- AgBioData-LIST - Main Bioinformatics Lab

REMINDER - Monthly Webinar Next Wed, Feb, 5th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us for the first monthly webinar of 2025! Next Wednesday, Feb. 5th, at 12 PM CDT, David Molik and Adam Wright from the Genome Assembly and Annotation Nomenclature working group will present their recent publication (https://doi.org/10.1093/genetics/iyaf006) and recommendations on gene and genome nomenclature. 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:* *Guidelines for Gene and Genome Assembly Nomenclature (GAAN)* Clear and informative naming schemes enhance the utility of genome assemblies and gene annotations. We present a comprehensive nomenclature framework which incorporates species, sequencing group, colony/breed/strain, version, and other critical metadata in a well-structured format. This approach aligns with standards from AgBioData discussions and ensures compatibility with major repositories such as those in the INSDC. To facilitate adoption, we developed the Gene and Genome Assembly Nomenclature (GAAN) tool for validating names under these guidelines. Future iterations of GAAN will integrate external databases like the Darwin Tree of Life Identifiers and the Vertebrate Breed Ontology for further validation. *| 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

2 months

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Join us at PAG 32 (Jan 10-15; San Diego)!

by Annarita Marrano

Dear everyone, AgBioData will be at PAG 32 in San Diego! If you are attending the conference, please join us: - For *our workshop* on *Friday, Jan. 10, at 4 PM in room Town and Country C*. There will be presentations from the current working groups and we will provide updates on the consortium's direction. More info on the workshop is available here <https://www.agbiodata.org/agb-pag32>. - At* booth #210! *We will be there with our member databases to meet you in person and answer questions. Looking forward to seeing you at PAG! Best, Annarita

2 months, 3 weeks

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REMINDER - TOMORROW Webinar at 12 PM CDT

by Annarita Marrano

Hi everybody, Join us TOMORROW, at 12 PM CDT, for our monthly webinar with Sarah Dyer. She will discuss Ensembl as a precious resource for annotated genomes across the tree of life. 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:* *Plants, pollinators, and pests in Ensembl - integrating genomics data for agriculturally relevant species* Ensembl is an open platform integrating publicly available genomic data to support the exploration of gene annotations, genetic variation, and comparative genomics. Increasing numbers of genomes are available for agriculturally relevant species, with multiple high-quality genomes now being generated for many crops. In addition, large-scale biodiversity projects are increasing the number of insect genomes available for pest and pollinator species. Providing ways to explore this genomic data is key to supporting research and breeding efforts for agricultural species. Ensembl Metazoa and Ensembl Plants now hold more than 380 invertebrate and almost 160 plant genomes, respectively. In addition, our new Ensembl site ( https://beta.ensembl.org) already holds more than 1,500 invertebrates and over 100 plant genomes. The new site will ultimately replace the current suite of Ensembl component sites, bringing annotated genomes together from across the Tree of Life. In this webinar, we will look at the species, data types, and tools you can find in Ensembl and ways you can access these resources. *| 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

4 months

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(no subject)

by Annarita Marrano

Hi everybody, Join us TOMORROW, at 12 PM CDT, for our monthly webinar with Sarah Dyer. She will discuss Ensembl as a precious resource for annotated genomes across the tree of life. 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:* *Plants, pollinators, and pests in Ensembl - integrating genomics data for agriculturally relevant species* Ensembl is an open platform integrating publicly available genomic data to support the exploration of gene annotations, genetic variation, and comparative genomics. Increasing numbers of genomes are available for agriculturally relevant species, with multiple high-quality genomes now being generated for many crops. In addition, large-scale biodiversity projects are increasing the number of insect genomes available for pest and pollinator species. Providing ways to explore this genomic data is key to supporting research and breeding efforts for agricultural species. Ensembl Metazoa and Ensembl Plants now hold more than 380 invertebrate and almost 160 plant genomes, respectively. In addition, our new Ensembl site ( https://beta.ensembl.org) already holds more than 1,500 invertebrates and over 100 plant genomes. The new site will ultimately replace the current suite of Ensembl component sites, bringing annotated genomes together from across the Tree of Life. In this webinar, we will look at the species, data types, and tools you can find in Ensembl and ways you can access these resources. *| 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

4 months

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REMINDER - Monthly Webinar Next Wed, Dec, 4th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us for our monthly webinar next Wednesday, Dec. 4th, at 12 PM CDT. Sarah Dyer will discuss Ensembl as a precious resource for annotated genomes across the tree of life. 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:* *Plants, pollinators, and pests in Ensembl - integrating genomics data for agriculturally relevant species* Ensembl is an open platform integrating publicly available genomic data to support the exploration of gene annotations, genetic variation, and comparative genomics. Increasing numbers of genomes are available for agriculturally relevant species, with multiple high-quality genomes now being generated for many crops. In addition, large scale biodiversity projects are increasing the number of insect genomes available for pest and pollinator species. Providing ways to explore this genomic data is key to supporting research and breeding efforts for agricultural species. Ensembl Metazoa and Ensembl Plants now hold more than 380 invertebrate and almost 160 plant genomes, respectively. In addition, our new Ensembl site ( https://beta.ensembl.org) already holds more than 1,500 invertebrate and over 100 plant genomes. The new site will ultimately replace the current suite of Ensembl component sites, bringing annotated genomes together from across the tree of life. In this webinar we will look at the species, data types and tools you can find in Ensembl and ways you can access these resources. *| 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

