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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$> repo and merging the changes into the main branch. AND NOW THE ANNOUNCEMENT At the end of July, I will be stepping away from my role as GMOD project coordinator, which on one hand, makes me very sad, but on the other, fills me with immense pride in what we as the GMOD community have achieved over the last 22 years. We have truly democratized organism genomics, allowing a small lab to distribute data on whatever organisms are of interest to them with (relatively) little effort. We can compare that to the MODs that existed in the early aughts, that had staffs of many software developers to make the same thing happen. We all did that, and I think the world is a better place for it. I can't say yet where I'm going, as I have a few opportunities on the table that haven't been finalized, but I hope to be fulfilling a similar role in another community. If you're really interested, you can follow me on Mastodon at @sco...@ge...cial. Thank you to all of you--I have really enjoyed working with and growing this community, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/<https://urldefense.com/v3/__http:/gmod.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLt_a75Ac4$>) 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 18:21:01
|
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: Ficklin, S. P. <ste...@ws...> - 2024-01-13 21:52:38
|
Dear Tripal Community, I am excited to announce that Tripal v4.0.0-alpha2 is now released! This release represents a major update to Tripal v4. Most importantly, site developers can now begin exploration for how to upgrade their Tripal v3 sites to Tripal v4 because we now have support for publishing all content types and we have most fields for all Chado content. This version is still alpha, and despite that we have more functional testing than ever before, there may be bugs or unexpected behavior. Please let the Tripal core development team know if you encounter any problems so we can prioritize fixes. Here are major items we working on for upcoming releases: * A default display layout for pages * Publication Importer * Bulk Loader * Searching via ElasticSearch and Drupal Views * Web services * Additional Documentation -- Stephen P. Ficklin, PhD Interim Department Chair of Horticulture Interim Director of the Integrated Plant Sciences degree program Associate Professor Computational Biology and Bioinformatics Department of Horticulture Washington State University 403A Plant Sciences Bldg. Pullman, WA 99164-6414 Office: 509-335-4295 http://ficklinlab.cahnrs.wsu.edu |
From: Ficklin, S. P. <ste...@ws...> - 2024-01-09 21:48:58
|
For those of you traveling to attend the yearly Tripal Codefest in San Diego, Jan 10th-11th, we will be meeting in the Golden State Boardroom at the Town and Country hotel. We will set up a camera, microphone, and projector for interaction with those who want to attend remotely. The meeting is from 9 am-5 pm US Pacific Time. The room will be available from 8 am for those who may want to arrive early. For those who want to attend by Zoom, the Zoom link is posted in the Tripal Slack space on the #codefest channel. Please feel free to reach out to me if you'd like me to email the Zoom connection details to you. We look forward to seeing everyone who can attend! Stephen |
From: Ficklin, S. P. <ste...@ws...> - 2023-10-30 22:50:42
|
CORRECTION: The dates for the Codefest are 10th and the 11th (Wed-Thur). Hope to see you there! -- Stephen P. Ficklin, PhD Interim Department Chair of Horticulture Interim Director of the Integrated Plant Sciences degree program Associate Professor Computational Biology and Bioinformatics Department of Horticulture Washington State University 403A Plant Sciences Bldg. Pullman, WA 99164-6414 Office: 509-335-4295 http://ficklinlab.cahnrs.wsu.edu ________________________________ From: Ficklin, Stephen Patrick Sent: Monday, October 30, 2023 9:57 AM To: gmo...@li... <gmo...@li...> Subject: Announcing the Tripal Codefest and Workshop at PAG 2024. Dear Tripal Community, We will be holding our annual Tripal Codefest and Workshop at the Plant and Animal Genome Conference this January! The Codefest will be Jan 11-12th (Thu-Fri) and the Workshop Jan 13th (Sat). Registration for the Codefest is open. You can find a link to register here: https://tripal.info/events/pag_2024 . If you would like to join the Codefest, please register and let us know the topics of interest you'd like to work on or discussion. The codefest is in person but we are seeking options to allow for remote attendance. Abstracts for the workshop at PAG are due by Nov 15th! We encourage anyone who would like to speak in about their Tripal site, a new or updated Tripal module or anything related to community-database development to please submit an abstract! We hope to see many of you there! |
