- AgBioData-LIST - Main Bioinformatics Lab

AgBiodata December 2025 webinar -- Heidi Imker on Database Sustainability during Instability

by MARCELA KAREY TELLO-RUIZ

Hi Everybody, On Wednesday, December 3rd, 12PM CT, Heidi Imker <https://databank.illinois.edu/featured_researchers/9>, Director of the Research Data Service at the University of Illinois Urbana-Champaign and Associate Professor at the University Library, will present the talk titled: “*Sustainability During Instability: Long-Lived Life Science Databases and Science Funding Outlook in the United States*”. Zoom link and abstract below. We hope you will join us. Kind regards, Marcela -- Wednesday, December 3rd, 12PM CT | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Decembe…> Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09M… ID: 820 3835 6125 Passcode: 160683-- Speaker: Heidi Imker, University of Illinois Urbana-Champaign Title: Sustainability During Instability: Long-Lived Life Science Databases and Science Funding Outlook in the United States Abstract: For many years, life science researchers have enjoyed free, open access to a wide range of online databases that make data sharing and reuse possible. But even long-established resources have always faced sustainability challenges and recent changes in U.S. science funding are making things even tougher. This presentation covers a study recently posted to bioRxiv which took a multiple mini–case study approach to document potential impacts for nine long-standing databases, including BHL, MorphoBank, OMIM, ORDB, rrnDB, VEuPathDB, WormAtlas, and two that preferred to remain anonymous. The results point to growing barriers to data access, a loss of valuable expertise, and disruptions to ongoing and future research. The presentation will conclude with a discussion of sustainability models given the current funding climate. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

2 weeks, 1 day

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Join the new AgBioData AI-Readiness Working Group!

by MARCELA KAREY TELLO-RUIZ

Dear AgBioData Community, *Do you want to contribute to the future of AI-Ready Ag data?* In its fifth year of NSF Research Coordination Network Award # 2126334, the AgBioData Consortium is launching a *new AI-Readiness Working Group*. This focused, 6–12 month group will: - define clear goals and deliverables, - develop a detailed timeline, and - nominate a chair and co-chair (if needed). Participation will require approximately 2–6 hours per month, including meetings and offline work. This is a valuable opportunity to help shape best practices for data archiving and management that benefit our entire community. Participation also offers: - professional networking, - leadership development, - authorship opportunities, and - eligibility for AgBioData Ambassador and Championship programs. Apply to join the AI-Readiness Working Group here: <https://forms.gle/B6pZP1aSDzYWScaT9> https://forms.gle/B6pZP1aSDzYWScaT9 For questions, contact Sarah Dyer (EMBL-EBI). Kind regards, Marcela On behalf of the AgBioData Steering Committee -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

1 month

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AgBiodata November webinar -- Barend Mons on "Stop data sharing: AgBioData and FAIR visitation"

by MARCELA KAREY TELLO-RUIZ

Hi everybody, On Wednesday, November 5th, we will have Barend Mons, Professor Emeritus at Leiden University, founder member of the LIFES Institute and GO-FAIR with a talk titled: "*Stop data sharing: AgBioData and FAIR visitation"*. Below you can find more details. We hope you will join us. Kind regards, Marcela --- Wednesday, November 5th, 12PM CT| 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+October…> Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09M… ID: 820 3835 6125 Passcode: 160683 --- *Speaker*: Barend Mons, Professor Emeritus at Leiden University, founder member of the LIFES Institute, and GO-FAIR *Title: *Stop data sharing: AgBioData and FAIR visitation One tap mobile +15642172000,,82038356125#,,,,*160683# US +16469313860,,82038356125#,,,,*160683# US Join instructions https://us06web.zoom.us/meetings/82038356125/invitations?signature=AOYF69Mt… -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

