- AgBioData-LIST - Main Bioinformatics Lab

AgBiodata April 2026 webinar -- Omar Harb on VEuPathDB, a pathogen database with a unique sustainability funding model

by MARCELA KAREY TELLO-RUIZ

Hello Everybody, Let's together explore how *VEuPathDB* integrates multi-omics data, advanced analytics, and AI-driven tools to accelerate infectious disease research, and learn about the innovative community-supported funding model designed to sustain this critical open resource! On Wednesday, April 1st, 1PM ET, *Omar Harb* <https://www.omarharb.org/>, Senior Project Manager & Director Scientific Outreach & Education(VEuPathDB.org) at the University of Pennsylvania, will present the talk titled: “VEuPathDB: A Comprehensive Informatics Resource for Eukaryotic Pathogen, Vector, and Host Biology”. Zoom link and abstract below. We hope you will join us! Marcela -- Wednesday, April 1st, 1PM ET | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time *here* <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+April+2…> . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- Speaker: *Omar Harb* <https://www.omarharb.org/> (Director of Scientific Outreach & Education; Project Manager, VEuPathDB) Title: VEuPathDB: A Comprehensive Informatics Resource for Eukaryotic Pathogen, Vector, and Host Biology Abstract: VEuPathDB (the Eukaryotic Pathogen, Vector, and Host Informatics Resource) is an integrated bioinformatics platform that empowers researchers with comprehensive data, advanced analytical tools, and emerging artificial intelligence capabilities to accelerate discovery in infectious disease biology. The resource consolidates high-quality genomic, transcriptomic, proteomic, and functional data for eukaryotic pathogens, vectors, and relevant host systems, coupled with curated metadata and standardized ontologies. VEuPathDB’s suite of tools enables complex in-silico analyses, including comparative genomics, gene expression profiling, metabolic pathway exploration, and customizable data mining workflows. Recent enhancements leverage AI-driven methods for summarizing transcriptomic data, facilitating hypothesis generation and the interpretation of large-scale experimental results. Through an intuitive web-based interface and APIs, VEuPathDB supports reproducible science and community-driven annotation efforts. To remain open access and sustain its development, maintenance, and ongoing expansion of data and computational capabilities, VEuPathDB employs a voluntary subscription-based funding model. Under this approach, participating labs, institutions, and companies contribute annual subscription fees that support core infrastructure, curation activities, and user support services. The model balances broad access for the scientific community with stable funding streams, enabling strategic investments in AI integration and responsive tool enhancement. Subscription revenues complement competitive grant funding and are essential for long-term platform growth, ensuring that VEuPathDB continues to meet evolving research needs in pathogen, vector, and host informatics. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

2 weeks

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2026 AgBioData Community Workshop -- Schedule and Registration

by MARCELA KAREY TELLO-RUIZ

Hi Everybody, We are pleased to share the schedule and *registration link* for the *AgBioData Community Workshop*, to be held April 20–22, 2026, in Olathe, Kansas, and *online*. *REGISTER:* https://tinyurl.com/agbiodata2026 If you plan to attend in person (and have not already registered), it is *very important* that you REGISTER no later than *Friday, March 6*, using the link above. Early next week, U.S.-based in-person participants will be contacted by a K-State travel agent to arrange flights to MCI and lodging (two nights). Ground transportation in Kansas City and meals will also be provided. International colleagues are welcome to participate in person with their own funding or join remotely. Details for virtual participation will be shared soon. We hope you will be able to join us. Kind regards, Marcela On behalf of AgBioData's Community Workshop Committee -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

4 weeks

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AgBioData March 2026 webinar -- John McNamara on Integrating Phenomics and Phenotypes into Agricultural Databases

