <https://www.open-bio.org/events/sponsors/> (more coming soon): GigaScience <https://academic.oup.com/gigascience>, GeneVia <https://geneviatechnologies.com/>, and Software Sustainability Institute <https://www.software.ac.uk/>! Keynote speakers [image: Sara El-Gebali] Sara El-Gebali <https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/> (SciLifeLab-DataCentre-Sweden): “A New Odyssey: Pioneering the Future of Scientific Progress Through Open Collaboration.” Joseph M. Yracheta <https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/> (Native BioData Consortium): “The Dissonance between Scientific Altruism & Capitalist Extraction: The Zero Trust and Federated Data Sovereignty Solution Abstract submission We encourage you to submit abstracts <https://www.open-bio.org/events/bosc-2023/submit/> (due April 20 – sorry, no extensions) on any topic relevant to open source bioinformatics or open science (see topic list below). After review, some abstracts will be selected for lightning talks, longer talks, or posters. A second “late poster” round of submissions will end May 18. Abstract submission is via ISMB’s EasyChair (linked from our submission page <https://www.open-bio.org/events/bosc-2023/submit/>). Note that ISMB 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. About BOSC Since 2000, the Bioinformatics Open Source Conference <https://www.open-bio.org/events/bosc-2021/about/> has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics and open science. As usual, BOSC 2023 <https://www.open-bio.org/events/bosc-2023/> will include keynote talks, longer and shorter (lightning) talks from submitted abstracts, posters, Birds of a Feather, and more! Like last year, BOSC and Bio-Ontologies <https://www.bio-ontologies.org.uk/ismb-annual-meeting/2023-meeting> will join forces for a joint session. BOSC topics include (but are not limited to): - Open Science and Reproducible Research - Open Biomedical Data - Citizen/Participatory Science - Standards and Interoperability - Data Science - Workflows - 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) 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 to be considered for a registration fee waiver right on the abstract submission form (your request will not be seen by reviewers). Fee waivers are made possible by our sponsors <https://www.open-bio.org/events/sponsors/>. Sponsors We welcome the first Silver sponsors <https://www.open-bio.org/events/sponsors/> of BOSC 2023! If you’re interested in becoming a sponsor, let us know! [image: Gigascience] <https://academic.oup.com/gigascience> <https://geneviatechnologies.com/> <https://www.software.ac.uk/> ------------------------------ Key Dates - April 20, 2023: Deadline for submitting talk/poster abstracts <https://www.open-bio.org/events/bosc-2023/submit/> - May 11: Talk/poster acceptance notifications - May 18: Late poster submission deadline - May 25: Late poster acceptance notifications - July 24-25: BOSC 2023 <https://www.open-bio.org/events/bosc-2023/> (part of ISMB/ECCB 2023 in Lyon, France, and online) - CollaborationFest <https://www.open-bio.org/events/bosc-2023/obf-bosc-collaborationfest-2023/> (CoFest) – July 22-23 (Lyon, France, and online) Join our community! - BOSC announcements mailing list: <http://lists.open-bio.org/mailman/listinfo/bosc-announce> https://groups.google.com/forum/#!forum/bosc-announce - Slack: https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew - Twitter: @OBF_BOSC <https://twitter.com/OBF_BOSC>, #BOSC2023 - Mastodon: https://genomic.social/@BOSC - Website: <https://www.open-bio.org/wiki/BOSC_2019> https://www.open-bio.org/events/bosc/ ------------------------------ We look forward to reading your abstract and seeing you (in person or virtually) at BOSC 2023! Sincerely, BOSC 2023 Organizing Committee (Nomi Harris, Karsten Hokamp, Hervé Ménager, Monica Munoz-Torres, Deepak Unni, Jason Williams, Chris Fields, Jessica Maia, Radhika Khetani) -- ------------------------------------------------------------------------ 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: Joe C. <jwc...@lb...> - 2023-03-29 21:38:56
|
Well, today we broke the limit with a chromosome longer than 1 Gbase and I tried to insert it into a chado record. Yes, the postgresql text field is unlimited in length, but there is a max of 1 Gbyte in a string buffer that is used for operations. So I cannot populate that field. I’m curious if anyone else has run into this issue before and what they’ve done about it. It seems that the thing to do is to separate the residues field from the feature table and divide residues into hunks of a more manageable size. The next milestone is when we break the 2G limit and need to make fmin and fmax in the featureloc table bigints. That, however, will be an easier fix. Joe (by the way, there is some info on large chado tables here https://www.mcgeeandco.com/products/chado-large-table-lamp <https://www.mcgeeandco.com/products/chado-large-table-lamp>) |
From: Scott C. <sc...@sc...> - 2022-08-19 03:34:19
|