1 month, 1 week

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TODAY at 12 pm CT!!! AgBiodata webinar -- Paige Kulzer on the Integrated Genome Browser

by MARCELA KAREY TELLO-RUIZ

Hi Everybody, Today we will have Paige Kulzer from the Loraine Lab at the University of North Carolina at Charlotte talking about the Integrated Genome Browser (IGB) for sustainable genomic data accessibility and visualization. Paige has kindly shared her slides for anyone interested in following her talk (attached and also available for download as PDF from the AgBioData website <https://www.agbiodata.org/sites/default/files/Kulzer_AgBioData_Webinar_Fina…> or go to Events --> Monthly Webinars). Zoom link and additional details below. We hope you will join us. Kind regards, Marcela --- Wednesday, October 1st, 12PM CT| 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+October…> Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09M… ID: 820 3835 6125 Passcode: 160683 --- *Speaker*: Page Kulzer, University of North Carolina at Charlotte *Title: *Toward Sustainable Genomic Data Accessibility and Visualization with the Integrated Genome Browser *Abstract: *Integrated Genome Browser (IGB, pronounced “ig-bee”) is a fast, feature-rich, open-source desktop genome browser thousands of researchers have used to explore and analyze genomic data. To make it as easy as possible for researchers to load their data in IGB, we provide built-in genome assemblies and annotations for model and non-model organisms. We obtained many of these from sources familiar to AgBioData members, including TAIR, Sol Genomics Network, and MaizeGDB. Other database and genome browser developers do similar work to disseminate genomic data to researchers, and some offer robust programmatic access to their data via APIs (application programmer interfaces). By accessing these computational resources, IGB can show new assemblies without our team needing to replicate assembly data files to our own servers. In this webinar, we’ll discuss IGB’s latest integrations with genome data providers and AgBioData members. We’re also excited to highlight the ongoing work of doctoral student Karthik Raveendran in our lab who is developing innovative methods for visualizing single-cell RNA-Seq data in the Integrated Genome Browser and how this new capability helps biologists understand, evaluate, and analyze these data better. Altogether, these integrations address one of the most important problems in data visualization in bioinformatics: Developing sustainable ways to make the vast wealth of genome-centric experimental data available to the community. One tap mobile +15642172000,,82038356125#,,,,*160683# US +16469313860,,82038356125#,,,,*160683# US Join instructions https://us06web.zoom.us/meetings/82038356125/invitations?signature=AOYF69Mt… -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

2 months, 2 weeks

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AgBiodata Oct 1st webinar: Paige Kulzer on The Integrated Genome Browser

by MARCELA KAREY TELLO-RUIZ

Hi everybody, Gentle reminder for our monthly webinar, THIS Wednesday, October 1st. We will have Paige Kulzer from the Loraine Lab at the University of North Carolina at Charlotte talking about the Integrated Genome Browser (IGB) for sustainable genomic data accessibility and visualization. More details below. We hope you will join us. Regards, Marcela --- Wednesday, October 1st, 12PM CT| 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+October…> Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09M… ID: 820 3835 6125 Passcode: 160683 --- *Speaker*: Page Kulzer, University of North Carolina at Charlotte *Title: *Toward Sustainable Genomic Data Accessibility and Visualization with the Integrated Genome Browser *Abstract: *Integrated Genome Browser (IGB, pronounced “ig-bee”) is a fast, feature-rich, open-source desktop genome browser thousands of researchers have used to explore and analyze genomic data. To make it as easy as possible for researchers to load their data in IGB, we provide built-in genome assemblies and annotations for model and non-model organisms. We obtained many of these from sources familiar to AgBioData members, including TAIR, Sol Genomics Network, and MaizeGDB. Other database and genome browser developers do similar work to disseminate genomic data to researchers, and some offer robust programmatic access to their data via APIs (application programmer interfaces). By accessing these computational resources, IGB can show new assemblies without our team needing to replicate assembly data files to our own servers. In this webinar, we’ll discuss IGB’s latest integrations with genome data providers and AgBioData members. We’re also excited to highlight the ongoing work of doctoral student Karthik Raveendran in our lab who is developing innovative methods for visualizing single-cell RNA-Seq data in the Integrated Genome Browser and how this new capability helps biologists understand, evaluate, and analyze these data better. Altogether, these integrations address one of the most important problems in data visualization in bioinformatics: Developing sustainable ways to make the vast wealth of genome-centric experimental data available to the community. One tap mobile +15642172000,,82038356125#,,,,*160683# US +16469313860,,82038356125#,,,,*160683# US Join instructions https://us06web.zoom.us/meetings/82038356125/invitations?signature=AOYF69Mt… -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