by MARCELA KAREY TELLO-RUIZ

Hi Everybody, On Wednesday, March 4th,12 PM CT, *John McNamara* <https://serc.carleton.edu/person/53858.html>, Professor Emeritus of Animal Sciences at Washington State University, will present the talk titled: “*Integrating phenomics and phenotypes into agricultural databases.*” Zoom link and abstract below. We hope you will join us. Kind regards, Marcela -- Wednesday, March 4th, 12PM CT | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time *here* <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+March+2…> . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- Speaker: *John McNamara* <https://serc.carleton.edu/person/53858.html>, Professor Emeritus of Animal Sciences at Washington State University Title: Integrating phenomics and phenotypes into agricultural databases Abstract: The United States agriculture and food systems research and education system remains the envy of the world, and the US Department of Agriculture and the Land-Grant University system lead the public and private partnerships that have improved agricultural productivity and human health phenomenally for over 160 years. The continuation of these improvements relies on equitable access to trustworthy data, particularly in genetics and phenomics, and the ability to leverage such data to address future scientific challenges. In the new article set forth by the Phenotypic Data Standardization and Management working group, we discuss the growing need in agriculture for phenomic databases that follow findable, accessible, interoperable, and reproducible (FAIR) data guidelines, as well as the need for public policy supporting a sustainable funding model for these databases. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

1 month

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Spots available for in-person participation at the AgBioData Annual Workshop (April 20–22, 2026)

by MARCELA KAREY TELLO-RUIZ

Dear Colleagues, We have some spots available to attend the AgBioData Annual Workshop IN PERSON. This hybrid event will be held on April 20–22, 2026, in Olathe, Kansas. To be eligible for support, you will need to be affiliated at a US-based institution. We will pay for airfare or equivalent, two nights lodging, meals and ground transportation in Kansas. Please let me know ASAP if you would be willing and able to participate in person. There is no cost for national and international participants to join remotely. We hope you will be able to join us! Marcela On behalf of AgBioData Community Workshop Organizing Committee -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

1 month, 2 weeks

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THIS Wednesday -- AgBiodata February 2026 webinar: Pascale Gaudet, Gene Ontology and Network Modeling

by MARCELA KAREY TELLO-RUIZ

Hi Everybody, This Wednesday, February 4th, 12PM CT, Pascale Gaudet, Gene Ontology Project Manager at the Swiss Institute Bioinformatics, will present the talk titled: “*Extending the Gene Ontology for Biological Network Modeling*”. Zoom link and abstract below. We hope you will join us! Kind regards, Marcela -- Wednesday, February 4th, 12PM CT | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Februar… . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- Speaker: Pascale Gaudet, Swiss Institute of Bioinformatics Title: Extending the Gene Ontology for Biological Network Modeling Abstract: The Gene Ontology (GO) is an essential resource in the bioinformatics landscape, supporting a wide range of applications. It serves both as a comprehensive encyclopedia of biological knowledge and as a key tool for interpreting high-throughput biological data. More recently, GO has expanded to support biological network modeling through the development of GO Causal Activity Models (GO-CAMs), which enable network analysis within the highly structured GO data framework. This presentation will introduce the GO-CAM data model, describe its relationship to standard GO annotations, and highlight ontology developments driven by GO-CAM requirements. It will also discuss how GO is leveraging artificial intelligence to enhance multiple aspects of the GO workflow, including ontology development, annotation, and quality control. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

1 month, 3 weeks

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AgBiodata February 2026 webinar -- Pascale Gaudet on Extending the Gene Ontology for Biological Network Modeling

by MARCELA KAREY TELLO-RUIZ

Hi Everybody, On Wednesday, February 4th, 12PM CT, Pascale Gaudet, Gene Ontology Project Manager at the Swiss Institute Bioinformatics, will present the talk titled: “*Extending the Gene Ontology for Biological Network Modeling*”. Zoom link and abstract below. We hope you will join us. Kind regards, Marcela -- Wednesday, February 4th, 12PM CT | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Februar…> . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- Speaker: Pascale Gaudet, Swiss Institute of Bioinformatics Title: Extending the Gene Ontology for Biological Network Modeling Abstract: The Gene Ontology (GO) is an essential resource in the bioinformatics landscape, supporting a wide range of applications. It serves both as a comprehensive encyclopedia of biological knowledge and as a key tool for interpreting high-throughput biological data. More recently, GO has expanded to support biological network modeling through the development of GO Causal Activity Models (GO-CAMs), which enable network analysis within the highly structured GO data framework. This presentation will introduce the GO-CAM data model, describe its relationship to standard GO annotations, and highlight ontology developments driven by GO-CAM requirements. It will also discuss how GO is leveraging artificial intelligence to enhance multiple aspects of the GO workflow, including ontology development, annotation, and quality control. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

2 months, 2 weeks

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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

3 months, 4 weeks

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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

4 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

4 months, 3 weeks

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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

6 months

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