AgBioData-LIST August 2024

agbiodata-list@bioinfo.wsu.edu

1 participants
2 discussions

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

3 months, 1 week

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

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AgBioData-LIST August 2024