Hi Jie Jin, Sorry about that; when gmod.org gets hammered by web crawlers, sometimes mysql goes down and I have to manually restart it. It should be back now. Please let us know if you have any questions we can help you with! Scott On Thu, Aug 18, 2022 at 8:05 PM Jie Jin <hel...@gm...> wrote: > Hello, > > I am looking for documentation of Chado. I found > https://chado.readthedocs.io/, there many useful information on this > site. > > But there are still many useful links pointed to http://gmod.org/, and > http://gmod.org/ is down. > > Is the downtime of gmod.org temporally? Will it come back sometime? > > Where can I find the full documentation including the wiki on gmod.org? > > 谢谢 > 金杰 (Jie Jin) > > > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > -- ------------------------------------------------------------------------ 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: Jie J. <hel...@gm...> - 2022-08-15 14:32:48
|
Hello, I am looking for documentation of Chado. I found https://chado.readthedocs.io/, there many useful information on this site. But there are still many useful links pointed to http://gmod.org/, and http://gmod.org/ is down. Is the downtime of gmod.org temporally? Will it come back sometime? Where can I find the full documentation including the wiki on gmod.org? 谢谢 金杰 (Jie Jin) |
From: Scott C. <sc...@sc...> - 2022-03-23 04:53:56
|
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: Ficklin, S. P. <ste...@ws...> - 2022-01-19 01:41:20
|
Dear Tripal and GMOD Community, Every Monday, Tripal developers meet via GatherTown, similar to a mini codefest. Anyone is welcome. Sometimes we have an agenda and sometimes we don't, but we get together to chat about code for anything Tripal related. Folks who want help with their Tripal sites are also welcome to drop in. On the first Monday of every month, starting in February, we are going to focus on Chado issues that we have, including submitting and reviewing pull requests made to the Chado GitHub repository. Members of the broader GMOD community are welcome to join us. You can meet with us on GatherTown by joining the Tripal Slack workspace (https://tripal.info/join/slack) which has a #chado channel. On the Tripal Slack you can request the GatherTown link. Alternatively, email me directly and I will send the link to you. If you would like to be involved in these discussions, please join us! Stephen Ficklin Tripal PMC Member |
From: Scott C. <sc...@sc...> - 2021-08-31 20:02:14
|
Hello all, A few years ago, Valentin created an issue and pull request for a natural diversity fact table (nd_fact) for collecting data/facts (climate data, temperature, etc) about observed conditions associated with natural diversity collections. Currently, there is a nd_geolocation table for identifying where a collection occurred, the nd_fact table would expand the ability to describe the conditions around the collection. Since this seems like a good idea to me but the issue has been sitting idle for a while, I'd like to get some feedback on the change. This change is a sort of "medium sized" change, since it's really a new sort of table. If you have the inclination, please take a look at https://github.com/GMOD/Chado/issues/107 and let me know what you think. Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Meg S. <me...@gm...> - 2021-08-20 00:40:21
|
Dear Researchers, Breeders, Database Providers, Funders, Editors, Students, Software Engineers, and other Scientists, *Do you want easy access to better quality data?* We are THRILLED to announce that AgBioData (https://www.agbiodata.org/) has received a three-year NSF RCN award to expand our community committed to improving quality and access to agricultural data. New activities will include organizing workshops, establishing new working groups, and developing FAIR curriculum for scientists. We are expanding the consortium and welcome new members, especially students, post-docs, big-data scientists, funding agency scientists and members of the scientific publishing community interested in solving common FAIR data issues. *We invite all of you to an important kickoff All-Hands Meeting on Sept 1st* at 10 am PDT (find your local time - https://bit.ly/389VeJA). At this meeting you will hear about our RCN objectives, the benefits of joining AgBioData, and how YOU can make a difference in the biological data environment for years to come. *Please pre-register* for this meeting at https://iastate.zoom.us/meeting/register/tJcld-iqqD4vE9awJKcFGnmHwxtCNc_a7UJM *We are also hiring a scientist to coordinate AgBioData activities*, outreach and curriculum development. Please help us publicize this opportunity! Applications should be submitted by August 31 to https://phoenix-bioinformatics.hirehive.com/job/83452/scientific-program-coordinator-newark?source=TAIR . Thank you! The AgBioData Steering Committee: Monica Poelchau, Sook Jung, Ethy Cannon, Jacqueline Campbell, Lisa Harper, Leonore Reiser, Marcela Tello-Ruiz, Laurel Cooper, Eva Hula, Meg Staton, and Darwin Campbell *About AgBioData:* https://www.agbiodata.org *AgBioData RCN*: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2126334 -- Margaret Staton Associate Professor Department of Entomology and Plant Pathology Office: 154 PBB Mail: 370 PBB, 2505 EJ Chapman Drive Knoxville, TN 37996-4560 she/her/hers 864-506-4515 Mobile mst...@ut... *Advanced Out of Office Notice* *October 11-15, 2021* |
