- AgBioData-LIST - Main Bioinformatics Lab

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 ***

4 days, 7 hours

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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

2 weeks, 3 days

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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 ***

2 weeks, 4 days

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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

3 weeks, 3 days

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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 month

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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 month, 2 weeks

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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 month, 2 weeks

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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 month, 3 weeks

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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 month, 3 weeks

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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 month, 3 weeks

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