- AgBioData-LIST - Main Bioinformatics Lab

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

5 months, 2 weeks

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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

6 months

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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

7 months

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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

7 months

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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

7 months, 2 weeks

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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.

8 months

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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.

8 months, 1 week

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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

9 months

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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

9 months

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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

9 months, 1 week

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AgBioData-LIST