2 months, 2 weeks

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AgBiodata October webinar -- Paige Kulzer on the Integrated Genome Browser

by MARCELA KAREY TELLO-RUIZ

Hi everybody, On Wednesday, October 1st, we will have Paige Kulzer from the Loraine Lab at the University of North Carolina at Charlotte talking about the Integrated Genome Browser (IGB) for sustainable genomic data accessibility and visualization. Below you can find more details. We hope you will join us. Kind regards, Marcela --- Wednesday, October 1st, 12PM CT| 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+October…> Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09M… ID: 820 3835 6125 Passcode: 160683 --- *Speaker*: Page Kulzer, University of North Carolina at Charlotte *Title: *Toward Sustainable Genomic Data Accessibility and Visualization with the Integrated Genome Browser *Abstract: *Integrated Genome Browser (IGB, pronounced “ig-bee”) is a fast, feature-rich, open-source desktop genome browser thousands of researchers have used to explore and analyze genomic data. To make it as easy as possible for researchers to load their data in IGB, we provide built-in genome assemblies and annotations for model and non-model organisms. We obtained many of these from sources familiar to AgBioData members, including TAIR, Sol Genomics Network, and MaizeGDB. Other database and genome browser developers do similar work to disseminate genomic data to researchers, and some offer robust programmatic access to their data via APIs (application programmer interfaces). By accessing these computational resources, IGB can show new assemblies without our team needing to replicate assembly data files to our own servers. In this webinar, we’ll discuss IGB’s latest integrations with genome data providers and AgBioData members. We’re also excited to highlight the ongoing work of doctoral student Karthik Raveendran in our lab who is developing innovative methods for visualizing single-cell RNA-Seq data in the Integrated Genome Browser and how this new capability helps biologists understand, evaluate, and analyze these data better. Altogether, these integrations address one of the most important problems in data visualization in bioinformatics: Developing sustainable ways to make the vast wealth of genome-centric experimental data available to the community. One tap mobile +15642172000,,82038356125#,,,,*160683# US +16469313860,,82038356125#,,,,*160683# US Join instructions https://us06web.zoom.us/meetings/82038356125/invitations?signature=AOYF69Mt… -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

3 months

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AgBioData monthly webinar - TOMORROW, Wed Sept. 3 (12 PM CET)

by Marcela Karey Tello-Ruiz

Please join us for our next monthly webinar on Sept 3, 12PM CDT. Dr. Sonia Balyan of the Indian Biological Data Centre will be presenting a talk entitled “Indian Crop Phenome Database: Advancing Crop Research Through Open Phenomic Data” | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 Abstract The Indian Crop Phenome Database (ICPD), developed at the Indian Biological Data Centre (IBDC), isa pioneering national initiative designed to address the challenges of managing large-scale phenotypic and associated datasets in agriculture. India generates vast volumes of phenotypic data from diverse crop species through field trials, breeding programs, and research projects; however, the absence of standardized formats and dedicated repositories has often left this wealth of information underutilized. ICPD addresses these gaps by fully embracing the FAIR principles — ensuring data are Findable, Accessible, Interoperable, and Re-usable. As the designated data hub for major mission-mode programs on Characterization of Genetic Resources supported by the Department of Biotechnology (DBT), India, ICPD offers a robust framework for digitization, curation, and sharing of crop phenotyping data, fostering seamless knowledge exchange across the scientific community. Each dataset receives a unique IBDC accession, ensuring traceability, proper citation, and long-term preservation. Supporting over 30 crop species, ICPD adopts international ontology standards for traits, tissues, developmental stages, and methodologies, while also allowing the creation of new ontology terms with temporary accessions that undergo expert curation. This generic framework enables the submission of any crop phenome data, providing both flexibility and standardization. By serving as a centralized, standards-driven, and FAIR-compliant repository, ICPD is poised to transform phenomics research in India — accelerating the development of climate-resilient, high-yield, and pest-resistant cultivars, and strengthening the scientific foundation for global food and nutritional security.