From: Ficklin, S. P. <ste...@ws...> - 2023-10-30 17:32:21
|
Dear Tripal Community, We will be holding our annual Tripal Codefest and Workshop at the Plant and Animal Genome Conference this January! The Codefest will be Jan 11-12th (Thu-Fri) and the Workshop Jan 13th (Sat). Registration for the Codefest is open. You can find a link to register here: https://tripal.info/events/pag_2024 . If you would like to join the Codefest, please register and let us know the topics of interest you'd like to work on or discussion. The codefest is in person but we are seeking options to allow for remote attendance. Abstracts for the workshop at PAG are due by Nov 15th! We encourage anyone who would like to speak in about their Tripal site, a new or updated Tripal module or anything related to community-database development to please submit an abstract! We hope to see many of you there! |
From: Muhonen, S. <sha...@uc...> - 2023-05-01 19:59:29
|
Hi everyone! Due to a scheduling conflict with the AgBioData Community Meeting that includes many Tripal users/developers, we will not be meeting for our quarterly TAC meeting this month (originally scheduled for tomorrow). Best, Shay Muhonen (they/their) Plant Computational Genomics Lab Manager and TreeGenes Program Manager Department of Ecology and Evolutionary Biology Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 Sha...@uc... |
From: Scott C. <sc...@sc...> - 2023-04-14 16:33:22
|
Hi Pushpa, By far the easiest way to get Chado (the PostgreSQL schema) is to install Tripal (https://tripal.info/) which is a Drupal-based PHP web application. Installing Tripal not only gets you Chado but a nice web interface for working with the data. Also, the Tripal community has several users in it that store phenotype and genotype data, so they can give you guidance on how to work with the data. There is a reasonably active Tripal Slack community as well (I can't invite you, but if you'd like to join I can put in touch with the people who can). Scott On Thu, Apr 13, 2023 at 10:08 PM Pushpavalli Raju <p....@uq...> wrote: > Hi > > I am Pushpavalli Raju working with University of Queensland on Arabidopsis > population development project that involves highthroughput phenotyping and > genotyping data. We would like to use GMOD for storing our data. Could you > kindly guide us how to get access to GMOD. > > > > Cheers > > Pushpa > -- ------------------------------------------------------------------------ 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: Muhonen, S. <sha...@uc...> - 2023-03-30 20:23:40
|
Hi everyone, You are invited to join us next Tuesday, April 4th, at 11 AM EST for our monthly Tripal Users meeting. This month, Valentin Guignon will be presenting on how to use the BrAPI module for Drupal 10, compatible with Tripal 4. The demo will include using external entities as data sources for wider use cases. The Zoom link will be: https://uconn-edu.zoom.us/j/91056131841?pwd=VUx4ZFplYmNFMTVhcVNmM0xHUCtUZz09 You can find the meeting time in your local timezone here: http://www.timeanddate.com/worldclock/meetingdetails.html?iso=20230404T1500&p1=179&p2=210&p3=224&p4=195&p5=33 Best, Shay Muhonen (they/their) Plant Computational Genomics Lab Manager and TreeGenes Program Manager Department of Ecology and Evolutionary Biology Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 Sha...@uc... |
From: Muhonen, S. <sha...@uc...> - 2023-02-28 22:53:02
|
