- AgBioData-LIST - Main Bioinformatics Lab

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

6 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

6 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

7 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

8 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

8 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

8 months, 4 weeks

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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 next Wednesday, Sept. 4th, 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

9 months

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REMINDER - Monthly Webinar TOMORROW, August 7th, at 12 PM CT

by Annarita Marrano

Hi everybody, This is a friendly reminder of tomorrow's webinar at 12 PM CDT. *Seth Murray <https://soilcrop.tamu.edu/people/murray-seth-c/> *(Texas A&M University, TAMU) will present on temporal field phenomics. I have included below more details about the webinar and the Zoom link to attend the webinar. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Abstracts:* *Capturing Nature AND Nurture with Temporal Field Phenomics to Breed Better Crops* An organism’s phenome results from genotype (nature), environment and management effects (nurture) and their interactions, as well as measurement error. For over 30 years, DNA sequencing and genomics tools have advanced genotyping to where genomes can now be routinely saturated with measurements. In contrast, most focus in high throughput phenotyping and phenomics to date has been on automating previously known “traits” as measurable and interpretable phenotypes; akin to focusing on measuring a single DNA marker rather than measuring a saturated genome. Tools such as unoccupied aerial systems (UAS, aka UAVs, drones) collecting temporal phenomic measurements in the field now allow novel methods in plant breeding and new insights into plant biology. Viewing phenomics as a platform for discovery, similar to genomics, opens new methods for capturing phenomena in nature and nurture. To date, our experience with phenomic prediction from UAS in maize breeding for cumulative, complex phenotypes such as grain yield suggests it’s possible to predict organismal performance in untested environments; in fact possibly better than gold-standard genomic methods. Surprising insights into biology have also been made in through these activities predicting plant disease and resistance, evaluating genotypic resilience to stress, and identifying early season growth periods for crop improvement that have not been able to be selected. Method development and data analytics in phenomics are large investments, but worth making. Successfully measuring the phenome will impact every aspect of science and society, in biological disciplines from germplasm curators, physiologists to breeders, to education, the courtroom and policy. *| 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

9 months, 3 weeks

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REMINDER - Monthly Webinar Next Wed, August 7th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wednesday, August 7th, at 12 PM CDT for our monthly webinar. *Seth Murray <https://soilcrop.tamu.edu/people/murray-seth-c/> *(Texas A&M University, TAMU) will present on temporal field phenomics. I have included below more details about the webinar and the Zoom link to attend the webinar. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Abstracts:* *Capturing Nature AND Nurture with Temporal Field Phenomics to Breed Better Crops* An organism’s phenome results from genotype (nature), environment and management effects (nurture) and their interactions, as well as measurement error. For over 30 years, DNA sequencing and genomics tools have advanced genotyping to where genomes can now be routinely saturated with measurements. In contrast, most focus in high throughput phenotyping and phenomics to date has been on automating previously known “traits” as measurable and interpretable phenotypes; akin to focusing on measuring a single DNA marker rather than measuring a saturated genome. Tools such as unoccupied aerial systems (UAS, aka UAVs, drones) collecting temporal phenomic measurements in the field now allow novel methods in plant breeding and new insights into plant biology. Viewing phenomics as a platform for discovery, similar to genomics, opens new methods for capturing phenomena in nature and nurture. To date, our experience with phenomic prediction from UAS in maize breeding for cumulative, complex phenotypes such as grain yield suggests it’s possible to predict organismal performance in untested environments; in fact possibly better than gold-standard genomic methods. Surprising insights into biology have also been made in through these activities predicting plant disease and resistance, evaluating genotypic resilience to stress, and identifying early season growth periods for crop improvement that have not been able to be selected. Method development and data analytics in phenomics are large investments, but worth making. Successfully measuring the phenome will impact every aspect of science and society, in biological disciplines from germplasm curators, physiologists to breeders, to education, the courtroom and policy. *| 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 ReplyForward

10 months

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REMINDER: Please participate to the AgBioData survey on FAIR data management

by Annarita Marrano

Dear all, Thank you for being part of the AgBioData community. We are almost at the end of a three-year National Science Foundation (NSF) RCN project. We want to estimate the impact of these years' efforts on increasing the awareness and implementation of FAIR practices in the ag research community. *If you haven't already*, we invite you to participate in a *brief survey* *on the impact of AgBioData activities on FAIR data management awareness*. This survey, which follows up on one we ran in 2022, will help us quantify any significant change in the implementation of FAIR practices since the beginning of the project. Click here <https://tinyurl.com/AgBioData24> to participate in this survey. Your participation in this survey is crucial for our mission to enhance FAIR data in agricultural research. It will provide insights to help us define the consortium's directions and secure future funding. We want to emphasize that your participation is entirely voluntary and anonymous. Best, Annarita

10 months, 1 week

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AgBioData-LIST