4 months

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REMINDER - Join us for a virtual round table on AI and biocuration TOMORROW (12 PM CT)

by Annarita Marrano

Dear all, We invite the AgBioData community to *a virtual roundtable on artificial intelligence* in agricultural genomics *TOMORROW (November 6) at 12 PM Central Time* (Zoom link <https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09> ). AI and natural language processing (NLP) for biocuration are becoming more popular in the community, allowing several applications and creating new data-related issues. *We invite the AgBioData member databases and the larger community to provide feedback on these challenges*, help us understand their importance for the AgBioData member databases, and define the focus of new AgBioData working groups. The meeting will be 1-hour long and will feature breakout room sessions on two main topics: - *How databases can make data ready for AI* - *NLP for biocuration.* Please forward this invite to anyone you think might be interested. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Virtual…> Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683

4 months, 3 weeks

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Join us for a virtual round table on AI and biocuration on November 6 (12 PM CT)

by Annarita Marrano

Dear all, We invite the AgBioData community to *a virtual roundtable on artificial intelligence* in agricultural genomics *next Wednesday (November 6) at 12 PM Central Time* (Zoom link <https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09> ). AI and natural language processing (NLP) for biocuration are becoming more popular in the community, allowing several applications and creating new data-related issues. *We invite the AgBioData member databases and the larger community to provide feedback on these challenges*, help us understand their importance for the AgBioData member databases, and define the focus of new AgBioData working groups. The meeting will be 1-hour long and will feature breakout room sessions on two main topics: - *How databases can make data ready for AI* - *NLP for biocuration.* Please forward this invite to anyone you think might be interested. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Virtual…> Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 Join Zoom Meeting Join Zoom Meeting Meeting ID: 820 3835 6125 Passcode: 160683

5 months

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REMINDER - Monthly Webinar TOMORROW at 12 PM CT

by Annarita Marrano

Hi everybody, Join us *tomorrow*, Oct. 2nd, *at 12 PM CDT*. Montana Smith will discuss the National Microbiome Data Collaborative (NMDC) initiative and its work on advancing microbiome science through FAIR and standardized metadata and data. 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:* *NMDC: Advancing microbiome science through FAIR and standardized metadata and data* The National Microbiome Data Collaborative (NMDC)’s mission is to support a FAIR microbiome data-sharing network through infrastructure, data standards, and community building that addresses pressing challenges in environmental sciences. In this webinar, we will dive into what the NMDC is and how standardized metadata capture enables FAIR data. We will walk through the 4 NMDC products and how they’re lowering barriers for experimental scientists to conduct their research in a way that ensures data re-use. *| 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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REMINDER - Monthly Webinar Next Wed, Oct, 2nd, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us for our monthly webinar next Wednesday, Oct. 2nd, at 12 PM CDT. Montana Smith will talk about the National Microbiome Data Collaborative (NMDC) initiative and their work on advancing microbiome science through FAIR and standardized metadata and data. 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:* *NMDC: Advancing microbiome science through FAIR and standardized metadata and data* The National Microbiome Data Collaborative (NMDC)’s mission is to support a FAIR microbiome data-sharing network through infrastructure, data standards, and community building that addresses pressing challenges in environmental sciences. In this webinar, we will dive into what the NMDC is and how standardized metadata capture enables FAIR data. We will walk through the 4 NMDC products and how they’re lowering barriers for experimental scientists to conduct their research in a way that ensures data re-use. *| 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, 1 week

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REMINDER - Monthly Webinar Next Wed, Sept. 4th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us for our monthly webinar tomorrow at 12 PM CDT! *Dr. David Emms from InstaDeep* will discuss AgroNT, a foundational large language model for plant genomics. 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:* *AgroNT: A Foundational Large Language Model for Plant Genomics* Foundational large language models can be pre-trained on large unlabelled datasets and subsequently fine-tuned to a wide range of specific tasks. We’ll present AgroNT (Agro Nucleotide Transformer), a foundational DNA large language model pre-trained on reference genomes from 48 plant species with a predominant focus on crops. We have shown that AgroNT can be fine-tuned to obtain state-of-the-art predictions of many genomic elements, including polyadenylation sites, splice sites, open chromatin and enhancer regions. Furthermore, AgroNT can be fine-tuned to e.g. predict tissue-specific gene expression levels or to prioritize functional variants. Building on our Nucleotide Transformer, the novel SegmentNT model is able to make nucleotide resolution predictions, well suited to tasks such as de novo genome annotation of previously unseen species. Both our AgroNT and SegmentNT models are open-sourced for academic research and non-commercial uses on our GitHub repository https://github.com/instadeepai/nucleotide-transformer and HuggingFace space https://huggingface.co/InstaDeepAI. *| 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

7 months

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AgBioData-LIST