- AgBioData-LIST - Main Bioinformatics Lab

Please participate to an AgBioData survey on FAIR data management

by Annarita Marrano

Dear AgBioData members, We'd like to invite you to participate *in a brief survey* to measure the impact of AgBioData activities on FAIR data management awareness. This is a follow-up survey from a similar one we ran in 2022 and will help us quantify the impact of our efforts during the three-year National Science Foundation (NSF) RCN project on increasing the awareness and implementation of FAIR practices in the AgBioData community. Your participation in this survey is crucial for our mission to enhance FAIR data in agricultural research and will provide insights that can help us define the consortium's directions and secure future funding. Click here <https://tinyurl.com/AgBioData24> to participate in this survey. Please submit your answers *by May 31*. We would like to emphasize that your participation in this survey is entirely voluntary and anonymous. For general questions or assistance accessing and completing the survey, please feel free to write to me or contact Dr Michael Coe at michael(a)cedarlakeresearch.com. Thanks for your contribution to AgBioData and for being part of our community! Best, Annarita

1 year, 6 months

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Charla Lambert on the SACNAS organization, this Monday (May 6) at 11 AM ET

by Annarita Marrano

Hi everybody, The DEI Recruiting WG invites everyone to join our meeting *this Monday, May 6, at 11 AM*. Dr Charla Lambert, president of the Advancing Chicanos/Hispanics and Native Americans in Science (SACNAS) organization, will talk about SACNAS, its 50-year history diversifying science in the U.S., and how it might benefit your group's outreach, networking, and recruitment activities. Zoom link to participate: https://us06web.zoom.us/j/89060768261?pwd=TC9EOWR3UVdQS3UxNGZWQTEvWDFaZz09. I hope you will join numerous. Best, Annarita

1 year, 7 months

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AG2PI upcoming events

by Scott, Nicole M [AGRON]

Dear AgBioData members, We have one new announcement and one reminder to share: 1. New: The next Agricultural Genome to Phenome Initiative (AG2PI) training workshop, "Combined GWAS and TWAS using SVEN" will be May 17 from 10 AM to 1 PM (CDT; UTC-5). The workshop series will cover: Fundamental of Bayesian hierarchical models in association studies; Demonstration of SVEN from R package bravo using data from a maize panel; and, Hands-on experience in using SVEN under the R statistical software. By the end of the workshop series, you'll be able to: Understand the marginal inclusion probability as an alternative to the p-value; Use SVEN to analyze your dataset; Summarize and visualize the output from SVEN. Register at https://www.ag2pi.org/workshops-and-activities/workshop-2024-05-17/. See flyer attached. 1. Reminder: The next AG2PI virtual Field Day will be "Digital Tools for Agriculture Research - AG2PI "Coconut" Grant Outcomes" and will be on Wednesday, April 24 from 10:30 AM to 12:00 PM (CDT, UTC-5). In this field day, we will first hear from Dr. Trevor Rife regarding how his app "Field Book" can be used as a tool for plant phenotyping. Then, Dr. Jinha Jung, Dr. Minyoung Jung and Benjamin Hancock will introduce their open source online platform for UAS HTP data management and sharing. Both of these presentations are outcomes from AG2PI "coconut" (large seed) grants. Register for this Zoom event at https://www.ag2pi.org/workshops-and-activities/field-day-2024-04-24/, where you will also find additional information. We look forward to seeing you at a future event! ------------------------ Nicole Scott, PhD Program Specialist Agricultural Genome to Phenome Initiative Iowa State University 1111 WOI Rd Ames, IA 50011 office: 1077 Roy J. Carver Co-Lab phone: 515-294-3945 ag2pi.org<https://www.ag2pi.org/> *** If you no longer wish to receive messages from AG2PI, then please visit https://www.ag2pi.org/join-ag2pi/unsubscribe/ to unsubscribe *** Please note, you cannot unsubscribe if you are receiving this message through a third party ***

1 year, 7 months

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2024 AgBioData community workshop (VIRTUAL; 04/29-30, 05/02) - REGISTRATION FORM

by Annarita Marrano

Dear everyone, Hurry up and register for the 2024 AGBioData community workshop! Registration is closing soon (April 15)! *The registration form is available here <https://forms.gle/FX9YgroWMQNnfYFXA>!* This year's community workshop will be wholly *VIRTUAL* and feature WG presentations and breakout room sessions from 9-11 AM CDT daily. A draft of the workshop's agenda is available on our website ( https://www.agbiodata.org/2024-agbcomworks). I hope you will be able to join us! Please let me know if you have any questions. Annarita

1 year, 8 months

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AG2PI Field Day: Digital Tools for Agriculture Research - AG2PI "Coconut" Grant Outcomes

by Scott, Nicole M [AGRON]