Greetings everyone! Next Tuesday, March 7, we will be holding our monthly Tripal Users meeting at 11 AM EST. We will be doing a Tripal 4 training session and revisiting topics from the Codefest we hosted at the Plant and Animal Genomics Conference in January. All are welcome! We will be using the following Zoom link: https://uconn-edu.zoom.us/j/91056131841?pwd=VUx4ZFplYmNFMTVhcVNmM0xHUCtUZz09 You can find the meeting time in your local timezone here: https://www.timeanddate.com/worldclock/meetingdetails.html?year=2023&month=3&day=7&hour=16&min=0&sec=0&p1=179&p2=210&p3=224&p4=195&p5=33 Best, Shay Muhonen (they/their) Plant Computational Genomics Lab Manager and TreeGenes Program Manager Department of Ecology and Evolutionary Biology Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 Sha...@uc... |
From: Muhonen, S. <sha...@uc...> - 2023-02-06 21:46:11
|
Good afternoon all, Tomorrow morning at 11 AM EST we will have our Quarterly TAC Tripal Leadership meeting. Although this is a required meeting for committee members, all are welcome to join! We will be discussing committee membership renewals for 2024, funding ideas, and creating a workgroup for the Tripal 4 publication. The link to join will be https://uconn-edu.zoom.us/j/91056131841?pwd=VUx4ZFplYmNFMTVhcVNmM0xHUCtUZz09 and you can find the time in your local timezone using the following link: http://www.timeanddate.com/worldclock/meetingdetails.html?iso=20230207T1600&p1=179 Best, Shay Muhonen (they/their) Plant Computational Genomics Lab Manager and TreeGenes Program Manager Department of Ecology and Evolutionary Biology Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 Sha...@uc... |
From: Muhonen, S. <sha...@uc...> - 2023-01-10 00:40:48
|
*Correction: The PAG Tripal Database Network and Initiatives seminar with various speakers on Saturday will be at the Town and Country instead of the Courtyard Marriot, only the Tripal Cofest will be held at the Courtyard Marriot. The screenshot from the website for Saturday’s schedule was attached to the last email and also can be viewed here: https://plan.core-apps.com/pag_2023/event/3cee484866e6d00c5e492240c4d4383b Best, Shay Muhonen (they/she) Plant Computational Genomics Lab Manager and TreeGenes Program Manager Department of Ecology and Evolutionary Biology Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 Sha...@uc... From: Muhonen, Shaylin<mailto:sha...@uc...> Sent: Monday, January 9, 2023 3:41 PM To: gmo...@li...<mailto:gmo...@li...> Subject: [Gmod-tripal] PAG Cofest Reminder and Tripal Database Networking and Initiatives Seminars *Message sent from a system outside of UConn.* Good afternoon all! In addition to the Tripal Cofest on Thursday and Friday next week, during the PAG Conference next Saturday various Tripal Database Network and Initiatives seminars will be starting at 4 PM PST. The speaker schedules and topics for Saturday have been attached. These will also be held at the Courtyard Marriot. As a reminder, all are welcome to join our Tripal Cofest as well from 8 AM – 5 PM PST on Thursday and from 8 AM – noon on Friday (either in-person in San Diego, CA at the Courtyard Marriot or by joining via Zoom). The Zoom link we will be using for Cofest is: https://uconn-edu.zoom.us/j/91056131841?pwd=VUx4ZFplYmNFMTVhcVNmM0xHUCtUZz09<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuconn-edu.zoom.us%2Fj%2F91056131841%3Fpwd%3DVUx4ZFplYmNFMTVhcVNmM0xHUCtUZz09&data=05%7C01%7Cshaylin.muhonen%40uconn.edu%7Ca63241b72e1d48314b4708daf29297c1%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C638089008715310593%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mQ%2F2JBB%2BdhaJ10G3co8Z1JLyCthJXGpreSkPNbINMVY%3D&reserved=0> The Cofest schedule and topics we will be covering can be found here: https://docs.google.com/document/d/1pXU00Fg_mEPb4PxQsh0qGeZNXgqxXmFivX7Ag2iF3EI/edit#<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1pXU00Fg_mEPb4PxQsh0qGeZNXgqxXmFivX7Ag2iF3EI%2Fedit%23&data=05%7C01%7Cshaylin.muhonen%40uconn.edu%7Ca63241b72e1d48314b4708daf29297c1%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C638089008715310593%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=XcNXk%2FatUVuEGsjQtcIWpQUAxtkpCzsijD3NfXt6tIw%3D&reserved=0> We hope to see you there! Best, Shay Muhonen (they/she) Plant Computational Genomics Lab Manager and TreeGenes Program Manager Department of Ecology and Evolutionary Biology Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 Sha...@uc... |
From: Muhonen, S. <sha...@uc...> - 2023-01-09 22:40:49
|