From: Scott C. <sc...@sc...> - 2021-07-27 21:01:52
|
Hi, Here's a reminder that "today" (that is, tomorrow morning for me) there is a Birds of a Feather meeting to discuss GMOD topics at ISMB/BOSC, including JBrowse but other GMOD topics as well. The BoF starts at 15:20 UTC (7:20 PDT, 10:20 EDT) on July 28. If you are attending ISMB, please feel free to drop in and chat about good stuff you're doing or want to do: https://ismbeccb2021.showcare.io/sessions/28-3-bof/ Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Scott C. <sc...@sc...> - 2021-07-21 17:46:31
|
Hello, If you are attending BOSC or any other ISCM meeting next week, please feel free to come to the GMOD/JBrowse Birds of a Feather on Wednesday, July 28 from 15:20 to 16:20 UTC (yes, that is 7:20 AM west coast US time). Several GMOD folks will be there; you can talk about new developments with JBrowse 2 or discuss any of several other GMOD components. https://www.iscb.org/ismbeccb2021-program/bof#bof4 The meeting will take place in the Research Exchange Forum, which hopefully will make sense when attending the meeting! :-) See you all next week! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Scott C. <sc...@sc...> - 2021-05-04 21:15:50
|
Don't forget to get your abstracts in for BOSC! ---------- Forwarded message --------- From: BOSC, the Bioinformatics Open Source Conference < bos...@gm...> Date: Tue, May 4, 2021 at 1:50 PM Subject: [bosc-announce] Reminder: BOSC abstract deadline is May 6! To: <bos...@go...> <https://www.open-bio.org/events/bosc/> The BOSC 2021 abstract submission <https://www.open-bio.org/events/bosc-2021/submit/> deadline is May 6th; see our announcement <https://www.open-bio.org/2021/03/24/join-us-at-bosc-2021/> for more info. This year’s BOSC is a track of ISMB/ECCB 2021 online <https://www.iscb.org/ismbeccb2021/>. What time on May 6th is the deadline? The official ISMB/ECCB deadline is 11:59pm EDT on May 6 (which is 03:59 UTC on May 7), but we convinced them to let us keep submissions for BOSC open until 11:59pm Hawaii time (which is six hours later, 09:59 UTC on May 7). We are unfortunately unable to grant any additional extensions. Late Poster deadline is June 3. If you can’t make the May 6th submission deadline, we encourage you to submit for a Late Poster (deadline June 3). As space permits, we will choose a few Late Poster submissions for Late-Breaking Lightning Talks. Fee assistance. Just check a box on the abstract submission form to request registration fee assistance! Join us on Slack! Our BOSC Slack workspace <https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew> is open to the community! Follow us on Twitter! @OBF_BOSC <http://twitter.com/OBF_BOSC>, #BOSC2021 -- You received this message because you are subscribed to the Google Groups "bosc-announce" group. To unsubscribe from this group and stop receiving emails from it, send an email to bos...@go.... To view this discussion on the web visit https://groups.google.com/d/msgid/bosc-announce/CAK27n1fyqV9KP1pR%2BOdYh%3D5rW%2BGdah-KQPJajCUxMMKXgqADZQ%40mail.gmail.com <https://groups.google.com/d/msgid/bosc-announce/CAK27n1fyqV9KP1pR%2BOdYh%3D5rW%2BGdah-KQPJajCUxMMKXgqADZQ%40mail.gmail.com?utm_medium=email&utm_source=footer> . -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Ficklin, S. P. <ste...@ws...> - 2020-12-01 23:48:31
|
Dear Tripal, Chado and GMOD communities. We will be hosting our yearly Tripal Codefest (Hackathon) Jan 11-15. Due to Covid-19, the Codefest will be held virtually via GatherTown (https://gather.town/) . Anyone interested in Tripal development (core or extensions) is welcome to attend. We also welcome those interested in Chado development, those interested in Tripal integration or any other GMOD tools. Please register and learn more by visiting http://tripal.info/events/codefest_2021 [cid:578172fc-b79c-4a23-b83d-1605d4acc6a8] |
From: Menolin S. <sha...@gm...> - 2020-09-02 05:02:49
|
Hi, I had loaded some organisms into the chado database. I had assumed loading the organisms would automatically create an organism_dbxref table for the organisms entered. However, the organism_dbxref table is empty. How can I link organisms to dbxref_id? I need these ids in order to be able to enter the stock information. Thank you, Menolin |
From: Menolin S. <sha...@gm...> - 2020-08-27 22:32:33
|
Hi, I have questions regarding loading the chado modules: 1. Which modules have a prebuilt script for loading data onto the chado schema? (I could figure out scripts for loading ontologies and gff3 files only so far) 2. Do I need to write my own script for loading the phenotype and other modules? Thank you very much for your help. Thank you, Menolin |