3 months, 2 weeks

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Reminder monthly webinar - Next Wed Sept. 3 (12 PM CET)

by Annarita Marrano

Join us for our next monthly webinar on Sept 3, 12PM CDT. Dr. Sonia Balyan of the Indian Biological Data Centre will be presenting a talk entitled “Indian Crop Phenome Database: Advancing Crop Research Through Open Phenomic Data” | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 Abstract The Indian Crop Phenome Database (ICPD), developed at the Indian Biological Data Centre (IBDC), isa pioneering national initiative designed to address the challenges of managing large-scale phenotypic and associated datasets in agriculture. India generates vast volumes of phenotypic data from diverse crop species through field trials, breeding programs, and research projects; however, the absence of standardized formats and dedicated repositories has often left this wealth of information underutilized. ICPD addresses these gaps by fully embracing the FAIR principles — ensuring data are Findable, Accessible, Interoperable, and Re-usable. As the designated data hub for major mission-mode programs on Characterization of Genetic Resources supported by the Department of Biotechnology (DBT), India, ICPD offers a robust framework for digitization, curation, and sharing of crop phenotyping data, fostering seamless knowledge exchange across the scientific community. Each dataset receives a unique IBDC accession, ensuring traceability, proper citation, and long-term preservation. Supporting over 30 crop species, ICPD adopts international ontology standards for traits, tissues, developmental stages, and methodologies, while also allowing the creation of new ontology terms with temporary accessions that undergo expert curation. This generic framework enables the submission of any crop phenome data, providing both flexibility and standardization. By serving as a centralized, standards-driven, and FAIR-compliant repository, ICPD is poised to transform phenomics research in India — accelerating the development of climate-resilient, high-yield, and pest-resistant cultivars, and strengthening the scientific foundation for global food and nutritional security.

3 months, 2 weeks

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REMINDER - Monthly Webinar TOMORROW at 12 PM CT

by Annarita Marrano

Hi everybody, Join us for our monthly webinar TOMORROW, *August 6th, at 12 PM CDT*. Trupti Joshi (Marshall University) will talk about translational bioinformatics resources and AI solutions for multiomics research. 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:* *Translational Bioinformatics Resources and AI Solutions for Multiomics Research* Next generation sequencing and multiomics data (bulk and single-cell) capturing molecular changes from genomics all the way to phenomics, have become an integral part of research in all domains including biomedical sciences, plants sciences, and others. This rapid revolution in the multiomics has posed a growing need for translational tools that can handle large amounts of data, are easily expandable, provide interpretable results and can be readily applied to any species. To address such translational needs, we have developed Soybean Knowledge Base (SoyKB) and Knowledge Base Commons (KBCommons) web-based frameworks, both fully equipped to handle the entire multiomics landscape for all organisms. Our developed tools, such as Allele Catalog, GenVarX, AccuTool, and MaDis, are specifically designed to provide the plant community with efficient data-driven solutions for better breeding strategies. Additionally, our G2PDeep, deep learning method, provides a comprehensive web-based resource for phenotype predictions using multiomics data for all organisms. *| 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, 1 week

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REMINDER - Monthly Webinar Next Wed, August 6th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us for our monthly webinar next Wed, *August 6th, at 12 PM CDT*. Trupti Joshi (Marshall University) will talk about translational bioinformatics resources and AI solutions for multiomics research. 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:* *Translational Bioinformatics Resources and AI Solutions for Multiomics Research* Next generation sequencing and multiomics data (bulk and single-cell) capturing molecular changes from genomics all the way to phenomics, have become an integral part of research in all domains including biomedical sciences, plants sciences, and others. This rapid revolution in the multiomics has posed a growing need for translational tools that can handle large amounts of data, are easily expandable, provide interpretable results and can be readily applied to any species. To address such translational needs, we have developed Soybean Knowledge Base (SoyKB) and Knowledge Base Commons (KBCommons) web-based frameworks, both fully equipped to handle the entire multiomics landscape for all organisms. Our developed tools, such as Allele Catalog, GenVarX, AccuTool, and MaDis, are specifically designed to provide the plant community with efficient data-driven solutions for better breeding strategies. Additionally, our G2PDeep, deep learning method, provides a comprehensive web-based resource for phenotype predictions using multiomics data for all organisms. *| 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, 2 weeks