Good afternoon all! In addition to the Tripal Cofest on Thursday and Friday next week, during the PAG Conference next Saturday various Tripal Database Network and Initiatives seminars will be starting at 4 PM PST. The speaker schedules and topics for Saturday have been attached. These will also be held at the Courtyard Marriot. As a reminder, all are welcome to join our Tripal Cofest as well from 8 AM – 5 PM PST on Thursday and from 8 AM – noon on Friday (either in-person in San Diego, CA at the Courtyard Marriot or by joining via Zoom). The Zoom link we will be using for Cofest is: https://uconn-edu.zoom.us/j/91056131841?pwd=VUx4ZFplYmNFMTVhcVNmM0xHUCtUZz09 The Cofest schedule and topics we will be covering can be found here: https://docs.google.com/document/d/1pXU00Fg_mEPb4PxQsh0qGeZNXgqxXmFivX7Ag2iF3EI/edit# We hope to see you there! Best, Shay Muhonen (they/she) Plant Computational Genomics Lab Manager and TreeGenes Program Manager Department of Ecology and Evolutionary Biology Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 Sha...@uc... |
From: Muhonen, S. <sha...@uc...> - 2023-01-05 01:43:49
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Hello everyone, You are invited to join us next Thursday and Friday (January 12th-13th) for a Tripal Cofest as part of the Plant and Animal Genomics Conference in San Diego, CA! Thursday we will meet from 8 AM – 5 PM PST, and Friday for a half-day from 8 AM until noon PST. In-person meetings will take place at the Courtyard Marriot in San Diego but you can also join remotely via Zoom using the following link: https://uconn-edu.zoom.us/j/91056131841?pwd=VUx4ZFplYmNFMTVhcVNmM0xHUCtUZz09 Discussion topics will include but are not limited to: navigating Tripal 4, creating fields, automating testing, designing modules with Drupal 9, and using Docker for app development. You can view the full schedule here: https://docs.google.com/document/d/1pXU00Fg_mEPb4PxQsh0qGeZNXgqxXmFivX7Ag2iF3EI/edit# All skill levels are welcome to participate - we hope to see you there! Best, Shay Muhonen (they/she) Plant Computational Genomics Lab Manager and TreeGenes Program Manager Department of Ecology and Evolutionary Biology, Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 Sha...@uc... |
From: Muhonen, S. <sha...@uc...> - 2022-12-02 21:12:54
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Hello everyone, Next Tuesday (Dec 6th) at 11 AM EST, we will be having our monthly Tripal Users meeting. Dr. Stephen Ficklin will be presenting on fields in Tripal v4. All are welcome! The Zoom link will be: https://uconn-edu.zoom.us/j/91056131841?pwd=VUx4ZFplYmNFMTVhcVNmM0xHUCtUZz09 You can find the start time in your area using the following website: https://www.timeanddate.com/worldclock/meetingdetails.html?iso=20221206T1600&p1=179 Best, Shay Muhonen (they/she) Plant Computational Genomics Lab Manager and TreeGenes Program Manager Department of Ecology and Evolutionary Biology Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 Sha...@uc... |
From: Muhonen, S. <sha...@uc...> - 2022-11-16 16:40:05
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Greetings all! This is a final call for short talks for the upcoming Plant and Animal Genome Conference in San Diego, CA - Jan 13-18, 2023. We are seeking a diverse set of contributions - this can be focused on a new (or existing) Tripal database, module development, etc. There are no requirement to be running a specific version of Tripal. Please reach out of you have any questions - submissions will be closing this Friday! Application Link: https://docs.google.com/forms/d/e/1FAIpQLSdej8UbbsbnWERq0X5yRJXbAGNwkaqEbv5eMhN5qUTluynV_A/viewform<Application%20Link:%20https:/docs.google.com/forms/d/e/1FAIpQLSdej8UbbsbnWERq0X5yRJXbAGNwkaqEbv5eMhN5qUTluynV_A/viewform> Best, Shay Muhonen (they/she) Plant Computational Genomics Lab Manager and TreeGenes Program Manager Department of Ecology and Evolutionary Biology Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 Sha...@uc... |
From: Muhonen, S. <sha...@uc...> - 2022-10-20 18:17:59
