- AgBioData-LIST - Main Bioinformatics Lab

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

6 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

6 months, 1 week

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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

8 months

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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

8 months, 1 week

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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

8 months, 4 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

9 months

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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

9 months, 1 week

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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

9 months, 2 weeks

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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

9 months, 3 weeks

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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

10 months

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AgBioData-LIST