Dear AgBioData community members, The next Agricultural Genome to Phenome Initiative (AG2PI) Field Day will be "Digital Tools for Agriculture Research - AG2PI "Coconut" Grant Outcomes" and will be on Wednesday, April 24 from 10:30 AM to 12:00 PM (CDT, UTC-5). In this field day, we will first hear from Dr. Trevor Rife regarding how his app "Field Book" can be used as a tool for plant phenotyping. Then, Dr. Jinha Jung, Dr. Minyoung Jung and Benjamin Hancock will introduce their open source online platform for UAS HTP data management and sharing. Both of these presentations are outcomes from AG2PI "coconut" (large seed) grants. We invite you to register for this Zoom event at https://www.ag2pi.org/workshops-and-activities/field-day-2024-04-24/, where you will also find additional information. Upon registration, you will receive a confirmation email with information about joining the meeting. If you are unable to attend the live session, then you will be able to find a recording at ag2pi.org/<https://www.ag2pi.org/>, at a later date. You do not need to register to view the recording; it is readily available on the AG2PI website soon after the close of the event (generally within 24 hours). Please share the attached, digitally accessible flyer with your colleagues or students and encourage them to attend. Kind regards, Nicole ------------------------ Nicole Scott, PhD Program Specialist Agricultural Genome to Phenome Initiative Iowa State University 1111 WOI Rd Ames, IA 50011 office: 1077 Roy J. Carver Co-Lab phone: 515-294-3945 ag2pi.org<https://www.ag2pi.org/> *** If you no longer wish to receive messages from AG2PI, then please visit https://www.ag2pi.org/join-ag2pi/unsubscribe/ to unsubscribe *** Please note, you cannot unsubscribe if you are receiving this message through a third party ***

1 year, 8 months

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REMINDER - Monthly Webinar TOMORROW, April 3rd, at 12 PM CT

by Annarita Marrano

Hi everybody, This is a friendly reminder of our monthly webinar tomorrow (April 3rd) at 12 PM CDT. Zachary Miller <https://www.maizegenetics.net/zackmiller> will talk about Practical Haplotype Graph (PHG), a streamlined and simple pangenome system. 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:* *The Practical Haplotype Graph Version 2: A Streamlined and Simple Pangenome System* The Practical Haplotype Graph (PHG) is a powerful tool for representing diverse plant pangenomes and imputing new sample genotypes for breeding programs and other purposes. Low-coverage sequencing data from various technologies (DaRT, GBS, etc.) is sufficient to identify paths through the graph, which can be stored efficiently within the PHG database or used to call variants and create custom genomes for alignment. PHGv2 refines and streamlines the original PHGv1 platform. *| 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

1 year, 8 months

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REMINDER - Monthly Webinar Next Wed, April 3rd, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wed, April 3rd, at 12 PM CDT for our monthly webinar. Zachary Miller <https://www.maizegenetics.net/zackmiller> from Cornell University will talk about Practical Haplotype Graph (PHG), a streamlined and simple pangenome system. 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:* *The Practical Haplotype Graph Version 2: A Streamlined and Simple Pangenome System* The Practical Haplotype Graph (PHG) is a powerful tool for representing diverse plant pangenomes and imputing new sample genotypes for breeding programs and other purposes. Low-coverage sequencing data from various technologies (DaRT, GBS, etc.) is sufficient to identify paths through the graph, which can be stored efficiently within the PHG database or used to call variants and create custom genomes for alignment. PHGv2 refines and streamlines the original PHGv1 platform. *| 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

1 year, 8 months

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REGISTRATION Open for the 2024 AgBioData community workshop (VIRTUAL; 04/29-30, 05/02)

by Annarita Marrano

Dear everyone, This is a friendly reminder to register for the *2024 AgBioData community workshop *(April 29-30; May 2)! This year's community workshop will be completely *VIRTUAL* and feature WG presentations, breakout room sessions, and more from 9-11 AM CDT daily. We are working on finalizing the workshop's agenda and will send it soon with other useful information. *Please register for the community workshop by completing this form (https://forms.gle/MjLhMcw75YS3dWmcA <https://forms.gle/MjLhMcw75YS3dWmcA>) **by April 15*. I hope you will be able to join us! Please let me know if you have any questions. Have a lovely week. Annarita

1 year, 9 months

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AG2PI Field Day: Phenomic Prediction & Bioinformatic Workflows - AG2PI "Coconut" Grant Outcomes

by Scott, Nicole M [AGRON]

