- AgBioData-LIST - Main Bioinformatics Lab

REMINDER - Monthly Webinar Next Wed, June 5th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wed, June 5th, at 12 PM CDT for our monthly webinar. *Ethy Cannon *(USDA-ARS) will talk about the *pan-genomic resources at MaizeGDB*. 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:* *Pan-genomic resources at MaizeGDB* Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genome assemblies within a clade, can be more useful than single reference genomes. This is especially true for Zea mays, which has a particularly diverse and complex genome. Presenting full pan-genome data is challenging, especially for a diverse species, but valuable when pan-genomic data can be linked to extensive gene models and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures, as is the case at MaizeGDB. I will present the pan-gene analysis pipeline Pandagma, and MaizeGDB’s pan-gene data centre, which offers a variety of browsing and visualizations, including sequence alignment visualization, gene trees and more, which enables exploration of pan-genes in Zea. *| 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, 5 months

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

by Annarita Marrano

Dear AgBioData members, This is a friendly reminder to participate in our *brief survey* on the impact of AgBioData activities on FAIR data management awareness if you haven't already done so. This survey is a follow-up to 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

2 years, 5 months

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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

2 years, 5 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

2 years, 6 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 ***

2 years, 6 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

2 years, 6 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 ***

2 years, 6 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

2 years, 7 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

2 years, 7 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

2 years, 7 months

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