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AgBioData Ambassador Program - NOW Accepting Applications!

by Annarita Marrano

Hi everybody, *Applications for the Ambassador Program are now open! * This program offers stipends of up to $2000 for individuals presenting AgBioData work at conferences and is *open to active or recent working group members*. The applicants will present a talk or poster specifically about AgBioData (as a whole or working group products) or represent the consortium at a conference or meeting. We accept applications from *members of U.S. institutions* and encourage Early-Career Researchers to apply. If you are or have been an active working group member and would like to attend *a conference before August 2026,* check if you are eligible and apply! *More information available at* https://www.agbiodata.org/agb-ambassador *Application form: *https://forms.gle/gepgiWwhYFP7K85U7 Please let us know if you have any questions. Best, Annarita

4 months, 3 weeks

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REMINDER - Monthly Webinar TOMORROW, June 4th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us for our monthly webinar *tomorrow* *at 12 PM CDT*. Sean Wilkinson will discuss the Workflows Community Initiative's FAIR Workflows Working Group (WCI-FW), a global and open community of researchers and developers working with computational workflows across disciplines and domains. 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:* *The FAIR Principles for Computational Workflow.* Recent trends in the computational and data sciences show an increasing recognition and adoption of computational workflows as tools for productivity and reproducibility that also democratize access to platforms and processing know-how. As digital objects to be shared, discovered, and reused, computational workflows benefit from the FAIR principles, which stand for Findable, Accessible, Interoperable, and Reusable. The Workflows Community Initiative's FAIR Workflows Working Group (WCI-FW), a global and open community of researchers and developers working with computational workflows across disciplines and domains, has systematically addressed the application of both FAIR data and software principles to computational workflows in a recent publication. This presentation will discuss the WCI-FW working group, some of the critical questions we needed to answer, the resulting set of FAIR principles for workflows, and opportunities for collaborating with the AgBioData Consortium to support FAIR workflow implementation. It is our hope that the FAIR recommendations for workflows proposed in the paper will maximize their value as research assets and facilitate their adoption by the wider community. *| 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

6 months, 2 weeks

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REMINDER - Monthly Webinar Next Wed, June 4th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us for our monthly webinar next Wed, *June 4th, at 12 PM CDT*. Sean Wilkinson will discuss the Workflows Community Initiative's FAIR Workflows Working Group (WCI-FW), a global and open community of researchers and developers working with computational workflows across disciplines and domains. 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:* *The FAIR Principles for Computational Workflow. * Recent trends in the computational and data sciences show an increasing recognition and adoption of computational workflows as tools for productivity and reproducibility that also democratize access to platforms and processing know-how. As digital objects to be shared, discovered, and reused, computational workflows benefit from the FAIR principles, which stand for Findable, Accessible, Interoperable, and Reusable. The Workflows Community Initiative's FAIR Workflows Working Group (WCI-FW), a global and open community of researchers and developers working with computational workflows across disciplines and domains, has systematically addressed the application of both FAIR data and software principles to computational workflows in a recent publication. This presentation will discuss the WCI-FW working group, some of the critical questions we needed to answer, the resulting set of FAIR principles for workflows, and opportunities for collaborating with the AgBioData Consortium to support FAIR workflow implementation. It is our hope that the FAIR recommendations for workflows proposed in the paper will maximize their value as research assets and facilitate their adoption by the wider community. *| 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

6 months, 3 weeks

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LAST CALL - Register NOW for the 2025 AgBioData community workshop on May 14-15

by Annarita Marrano

Hi everybody, This is your last chance to register for the *2025 AgBioData community workshop! REGISTER by Thursday (May 8)* at *https://forms.gle/rBZbEYKj73Lz9H9J8 <https://forms.gle/rBZbEYKj73Lz9H9J8> *and share the registration link with anybody you think might be interested. This two-day workshop (*May 14-15, 9:00 AM - 1:00 PM US Central Time*) will feature presentations from current working groups, keynote speakers, and discussions on relevant data-related topics, such as AI and database sustainability. A* draft of the meeting agenda is available here <https://www.agbiodata.org/2025-agbcomworks>.* I hope you will join us. Have a lovely week. Best, Annarita