Dear AgBioData community members, The next Agricultural Genome to Phenome Initiative (AG2PI) Field Day will be "Phenomic Prediction & Bioinformatic Workflows - AG2PI "Coconut" Grant Outcomes" and will be on Wednesday, March 20 from 10:30 AM to 12:00 PM (CDT, UTC-5). In this field day, we will first hear from Dr. Daniel Runcie regarding how phenomic prediction can be used as a tool for plant breeding. Then, Dr. Fiona McCarthy will review new bioinformatic workflows her team has developed to support genomic analyses. Both of these presentations are outcomes from AG2PI "coconut" (large seed) grants. We invite you to register for this Zoom event at https://www.ag2pi.org/workshops-and-activities/field-day-2024-03-20/, where you will also find additional information. Upon registration, you will receive a confirmation email with information about joining the meeting. If you are unable to attend the live session, then you will be able to find a recording at ag2pi.org/<https://www.ag2pi.org/>, at a later date. You do not need to register to view the recording; it is readily available on the AG2PI website soon after the close of the event (generally within 24 hours). Please share the attached, digitally accessible flyer with your colleagues or students and encourage them to attend. Kind regards, Nicole ------------------------ Nicole Scott, PhD Program Specialist Agricultural Genome to Phenome Initiative Iowa State University 1111 WOI Rd Ames, IA 50011 office: 1077 Roy J. Carver Co-Lab phone: 515-294-3945 ag2pi.org<https://www.ag2pi.org/> *** If you no longer wish to receive messages from AG2PI, then please visit https://www.ag2pi.org/join-ag2pi/unsubscribe/ to unsubscribe *** Please note, you cannot unsubscribe if you are receiving this message through a third party ***

1 year, 9 months

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REMINDER - Monthly Webinar TOMORROW at 12 PM CT

by Annarita Marrano

Hi everybody, Join us tomorrow, March. 6th, at 12 PM CDT, for our monthly webinar. Cyril Pommier <https://orcid.org/0000-0002-9040-8733> will talk about FAIR plant phenomics data management tools and guidelines from the ELIXIR and Emphasis European infrastructures. 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:* *FAIR Plant Phenomics Data Management Tools and Guidelines from ELIXIR and Emphasis European Infrastructures* Plant phenomics data has been greatly facilitated over the past ten years at several levels: data standards to organize and describe data, databases for the management of the experiments, data repositories to ensure long-term accessibility supplemented by data portals to maximise findability and finally, guidelines to ease their usage. We will review the recent advances from joint initiatives involving two European infrastructures: ELIXIR (Life science data) and EMPHASIS (Plant phenomics). First, we will update the current status of MIAPPE (www.miappe.org), a data standard interoperable with the Breeding API that enables not only phenotyping experiment formalisation but also their linking with genotyping. We will also give an overview of its usage in generic data repositories such as Dataverse or Zenodo and their relation with experimental databases such as PHIS. Finding the right documentation to use those tools and standards is not always straightforward. The RDMKit ( https://rdmkit.elixir-europe.org/) is a guidelines portal that has been built to help researchers find the information subset they need. Through a dedicated section, such as the plant domain page ( https://rdmkit.elixir-europe.org/), it shows the complementarity between standards and tools and provides the guidance needed for data management. Finally, we will also update the status of FAIDARE ( https://urgi.versailles.inrae.fr/faidare/), a global data portal that indexes 30 databases using either BrAPI or a generic minimal format. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+March+W…> *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

1 year, 9 months

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2024 AgBioData community workshop (VIRTUAL; 04/29-30, 05/02) - REGISTRATION FORM

by Annarita Marrano

Dear everyone, We are happy to announce that the registration for the *2024 AgBioData community workshop *(April 29-30; May 2) is now *OPEN*! This year's community workshop will be completely *VIRTUAL* and feature WG presentations and breakout room sessions from 9-11 AM CDT daily. We will soon share more details on the workshop agenda and other helpful information. *Please register for the community workshop by completing this form (https://forms.gle/MjLhMcw75YS3dWmcA <https://forms.gle/MjLhMcw75YS3dWmcA>) **by April 15*. I hope you will be able to join us! Please let me know if you have any questions. Have a lovely week. Annarita

1 year, 9 months

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Job alert: "Genomics Data Engineer (Joint Genome Institute)"

by Annarita Marrano

Hi everybody, Please see below for details about a position as "Genomic Data Engineer" in the Plant Comparative Analysis Group at the Joint Genome Institute: *http://phxc1b.rfer.us/LBLbNj9kY <http://phxc1b.rfer.us/LBLbNj9kY>* Best, Annarita

1 year, 9 months

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REMINDER - Monthly Webinar Next Wed, March. 6th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wed, March. 6th, at 12 PM CDT, for our monthly webinar. Cyril Pommier <https://orcid.org/0000-0002-9040-8733> will talk about FAIR plant phenomics data management tools and guidelines from the ELIXIR and Emphasis European infrastructures. 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:* *FAIR Plant Phenomics Data Management Tools and Guidelines from ELIXIR and Emphasis European Infrastructures* Plant phenomics data has been greatly facilitated over the past ten years at several levels: data standards to organize and describe data, databases for the management of the experiments, data repositories to ensure long-term accessibility supplemented by data portals to maximise findability and finally, guidelines to ease their usage. We will review the recent advances from joint initiatives involving two European infrastructures: ELIXIR (Life science data) and EMPHASIS (Plant phenomics). First, we will update the current status of MIAPPE (www.miappe.org), a data standard interoperable with the Breeding API that enables not only phenotyping experiment formalisation but also their linking with genotyping. We will also give an overview of its usage in generic data repositories such as Dataverse or Zenodo and their relation with experimental databases such as PHIS. Finding the right documentation to use those tools and standards is not always straightforward. The RDMKit ( https://rdmkit.elixir-europe.org/) is a guidelines portal that has been built to help researchers find the information subset they need. Through a dedicated section, such as the plant domain page ( https://rdmkit.elixir-europe.org/), it shows the complementarity between standards and tools and provides the guidance needed for data management. Finally, we will also update the status of FAIDARE ( https://urgi.versailles.inrae.fr/faidare/), a global data portal that indexes 30 databases using either BrAPI or a generic minimal format. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+March+W…> *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

