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
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
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
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.
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.
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
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
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
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
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