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Hi all, If you have not already, please use the form below to indicate your interest, or submit an abstract or discussion topics for the upcoming Plant and Animal Genomics Conference (and Codefest beforehand) in January 2023! https://docs.google.com/forms/d/e/1FAIpQLSdej8UbbsbnWERq0X5yRJXbAGNwkaqEbv5eMhN5qUTluynV_A/viewform Best, Shay Muhonen (they/she) Plant Computational Genomics Lab Manager and TreeGenes Program Manager Department of Ecology and Evolutionary Biology Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 Sha...@uc... |
From: Muhonen, S. <sha...@uc...> - 2022-10-18 20:22:44
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Hello all, As a reminder, there are just two weeks remaining in Hacktoberfest! Everyone is welcome to participate on the Tripal GitHub (Tripal 3: https://github.com/tripal/tripal , Tripal 4: https://github.com/tripal/t4d8). If you complete the challenge you will receive a free T-Shirt or a tree planted in your name! We also need folks to help us with easier contributions to the documentation (e.g. improving clarity or content, updates) - small bug fixes, and bug reports still make a big impact in supporting open-source projects! Visit https://hacktoberfest.com/ for more information on available projects! Best, Shay Muhonen (they/she) Plant Computational Genomics Lab Manager and TreeGenes Program Manager Department of Ecology and Evolutionary Biology Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 Sha...@uc... |
From: Muhonen, S. <sha...@uc...> - 2022-10-11 17:40:27
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Hi everyone, We will be hosting a Codefest a couple days in advance of the Plant and Animal Genomics Conference (January 13-18, 2023 in San Diego, CA), and we will also be hosting a workshop during the meeting where members of the community are invited to present. You are invited to one or both! Please use the following form to respond with your interest, to submit an abstract, or provide a potential topic for Codefest discussion! https://docs.google.com/forms/d/e/1FAIpQLSdej8UbbsbnWERq0X5yRJXbAGNwkaqEbv5eMhN5qUTluynV_A/viewform Best, Shay Muhonen (they/she) Plant Computational Genomics Lab Manager and TreeGenes Program Manager Department of Ecology and Evolutionary Biology Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 Sha...@uc... |
From: Buble, K. <kat...@ws...> - 2022-10-06 02:17:40
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Dear Tripal Community, Tripal MapViewer v2.0 is now released. New features include genome comparison view with JBrowse integration and Dot plot and Correspondence Matrix support. Please see the release notes<https://gitlab.com/mainlabwsu/tripal_map/-/releases/Tripal_MapViewer/7.x-2.0> for details. Thank you to those who contributed issues and code fixes. Katheryn Buble MainLab Bioinformatics |
From: Muhonen, S. <sha...@uc...> - 2022-10-03 21:44:22
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Hello everyone! We will be having our quarterly TAC meeting tomorrow at 11 AM EST (all are welcome to join!). The Zoom link is here: https://uconn-edu.zoom.us/j/7301904581?pwd=d0VoNkJ2VEdFZzFzZ2RtOWkzSHBRdz09 Please add your topics and updates to the agenda: https://docs.google.com/document/d/1nAQUjPz3UbguQSpU-7vlvs6t2ky9_XU4FeWQ6JzyO0Y/edit You can also look up your timezone for the meeting here: http://www.timeanddate.com/worldclock/meetingdetails.html?iso=20221004T1500&p1=179&p2=195&p3=137 Best, Shay Muhonen (they/she) Plant Computational Genomics Lab Manager and TreeGenes Program Manager Department of Ecology and Evolutionary Biology Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 Sha...@uc... |
From: Cheng, Chun-H. <chu...@ws...> - 2022-09-22 19:46:53
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Dear Tripal Community, We're happy to announce the release of Tripal MegaSearch v1.4.0 (https://gitlab.com/mainlabwsu/tripal_megasearch/-/tags/v1.4.0). We welcome your feedback and please give it a try. Release Note: Tripal MegaSearch v1.4.0 contains bug fixes and new features, including: 1. Extra fields/filters on static forms - Updated static forms with extra fields/filters for Marker/Map/QTL/Pub/Gene Search 2. New search - Added Ortholog/Paralog Search 3. Subset download - Allowed downloading subset of results by selecting row(s) from the table. Can be turned on/off with the 'checkbox_filter' setting in the MView definition conf file. 4. MView stats - Displayed MView statistics and dates on MegaSearch landing page (See screenshot in the README) 5. Sequence