1 year, 9 months

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Genome assembly graph resolution workshop at the AGBT-Ag conference

by Annarita Marrano

Forwarding this announcement from Timothy P.L. Smith (USDA-ARS, Meat Animal Research Center): ------------------------------------------------------------------------- We are pleased to announce that Drs. Arang Rhie and Sergey Koren, from the Center for Genomics and Data Science Research at the National Institutes of Health, have agreed to conduct an in-person hands- on workshop on inspecting and resolving genome assembly graphs in conjunction with the Advances in Genome Biology and Technology Agriculture conference (AGBT-Ag) in Phoenix on Sunday, April 14, 7-9 pm (following the RCN workshop). The workshop will be organized by Drs. Brenda Murdoch and Ben Rosen, and requires registration for the conference at www.agbt.org. Resolving assembly graphs is an important component of generating full haplotype separated diploid or polyploid assemblies in animals or plants, and particularly important in the context of “complete” telomere-to-telomere (T2T) assembly. The Ruminant T2T project aims to generate T2T assemblies of cetartiodactyla species and other species that can generate the appropriate data types but the graph resolution step is a manual process and additional trained personnel would be beneficial to speed progress and accelerate other T2T efforts. The training will cover evaluating assembly graphs in bandage, resolving tangles that are amenable to manual resolution, and generating assemblies with resolved sequence. Some easy and difficult graphs will be examined during the two hour workshop. We are very grateful that Arang and Sergey are willing to develop this tutorial and provide their expertise. Please email Kelsey McClure at kelsey.mcclure(a)usda.gov if you want to attend the workshop by March 5, so that we can make sure we can accommodate the number of interested participants. If you hope to attend but do not know if you will be able to by that deadline, please go ahead and email with a statement to that effect.

1 year, 10 months

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AG2PI field day, new RFP, travel awards

by Scott, Nicole M [AGRON]

Dear AgBioData members, We, Agricultural Genome to Phenome Initiative (AG2PI), have three announcements to share: 1. AG2PI virtual field days are back! The next field day will be held February 21, 10:30 AM to 12:00 PM (CST, UTC-6) and will highlight the "coconut" (large seed) grant projects led by Dr. Pankaj Jaiswal on plant stress ontology and by Dr. Seth Murray on building a more connected unmanned aerial systems (UAS) community. For more information and to register, visit https://www.ag2pi.org/workshops-and-activities/field-day-2024-02-21/. 1. Reminder: AG2PI is offering student conference travel grants up to $1500 to any* undergraduate and graduate students attending an institution in the US. Details and instructions to apply can be found on the AG2PI website (https://www.ag2pi.org/seed-grants/student-conference-travel-awards-2023-11-…). These will be awarded on a rolling basis until all funds are committed, so apply soon! Application portal will close by June 1, 2024 and all travel must be completed by August 1, 2024. (*students must be engaged in AG2PI-related research, broadly, to apply) 1. A Request for Proposals has been released by USDA NIFA for FY2024 regarding the AG2PI program. There will be a NIFA Technical Assistance Webinar for the RFP on March 21, 2024. Registration details can be found here: https://www.nifa.usda.gov/events/technical-assistance-webinar-agricultural-…. Please share this message with anyone you think might be interested in either of these opportunities. Have a wonderful week, Nicole ------------------------ Nicole Scott, PhD Program Specialist Agricultural Genome to Phenome Initiative Iowa State University 1111 WOI Rd Ames, IA 50011 office: 1077 Roy J. Carver Co-Lab phone: 515-294-3945 ag2pi.org<https://www.ag2pi.org/> *** If you no longer wish to receive messages from AG2PI, then please visit https://www.ag2pi.org/join-ag2pi/unsubscribe/ to unsubscribe *** Please note, you cannot unsubscribe if you are receiving this message through a third party ***