7 months, 2 weeks

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REMINDER - Register NOW for the 2025 AgBioData community workshop on May 14-15

by Annarita Marrano

Hi everybody, You are still on time to register for the *2025 AgBioData community workshop! REGISTER NOW* at *https://forms.gle/rBZbEYKj73Lz9H9J8 <https://forms.gle/rBZbEYKj73Lz9H9J8> *and share the registration link with anybody you think might be interested. This two-day workshop (*May 14-15, 9:00 AM - 1:00 PM US Central Time*) will feature presentations from current working groups, keynote speakers, and discussions on relevant data-related topics, such as AI and database sustainability. A* draft of the meeting agenda is available here <https://www.agbiodata.org/2025-agbcomworks>.* *Register NOW* and contribute your valuable experience and insights on data generation, management, and reuse. I hope you will join us. Have a lovely week. Best, Annarita

7 months, 2 weeks

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REMINDER - Register NOW for the 2025 AgBioData community workshop on May 14-15

by Annarita Marrano

Hi everybody, A friendly reminder to register for the *2025 AgBioData community workshop* *by May 5* at *https://forms.gle/rBZbEYKj73Lz9H9J8 <https://forms.gle/rBZbEYKj73Lz9H9J8>*! This two-day workshop (*May 14-15, 9:00 AM - 1:00 PM US Central Time*) will feature presentations from current working groups, keynote speakers, and discussions on relevant data-related topics, such as AI and database sustainability. You can see *a draft of the meeting agenda here <https://www.agbiodata.org/2025-agbcomworks>.* *Register NOW* and contribute your valuable experience and insights on data generation, management, and reuse. I hope you will join us. Have a lovely week. Best, Annarita

7 months, 3 weeks

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Register NOW for the 2025 AgBioData community workshop on May 14-15

by Annarita Marrano

Hi everybody, The registration for the *2025 AgBioData community workshop* is OPEN! This two-day workshop (*May 14-15, 9:00 AM - 1:00 PM CDT*) will feature presentations from current working groups, keynote speakers, and discussions on relevant data-related topics, such as AI and database sustainability. We'll share more details about the meeting agenda soon! *Register by May 5* and contribute your valuable experience and insights on data generation, management, and reuse. *Registration link (https://forms.gle/rBZbEYKj73Lz9H9J8 <https://forms.gle/rBZbEYKj73Lz9H9J8>).* I hope you will join us. Have a lovely weekend. Best, Annarita

8 months

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Registration open for the 2025 AgBioData community workshop on May 14-15

by Annarita Marrano

Dear everybody, The registration for the *2025 AgBioData community workshop* is now OPEN! This two-day workshop (*May 14-15, 9 AM - 1 PM CDT*) will feature presentations from current working groups, keynote speakers, and discussions on relevant data-related topics (e.g., AI, database sustainability). We will share more details on the meeting agenda soon! *Register by May 5* and contribute with your valuable experience and insights on data generation, management, and reuse. *Registration link (https://forms.gle/rBZbEYKj73Lz9H9J8 <https://forms.gle/rBZbEYKj73Lz9H9J8>).* I hope you will join us. Have a lovely weekend. Best, Annarita

8 months, 1 week

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

by Annarita Marrano

Hi everybody, Join us tomorrow, *April 2nd, at 12 PM CDT,* and meet iBeetle-Base <https://ibeetle-base.uni-goettingen.de/>, the new AgBioData member database. *Gregor Bucher *from the University of Gottingen will discuss this integrated genomic and phenotypic information resource for red flour beetle research. 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

8 months, 2 weeks

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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

8 months, 3 weeks

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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

9 months, 2 weeks

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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

9 months, 3 weeks

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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

9 months, 3 weeks

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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

10 months

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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

10 months, 1 week

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