- AgBioData-LIST - Main Bioinformatics Lab

REMINDER - Monthly Webinar Next Wed, April 2nd, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wednesday, *April 2nd, at 12 PM CDT* for our monthly webinar with *Gregor Bucher* from the University of Gottingen. He will present iBeetle-Base <https://ibeetle-base.uni-goettingen.de/>, an integrated genomic and phenotypic information resource for red flour beetle research and a new AgBioData member database. I have included more details about the webinar and the Zoom link to attend the webinar below. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Abstracts:* *iBeetle-Base - a phenotypic database with community edition* The red flour beetle *Tribolium castaneum* has become an important insect model organism to study gene function and RNAi mediated pest control. iBeetle-Base was developed to document morphological phenotypes from the genome-wide RNAi gene-knockdown screen iBeetle and has become an integrated resource of genomic and phenotypic information for *Tribolium castaneum* research. Since our last release in 2024, iBeetle-Base allows the community to contribute RNAi phenotypes and associate Gene Ontology terms and publications with *Tribolium* genes (“community addition”). This novel functionality overcomes the lack of curators for databases of small communities. Further, we improved data accessibility, via programming interfaces alongside traditional HTML pages, which facilitates the automatic usage of the database by scripting and third-party tools. Importantly, this phenotypic database with its special adaptations to small research communities could become the nucleus for other interlinked databases in the future. iBeetle-Base is freely accessible at https://ibeetle-base.uni-goettingen.de/ *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> *Join Zoom Meetinghttps://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 <https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09>* Meeting ID: 820 3835 6125 Passcode: 160683

5 days, 16 hours

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REMINDER - Monthly Webinar TOMORROW, March 5th, at 12 PM CT

by Annarita Marrano

Hi everybody, This is a friendly reminder of the monthly webinar TOMORROW at 12 PM CDT with *Alenka Hafner*. Alenka will present the current recommendations and future directions of the AgBioData Data Reuse working group, recently published on GigaScience (https://doi.org/10.1093/gigascience/giae106). I have included more details about the webinar and the Zoom link to attend the webinar below. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Abstracts:* *AgBioData's Data Reuse WG: our current guidelines and future considerations* The scientific community has long benefited from the opportunities provided by data reuse. Recognizing the need to identify the challenges and bottlenecks to reuse in the agricultural research community and propose solutions for them, the data reuse working group was started within the AgBioData consortium framework. Throughout two years of remote meetings and asynchronous discussion, we identified the limitations of data standards, metadata deficiencies, data interoperability, data ownership, data availability, user skill level, resource availability, and equity issues, with a specific focus on agricultural genomics research. We described these in a white paper, out now in GigaScience ( https://doi.org/10.1093/gigascience/giae106), while proposing possible solutions stakeholders could implement to mitigate and overcome these challenges and providing an optimistic perspective on the future of genomics and transcriptomics data reuse. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=Alenka+Hafner+on+…> *Join Zoom Meetinghttps://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 <https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09>* Meeting ID: 820 3835 6125 Passcode: 160683

3 weeks, 6 days

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REMINDER - Monthly Webinar Next Wed, March 5th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wed., March 5th, at 12 PM CDT for our monthly webinar with Alenka Hafner. Alenka will present the current recommendations and future directions of the AgBioData Data Reuse working group, recently published on GigaScience (https://doi.org/10.1093/gigascience/giae106). I have included more details about the webinar and the Zoom link to attend the webinar below. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Abstracts:* *AgBioData's Data Reuse WG: our current guidelines and future considerations* The scientific community has long benefited from the opportunities provided by data reuse. Recognizing the need to identify the challenges and bottlenecks to reuse in the agricultural research community and propose solutions for them, the data reuse working group was started within the AgBioData consortium framework. Throughout two years of remote meetings and asynchronous discussion, we identified the limitations of data standards, metadata deficiencies, data interoperability, data ownership, data availability, user skill level, resource availability, and equity issues, with a specific focus on agricultural genomics research. We described these in a white paper, out now in GigaScience ( https://doi.org/10.1093/gigascience/giae106), while proposing possible solutions stakeholders could implement to mitigate and overcome these challenges and providing an optimistic perspective on the future of genomics and transcriptomics data reuse. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=Alenka+Hafner+on+…> *Join Zoom Meetinghttps://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 <https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09>* Meeting ID: 820 3835 6125 Passcode: 160683