1 year, 10 months

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REMINDER - Monthly Webinar, TODAY, at 12 PM CT - Zoom link

by Annarita Marrano

Hi everybody, Join us today* at 12 PM CT *for our monthly webinar. We will have Alex Ignatchenko and Paul Thomas talking about TreeGrafter, a method of predicting Gene Ontology annotations, and other tools implemented in InterProScan. *Zoom link: https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 <https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09>.* Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Abstracts:* *Alex Ignatchenko (EMBL-EBI):* Gene Ontology (GO) Annotation (GOA) project at EMBL-EBI aims to provide high-quality GO annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. Currently, the GOA database hosts 5 million manually curated GO annotations from over 70 research groups. This set is used as a foundation for 15 automatic GO annotation pipelines. The output data re-generated ever 2 month and commonly referred to as Inferred from Electronic Annotation (IEA). The IEA pipelines use range of statistical, rule-based and machine learning algorithms to enrich existing GO annotation coverage. The generated IEA set of over 1.1 billion GO annotations is subject to over 130 checks, constraints and filters to ensure the quality of predicted GO annotations. The GOA data is publicly available from GOA ftp and the GO annotation browser QuickGO. The GOA team is constantly looking for ways to improve the quality of GO annotations and gene product coverage. The TreeGrafter is a method of prediction of GO annotations based on PANTHER family/subfamily and the InterPro signatures. The project is a collaboration between PANTHER and the InterPro team at EMBL-EBI. The algorithm was published in 2019, and it was incorporated into the InterPro in the second half of 2023. The TreeGrafter mappings were processed and added to the GOA database for testing shortly after. This implementation resulted in about 301 million GO annotations after the GOA pipeline checks and filters. More importantly, the final set has over 200 million GO annotations, which is not predicted by any other IEA methods. The GOA team plans to intergrade TreeGrafter GO annotation pipeline into the GOA database and release it to public in a first half of 2024. *Paul D. Thomas (University of Southern California and Gene Ontology Consortium)Accurate annotation of protein sequences at large scale, using evolutionary modeling* Inferring (aka “annotating” or “predicting”) the functions of the vast numbers of known protein sequences has been a longstanding challenge in genomics. Over the last decade, a comprehensive system has been developed for addressing this challenge based on constructing and applying models of function evolution in protein families. The main components of the system– including PANTHER phylogenetic trees, Gene Ontology phylogenetic annotations and TreeGrafter software (now implemented in InterProScan)– work together in an integrated software and data suite that is now beginning to be broadly used to annotate the functions of protein-coding genes. I will describe each of these components, as well as how the tool can be easily used to annotate any set of protein-coding genes and how users can give feedback to help improve the annotations. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…>

1 year, 10 months

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

by Annarita Marrano

Hi everybody, This is a friendly reminder of our monthly webinar *tomorrow, Feb. 7th, at 12 PM CT*. Alex Ignatchenko and Paul Thomas will talk about TreeGrafter, a method of predicting Gene Ontology annotations, and other tools implemented in InterProScan. 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:* *Alex Ignatchenko (EMBL-EBI):* Gene Ontology (GO) Annotation (GOA) project at EMBL-EBI aims to provide high-quality GO annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. Currently, the GOA database hosts 5 million manually curated GO annotations from over 70 research groups. This set is used as a foundation for 15 automatic GO annotation pipelines. The output data re-generated ever 2 month and commonly referred to as Inferred from Electronic Annotation (IEA). The IEA pipelines use range of statistical, rule-based and machine learning algorithms to enrich existing GO annotation coverage. The generated IEA set of over 1.1 billion GO annotations is subject to over 130 checks, constraints and filters to ensure the quality of predicted GO annotations. The GOA data is publicly available from GOA ftp and the GO annotation browser QuickGO. The GOA team is constantly looking for ways to improve the quality of GO annotations and gene product coverage. The TreeGrafter is a method of prediction of GO annotations based on PANTHER family/subfamily and the InterPro signatures. The project is a collaboration between PANTHER and the InterPro team at EMBL-EBI. The algorithm was published in 2019, and it was incorporated into the InterPro in the second half of 2023. The TreeGrafter mappings were processed and added to the GOA database for testing shortly after. This implementation resulted in about 301 million GO annotations after the GOA pipeline checks and filters. More importantly, the final set has over 200 million GO annotations, which is not predicted by any other IEA methods. The GOA team plans to intergrade TreeGrafter GO annotation pipeline into the GOA database and release it to public in a first half of 2024. *Paul D. Thomas (University of Southern California and Gene Ontology Consortium)Accurate annotation of protein sequences at large scale, using evolutionary modeling* Inferring (aka “annotating” or “predicting”) the functions of the vast numbers of known protein sequences has been a longstanding challenge in genomics. Over the last decade, a comprehensive system has been developed for addressing this challenge based on constructing and applying models of function evolution in protein families. The main components of the system– including PANTHER phylogenetic trees, Gene Ontology phylogenetic annotations and TreeGrafter software (now implemented in InterProScan)– work together in an integrated software and data suite that is now beginning to be broadly used to annotate the functions of protein-coding genes. I will describe each of these components, as well as how the tool can be easily used to annotate any set of protein-coding genes and how users can give feedback to help improve the annotations. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Topic: AgBioData - SC bi-weekly meeting Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/83731466263?pwd=Q2ZZbHB2UEcrRHAvNzZxV3BRRlBuUT09 Meeting ID: 837 3146 6263 Passcode: 827841 --- One tap mobile +15642172000,,83731466263#,,,,*827841# US +16469313860,,83731466263#,,,,*827841# US --- Dial by your location • +1 564 217 2000 US • +1 646 931 3860 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US • +1 929 205 6099 US (New York) • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US Meeting ID: 837 3146 6263 Passcode: 827841 Find your local number: https://us06web.zoom.us/u/kekUSg0LV1

