- AgBioData-LIST - Main Bioinformatics Lab

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, 11 months

1
0
0 0

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, 12 months

1
0
0 0

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

2 years

1
0
0 0

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

2 years

1
0
0 0

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 ***

2 years

1
0
0 0

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

2 years

1
0
0 0

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

2 years

1
0
0 0

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

2 years

1
0
0 0

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

2 years, 1 month

1
0
0 0

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.

2 years, 1 month

1
0
0 0

2026

2025

2024

2023

2022

2021

2020

2019

AgBioData-LIST