AgBioData-LIST September 2025

agbiodata-list@bioinfo.wsu.edu

2 participants
3 discussions

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, 4 weeks

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, 1 week

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, 3 weeks

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AgBioData-LIST September 2025