1 year, 10 months

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

by Annarita Marrano

Hi everybody, After the holiday break and PAG 31, we are ready to restart our monthly webinar series! Join us next Wed, Feb. 7th, at 12 PM CT for our monthly webinar. Alex Ignatchenko and Paul Thomas will talk about TreeGrafter, a method of predicting Gene Ontology annotations, and other tools implemented in InterProScan. 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:* *Alex Ignatchenko (EMBL-EBI):* Gene Ontology (GO) Annotation (GOA) project at EMBL-EBI aims to provide high-quality GO annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. Currently, the GOA database hosts 5 million manually curated GO annotations from over 70 research groups. This set is used as a foundation for 15 automatic GO annotation pipelines. The output data re-generated ever 2 month and commonly referred to as Inferred from Electronic Annotation (IEA). The IEA pipelines use range of statistical, rule-based and machine learning algorithms to enrich existing GO annotation coverage. The generated IEA set of over 1.1 billion GO annotations is subject to over 130 checks, constraints and filters to ensure the quality of predicted GO annotations. The GOA data is publicly available from GOA ftp and the GO annotation browser QuickGO. The GOA team is constantly looking for ways to improve the quality of GO annotations and gene product coverage. The TreeGrafter is a method of prediction of GO annotations based on PANTHER family/subfamily and the InterPro signatures. The project is a collaboration between PANTHER and the InterPro team at EMBL-EBI. The algorithm was published in 2019, and it was incorporated into the InterPro in the second half of 2023. The TreeGrafter mappings were processed and added to the GOA database for testing shortly after. This implementation resulted in about 301 million GO annotations after the GOA pipeline checks and filters. More importantly, the final set has over 200 million GO annotations, which is not predicted by any other IEA methods. The GOA team plans to intergrade TreeGrafter GO annotation pipeline into the GOA database and release it to public in a first half of 2024. *Paul D. Thomas (University of Southern California and Gene Ontology Consortium)Accurate annotation of protein sequences at large scale, using evolutionary modeling* Inferring (aka “annotating” or “predicting”) the functions of the vast numbers of known protein sequences has been a longstanding challenge in genomics. Over the last decade, a comprehensive system has been developed for addressing this challenge based on constructing and applying models of function evolution in protein families. The main components of the system– including PANTHER phylogenetic trees, Gene Ontology phylogenetic annotations and TreeGrafter software (now implemented in InterProScan)– work together in an integrated software and data suite that is now beginning to be broadly used to annotate the functions of protein-coding genes. I will describe each of these components, as well as how the tool can be easily used to annotate any set of protein-coding genes and how users can give feedback to help improve the annotations. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +15642172000,,82038356125#,,,,*160683# US +16469313860,,82038356125#,,,,*160683# US --- Dial by your location • +1 564 217 2000 US • +1 646 931 3860 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US • +1 929 205 6099 US (New York) • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

1 year, 10 months

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Where can you find AgBioData at PAG 31!!!

by Annarita Marrano

Hello everyone, AgBioData will be at PAG 31 in San Diego on Jan. 12-17! Here are some information on when and where you can find us at PAG: - Join us for *our workshop *"*The AgBioData Consortium: Challenges and Recommendations for FAIR Genetic, Genomic and Breeding Data*" on *Friday, Jan. 12, at 4 PM* in room Town and Country C. Some of our working groups and two talented early-career AgBioData members will present their works. More details are available here <https://www.agbiodata.org/agb-pag31>. - *Join us at booth #422* and meet our member database resources. We will be there during exhibit hours to discuss our mission and answer your questions. - AgBioData will have two posters on Monday, Jan. 15, from 3-4.40. - *PO0727* - *PO0643 * - Our steering committee member, *Leonore Reiser*, will present about AgBioData and our NSF RCN grant during the workshop "*Beyond the National Plant Genome Initiative: New Frontiers and Grand Challenges in Plant Genomics*." Her talk <https://plan.core-apps.com/pag_2024/event/2562157f06c9714c1a4dcc7037839c83> is scheduled for *Sunday, Jan. 14, at 2:10 PM.* In addition, Ag2PI organized the workshop "*Supporting Agricultural Genomics Through Bioinformatics*" on Tuesday, Jan. 16, at 6.20 PM in room Palm 8. During the workshop, there will be a roundtable discussion about how bioinformaticians can support the agricultural genomics community in analyzing genomics data. This discussion will be led by plant and animal researchers with a mixture of bioinformatics expertise and topics include: - current barriers to doing reproducible genomic analyses - how bioinformatics experts can more effectively support agricultural researchers - how to ensure students have the bioinformatics skills they will need - commonalities for genomic analyses across plant, animal and microbial data sets Best regards, Annarita

