- AgBioData-LIST - Main Bioinformatics Lab

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

3 months

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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

3 months, 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

3 months, 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

3 months, 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

3 months, 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

4 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

4 months

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Join us at PAG 32 (Jan 10-15; San Diego)!

by Annarita Marrano

Dear everyone, AgBioData will be at PAG 32 in San Diego! If you are attending the conference, please join us: - For *our workshop* on *Friday, Jan. 10, at 4 PM in room Town and Country C*. There will be presentations from the current working groups and we will provide updates on the consortium's direction. More info on the workshop is available here <https://www.agbiodata.org/agb-pag32>. - At* booth #210! *We will be there with our member databases to meet you in person and answer questions. Looking forward to seeing you at PAG! Best, Annarita

4 months, 3 weeks

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REMINDER - TOMORROW Webinar at 12 PM CDT

by Annarita Marrano

Hi everybody, Join us TOMORROW, at 12 PM CDT, for our monthly webinar with Sarah Dyer. She will discuss Ensembl as a precious resource for annotated genomes across the tree of life. 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:* *Plants, pollinators, and pests in Ensembl - integrating genomics data for agriculturally relevant species* Ensembl is an open platform integrating publicly available genomic data to support the exploration of gene annotations, genetic variation, and comparative genomics. Increasing numbers of genomes are available for agriculturally relevant species, with multiple high-quality genomes now being generated for many crops. In addition, large-scale biodiversity projects are increasing the number of insect genomes available for pest and pollinator species. Providing ways to explore this genomic data is key to supporting research and breeding efforts for agricultural species. Ensembl Metazoa and Ensembl Plants now hold more than 380 invertebrate and almost 160 plant genomes, respectively. In addition, our new Ensembl site ( https://beta.ensembl.org) already holds more than 1,500 invertebrates and over 100 plant genomes. The new site will ultimately replace the current suite of Ensembl component sites, bringing annotated genomes together from across the Tree of Life. In this webinar, we will look at the species, data types, and tools you can find in Ensembl and ways you can access these resources. *| 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 months, 4 weeks

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(no subject)

by Annarita Marrano

Hi everybody, Join us TOMORROW, at 12 PM CDT, for our monthly webinar with Sarah Dyer. She will discuss Ensembl as a precious resource for annotated genomes across the tree of life. 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:* *Plants, pollinators, and pests in Ensembl - integrating genomics data for agriculturally relevant species* Ensembl is an open platform integrating publicly available genomic data to support the exploration of gene annotations, genetic variation, and comparative genomics. Increasing numbers of genomes are available for agriculturally relevant species, with multiple high-quality genomes now being generated for many crops. In addition, large-scale biodiversity projects are increasing the number of insect genomes available for pest and pollinator species. Providing ways to explore this genomic data is key to supporting research and breeding efforts for agricultural species. Ensembl Metazoa and Ensembl Plants now hold more than 380 invertebrate and almost 160 plant genomes, respectively. In addition, our new Ensembl site ( https://beta.ensembl.org) already holds more than 1,500 invertebrates and over 100 plant genomes. The new site will ultimately replace the current suite of Ensembl component sites, bringing annotated genomes together from across the Tree of Life. In this webinar, we will look at the species, data types, and tools you can find in Ensembl and ways you can access these resources. *| 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 months, 4 weeks

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