1 month

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REMINDER - Nomination for a new AgBioData steering committee member

by Annarita Marrano

Hi everybody, You have till Friday, Feb. 28, to nominate yourself and someone else as a NEW AgBioData steering committee (SC) member ( https://forms.gle/1dTTbEhN8FDs6Ep5A*)*! The SC is a vibrant, collaborative, and inclusive environment that offers opportunities to expand leadership skills, network with agricultural research community stakeholders, and help achieve a FAIR agricultural data ecosystem. We are looking for candidates to serve as members of the AgBioData SC who are willing to commit a proportion of *their time to AgBioData activities (approximately 2 hours/week) for 3 years. * Please let me know if you have any questions. Best, Annarita

1 month

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NOW OPEN Nomination for a new AgBioData steering committee member + REGISTRATION for the NLP4Biocuration WG

by Annarita Marrano

Hi everybody, Please *see below two important opportunities*: - The AgBioData steering committee (SC) is calling *for nominations for new SC members*! Do you want to take a leadership role within the AgBioData consortium? Do you know someone who can contribute significantly to the AgBioData steering committee? Nominate* yourself or somebody you think might fit the position by next Friday, February 28, at * https://forms.gle/1dTTbEhN8FDs6Ep5A *! *The SC is a vibrant, collaborative, and inclusive environment that offers opportunities to expand leadership skills, network with agricultural research community stakeholders, and help achieve a FAIR agricultural data ecosystem. *We are looking for candidates to serve as members of the AgBioData SC who are willing to commit a proportion of their time to AgBioData activities (approximately 2 hours/week) for 3 years. * - You have until Friday, February 21, to register for the new AgBioData working group on *Natural Language Processing for biocuration (NLP4Biocuration WG)! The NLP4Biocuration WG will explore the application of existing NLP tools to biocuration and identify their limitations with AgBioData-curated content. Join it by completing this form <https://docs.google.com/forms/d/e/1FAIpQLSe0exyHDowMCnL1_VkCBsff6T0sSPTl3pg…> by February 21! The commitment will generally be between 2-6 hours monthly, including meeting attendance and offline work (e.g., literature, writing, etc.). Please share the registration link with anybody who you think is interested.* Please let me know if you have any questions. Have a lovely week! Annarita

1 month, 1 week

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REGISTRATION OPEN - New Working Group on Natural Language Processing for biocuration!

by Annarita Marrano

Dear all, This is a friendly reminder to register for the new working group (WG) on *Natural Language Processing (NLP) for biocuration*! The NLP4Biocuration WG will explore the application of existing NLP tools to biocuration and identify their limitations with AgBioData-curated content. *Complete this form to join the working group by February 21! * *The commitment will generally be between 2-6 hours monthly*, including meeting attendance and offline work (e.g., literature, writing, etc.). This is your opportunity to shape the future of our research community by contributing to developing best data archiving and management practices that can benefit you and all the other stakeholders. Participating in the AgBioData working groups will also offer you opportunities for - professional networking - leadership skill development - authorship in impactful manuscripts - possibility to join the AgBioData Ambassador and Championship programs Please share the registration link with anybody who you think is interested. Best, Annarita

1 month, 2 weeks

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REGISTRATION OPEN - New Working Group on Natural Language Processing for biocuration!

by Annarita Marrano

Dear all, Registration for the new working group (WG) on *Natural Language Processing (NLP) for biocuration* is now OPEN! The NLP4Biocuration WG will explore the application of existing NLP tools to biocuration and identify their limitations with AgBioData-curated content. *Join the NLP4biocuration working group by completing this form <https://docs.google.com/forms/d/e/1FAIpQLSe0exyHDowMCnL1_VkCBsff6T0sSPTl3pg…> by February 21! * *The commitment will generally be between 2-6 hours monthly*, including meeting attendance and offline work (e.g., literature, writing, etc.). This is your opportunity to shape the future of our research community by contributing to developing best practices of data archiving and management that can benefit you and all the other stakeholders. Participating in the AgBioData working groups will also offer you opportunities for - professional networking - leadership skill development - authorship in impactful manuscripts - possibility to participate in the AgBioData Ambassador and Championship programs Please share the registration link with anybody that you think can be interested. Best, Annarita