retrieval tool - Added Sequence Retrieval Tool for inclusion of flanking sequences in the Download for Gene/Marker Search. (Enabled from the Admin interface, screenshot in the README) 6. Direct URL for search - Added direct URL link for individual search. For example, path '/tripal_megasearch?datatype=tripal_megasearch_gene' leads directly to the MegaSearch Gene Search 7. Short static forms - Through Chado Search settings (under the User Interface section, i.e. /admin/mainlab/chado_search/settings), configure fieldsets to open/close like an accordion which make the static forms shorter and more succinct 8. Performance optimization - drush commands for managing MView indexes and partitioning tables (See the 'Performance' section in the README) 9. UI refresh for Ajax calls - Updated UI theme when AJAX calls are made 10. Maintenance message - For long maintenance operations such as populating a big MView, allowed displaying a maintenance message if 'maintenance' = TRUE is set in the MView definition conf file. Thank you, Chun-Huai Cheng Mainlab Bioinformatics |
From: Wegrzyn, J. <jil...@uc...> - 2022-09-06 04:36:10
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Greetings all, The Tripal Users Meeting will be held at 11am EST tomorrow (Tuesday, September 6th) Zoom link: https://uconn-edu.zoom.us/j/91056131841?pwd=VUx4ZFplYmNFMTVhcVNmM0xHUCtUZz09 Agenda - Please add any discussion items/updates to the agenda - https://docs.google.com/document/d/1nAQUjPz3UbguQSpU-7vlvs6t2ky9_XU4FeWQ6JzyO0Y/edit Correction on the time for the meeting: https://www.timeanddate.com/worldclock/meetingdetails.html?year=2022&month=9&day=6&hour=15&min=0&sec=0&p1=234&p2=195 Best, Jill Jill L. Wegrzyn Associate Professor Department of Ecology and Evolutionary Biology Institute for Systems Genomics: Computational Biology Core University of Connecticut 67 N. Eagleville Road Storrs CT 06269-3214 jil...@uc...<mailto:jil...@uc...> +1 860-486-8742 Research: http://plantcompgenomics.com<http://plantcompgenomics.com/> CBC Core: http://bioinformatics.uconn.edu<http://bioinformatics.uconn.edu/> Office (Gant 419) / Lab Gant 401) On Sep 5, 2022, 11:49 AM -0400, Ficklin, Stephen Patrick via Gmod-tripal <gmo...@li...>, wrote: *Message sent from a system outside of UConn.* Dear Tripal Community Apologies for the short notice. Tomorrow Sept 6th we will restart our monthly Tripal Users Meeting. We will be talking about Tripal 4 and providing a status update. Please join us! You can find the start time in your Livan area at this link https://www.timeanddate.com/worldclock/fixedtime.html?iso=20220906T0300<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.timeanddate.com%2Fworldclock%2Ffixedtime.html%3Fiso%3D20220906T0300&data=05%7C01%7C%7C144d20db6f8043e665b508da8f5621f8%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637979897433313856%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4LohlxoVWSgoPndjI5fJnCtoFY%2BbGsyF2KfjvK5pp6I%3D&reserved=0> Hope to see you there. |
From: Ficklin, S. P. <ste...@ws...> - 2022-09-05 15:48:44
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Dear Tripal Community Apologies for the short notice. Tomorrow Sept 6th we will restart our monthly Tripal Users Meeting. We will be talking about Tripal 4 and providing a status update. Please join us! You can find the start time in your Livan area at this link https://www.timeanddate.com/worldclock/fixedtime.html?iso=20220906T0300 Hope to see you there. |
From: Ficklin, S. P. <ste...@ws...> - 2022-08-12 22:17:48
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The Tripal Project Management Committee (PMC) has just released Tripal v3.9. You can upgrade using the common approach for upgrading any Drupal modules. For example, on the command-line: drush pm-update tripal The following changes are present in this release: 1. Bug fixes in the Organism API functions. 2. Bug fixes in some fields: sbo__database_cross_reference, sep__protocol, . 3. Bug fixes when selecting terms for content types and fields. 4. Bug fix to correct missing definitions in controlled vocabulary terms. 5. Improvements to species nomenclature text. 6. Some Fixes for PHP 8 compatibility. 7. Fixes for functional testing. 8. Bug fix in web services Special thanks to Douglas Senalik for many of the fixes in this release! |