1 year, 11 months

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REMINDER - Monthly Webinar TOMORROW, Dec. 6th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us TOMORROW, Dec. 6th, at 12 PM Central Time for our monthly webinar. This webinar will focus on single-cell data and metadata management in livestock and plants Benjamin Cole <https://jgi.doe.gov/our-science/scientists-jgi/benjamin-cole-genomics-of-pl…> , Christopher Tuggle <https://faculty.sites.iastate.edu/cktuggle/>, and Muskan Kapoorand <https://github.com/kapoormuskan>. 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:* *Benjamin Cole (Joint Genome Institute) on "Data management considerations for plant single-cell genomics."* While plants have arrived on the single-cell scene relatively late, the number and complexity of plant single-cell datasets have exploded over the past four years. With that massive increase in data has come a pressing need to ensure accurate documentation of the experimental provenance of plant single-cell datasets, not only for reproducibility but also for reusability in meta-analyses. During this presentation, I will discuss the current state of plant single-cell research as well as the most common practices for data storage. I will also argue for the need for better standards in the field, and what that could potentially enable. *Christopher Tuggle (Iowa State University) & Muskan Kapoor (Iowa State University) on "Single-Cell genomics data incorporation into agricultural G2P research by building a FAIR data ecosystem."* We will describe a pilot-scale project to determine if our current metadata standards for livestock and crops can be used to ingest scRNAseq datasets in a manner consistent with HCA DCP standards and if established resources (e.g., Terra) can be used to analyze the ingested data. Currently, the most comprehensive data ingestion portal for high throughput sequencing datasets from plants, fungi, protists, and animals/humans is Annotare (located at EMBL-European Bioinformatics Institute). For agricultural animal datasets, another EMBL-EBI portal, the FAANG portal, has been developed. scRNAseq data/metadata can be submitted to FAANG using a semi-automated process. We have extended this tool for scRNAseq data so that files can be validated using the HCA DCP metadata and data validation service. These files are incorporated using EMBL-EBI’s HCA DCP ingestion service and transferred to Terra for further analysis. We will also describe a Shiny-based web application, implemented in R and called Shiny-PIGGI, for the single cell-level transcriptomic study of pig immune tissues and peripheral blood mononuclear cells, which will be an important resource for improved annotation of porcine immune genes and cell types ( https://shinypiggi.ansci.iastate.edu). We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem to facilitate single cell-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) --- Dial by your location • +1 929 205 6099 US (New York) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

2 years

1
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Board on Agriculture and Natural Resources Winter Meeting - Tomorrow, Dec. 5

by Annarita Marrano

Hi everybody, The Board on Agriculture and Natural Resources is holding a seminar on Access to Data *tomorrow, Dec. 5, at 11 AM ET.* The meeting will explore a range of topics of interest to the food, agriculture, and natural resources communities. The open sessions of the meeting will include a presentation on research priorities of the USDA Economic Research Service, a panel on disparities in access to data and journal publications, a briefing on a new National Academies report on Accelerating Decarbonization, and a presentation from Colorado State University researchers on a National Climate Change Roadmap: A Research Framework for U.S. Agriculture, Forestry, and Working Lands. You can find more information here <https://www.nationalacademies.org/event/41526_12-2023_board-on-agriculture-…> . Best, Annarita