1 month, 3 weeks

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REMINDER - Monthly Webinar TOMORROW, Feb, 5th, at 12 PM CT

by Annarita Marrano

Hi everybody, Don't miss our monthly webinar TOMORROW, Feb. 5th, at 12 PM CDT. David Molik and Adam Wright from the Genome Assembly and Annotation Nomenclature working group will present their recent publication ( https://doi.org/10.1093/genetics/iyaf006) and recommendations on gene and genome nomenclature. I have included more details about the webinar and the Zoom link to attend the webinar below. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Abstracts:* *Guidelines for Gene and Genome Assembly Nomenclature (GAAN)* Clear and informative naming schemes enhance the utility of genome assemblies and gene annotations. We present a comprehensive nomenclature framework which incorporates species, sequencing group, colony/breed/strain, version, and other critical metadata in a well-structured format. This approach aligns with standards from AgBioData discussions and ensures compatibility with major repositories such as those in the INSDC. To facilitate adoption, we developed the Gene and Genome Assembly Nomenclature (GAAN) tool for validating names under these guidelines. Future iterations of GAAN will integrate external databases like the Darwin Tree of Life Identifiers and the Vertebrate Breed Ontology for further validation. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=David+Molik+and+A…> *Join Zoom Meetinghttps://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 <https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09>* Meeting ID: 820 3835 6125 Passcode: 160683

1 month, 3 weeks

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2nd Announcement: details for attending on-line Single Cell Genomics Field Days! *ALSO: a reminder on travel funding for in-person March SC Workshop!*

by Annarita Marrano

Dear agricultural genome or phenome researcher: This is a further announcement of the series of four “Field Days” on Single Cell genomics in agriculture. Also, please see below for a second reminder on travel funding for attending the AG2PI Single Cell Workshop March 29-30! Details on the four sessions can be found at: https://www.faang.org/bbs?s=2025_wkshop..txt If you are interested in attending one or more of these *free* online sessions, please register at least 2 days in advance at: https://docs.google.com/forms/d/1W2aSNN0QEE-yzqehj2DHsGKa9N3fvCXHPMY9gAeZa7… We will follow up with registered people to provide Zoom information one day before the session and provide information on obtaining the sessions' recordings once they are available. *ALSO:* **We still have a handful of seats available for early career researchers to request $600 funding that will cover costs for the SC Workshop in Orlando, Florida: https://www.agbt.org/home/home/agbt-ag/agworkshops/#workshop3 If you are interested in this, have your advisor send confirmation you are eligible: that you are currently in graduate school or within 5 years of attaining your PhD.** Thanks for your interest! Chris Tuggle for the AG2PI Single Cell Workshop Organizing Committee

2 months

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REMINDER - Monthly Webinar Next Wed, Feb, 5th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us for the first monthly webinar of 2025! Next Wednesday, Feb. 5th, at 12 PM CDT, David Molik and Adam Wright from the Genome Assembly and Annotation Nomenclature working group will present their recent publication (https://doi.org/10.1093/genetics/iyaf006) and recommendations on gene and genome nomenclature. I have included more details about the webinar and the Zoom link to attend the webinar below. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Abstracts:* *Guidelines for Gene and Genome Assembly Nomenclature (GAAN)* Clear and informative naming schemes enhance the utility of genome assemblies and gene annotations. We present a comprehensive nomenclature framework which incorporates species, sequencing group, colony/breed/strain, version, and other critical metadata in a well-structured format. This approach aligns with standards from AgBioData discussions and ensures compatibility with major repositories such as those in the INSDC. To facilitate adoption, we developed the Gene and Genome Assembly Nomenclature (GAAN) tool for validating names under these guidelines. Future iterations of GAAN will integrate external databases like the Darwin Tree of Life Identifiers and the Vertebrate Breed Ontology for further validation. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> *Join Zoom Meetinghttps://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 <https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09>* Meeting ID: 820 3835 6125 Passcode: 160683

2 months

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AgBioData-LIST