2 years

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REMINDER - Monthly Webinar Next Wed, Nov 1st, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wed, Dec. 6th, at 12 PM CT for our monthly webinar. This webinar will focus on single-cell data and metadata management in livestock and plants Benjamin Cole <https://jgi.doe.gov/our-science/scientists-jgi/benjamin-cole-genomics-of-pl…> , Christopher Tuggle <https://faculty.sites.iastate.edu/cktuggle/>, and Muskan Kapoorand <https://github.com/kapoormuskan>. 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:* *Benjamin Cole (Joint Genome Institute) on "Data management considerations for plant single-cell genomics."* While plants have arrived on the single-cell scene relatively late, the number and complexity of plant single-cell datasets have exploded over the past four years. With that massive increase in data has come a pressing need to ensure accurate documentation of the experimental provenance of plant single-cell datasets, not only for reproducibility but also for reusability in meta-analyses. During this presentation, I will discuss the current state of plant single-cell research as well as the most common practices for data storage. I will also argue for the need for better standards in the field, and what that could potentially enable. *Christopher Tuggle (Iowa State University) & Muskan Kapoor (Iowa State University) on "Single-Cell genomics data incorporation into agricultural G2P research by building a FAIR data ecosystem."* We will describe a pilot-scale project to determine if our current metadata standards for livestock and crops can be used to ingest scRNAseq datasets in a manner consistent with HCA DCP standards and if established resources (e.g., Terra) can be used to analyze the ingested data. Currently, the most comprehensive data ingestion portal for high throughput sequencing datasets from plants, fungi, protists, and animals/humans is Annotare (located at EMBL-European Bioinformatics Institute). For agricultural animal datasets, another EMBL-EBI portal, the FAANG portal, has been developed. scRNAseq data/metadata can be submitted to FAANG using a semi-automated process. We have extended this tool for scRNAseq data so that files can be validated using the HCA DCP metadata and data validation service. These files are incorporated using EMBL-EBI’s HCA DCP ingestion service and transferred to Terra for further analysis. We will also describe a Shiny-based web application, implemented in R and called Shiny-PIGGI, for the single cell-level transcriptomic study of pig immune tissues and peripheral blood mononuclear cells, which will be an important resource for improved annotation of porcine immune genes and cell types ( https://shinypiggi.ansci.iastate.edu). We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem to facilitate single cell-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) --- Dial by your location • +1 929 205 6099 US (New York) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

2 years

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Sign-Up for New AgBioData Working Groups OPEN!!!

by Annarita Marrano

Hello AgBioData community, We are happy to announce that the sign-up for AgBioData working groups is now OPEN! *Please complete this form <https://forms.gle/MeZZrCeSvUywxkQo6> by November 22 at 12 p.m. ET to join one or more of our working groups.* We will have two new working groups starting from January 2023, which are the "*Phenotypic Data Standardization and Management*" and the "*scRNAseq BIOCURATION*" working groups. Two current working groups (i.e., the *DEI Recruiting* and *FAIR Scientific Literature WGs*) are also recruiting new members to join their incredible efforts. You can find more details about them in the form. *We anticipate the commitment will generally be between 2-6 hours per month*, including meeting attendance and offline work (e.g., literature, writing, etc.). This is your opportunity to shape the future of our research community by contributing to developing best practices of data archiving and management that can benefit you and all the other stakeholders. Participating in the AgBioData working groups will also offer you opportunities for - professional networking - leadership skill development - authorship in impactful manuscripts Please share the registration link with anybody that you think can be interested. Thanks, Annarita

2 years, 1 month

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Nomination for a new AgBioData steering committee member due to Nov. 3rd

by Annarita Marrano

Hi everybody, The AgBioData steering committee (SC) is calling for nominations for new SC members! The SC is a vibrant, collaborative, and inclusive environment that offers opportunities to expand your leadership skills, network with agricultural research community stakeholders, and help achieve a FAIR agricultural data ecosystem. *We are looking for candidates to serve as members of the AgBioData SC willing to commit a proportion of time to AgBioData activities (approximately 2 hours/week) for a term of 3 years. * *Nominate yourself or somebody you think might fit the position by this Friday, November 3rd at https://forms.gle/jVN6GZvbhS5QnJkB7 <https://forms.gle/jVN6GZvbhS5QnJkB7>.* Best, Annarita

2 years, 1 month

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REMINDER - Monthly Webinar TOMORROW, Nov. 1st, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us *TOMORROW, Nov. 1st, at 12 PM CT* for our monthly webinar. We will host Ben Rosen <https://www.ars.usda.gov/northeast-area/beltsville-md-barc/beltsville-agric…>, who will talk about telomere-to-telomere genome assemblies of ruminant species and how they will help answer important evolutionary questions. 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 :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Presenters: * Ben Rosen, USDA-ARS *Abstract:* *The Ruminant T2T Consortium* The first draft of the human genome assembly was released over twenty years ago. However, a gapless telomere-to-telomere (T2T) “complete” assembly remained elusive until last year. The highly repetitive nature of pericentromeric, subtelomeric, and duplicated gene families, such as rRNA arrays, made them impossible to assemble. It was only with advances in long-read sequencing technologies and new bioinformatic tools that these structures were resolved. Recently, we proposed the application of these new resources, tools, and knowledge in support of a “Ruminant T2T Consortium.” Our goal is to generate complete genomes for the ruminant evolutionary lineage. The ruminant Suborder comprises six Families and 66 living genera. These species are found in geographically dispersed areas and have adapted to a wide variety of environments. They have also been subjected to both natural and artificial selection. Our hypothesis is that T2T assemblies of ruminant species with relatedness varying from those capable of interbreeding to higher evolutionary distances (up to the estimated 25 million years ago last common ancestor) will inform our understanding of the underpinnings of ruminant evolution. It will also shed light on the genomic consequences of domestication and enhance our knowledge of the functional roles of heterochromatin and other repeat regions of the genome. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) --- Dial by your location • +1 929 205 6099 US (New York) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

2 years, 1 month

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