- AgBioData-LIST - Main Bioinformatics Lab

"Inequalities in plant science literature", Rose Marks at the DEI Recruiting WG open meeting series

by Annarita Marrano

Hi everybody, The AgBioData DEI Recruiting working group (WG) will feature a series of open meetings on subjects and resources related to disparity and inclusion in STEM science. The first event of this series will be *next Monday (July 24) at 3 PM ET* with Dr. Rose Marks from Michigan State University. Rose will present her recent publication in PNAS <https://doi.org/10.1073/pnas.2217564120> about inequalities in plant science literature. Below you can find more information about her talk and the Zoom link. I hope you will join us! Best, Annarita *Speaker: *Rose Marks, Ph.D., Michigan State University *Global disparities in plant science: a legacy of colonialism, patriarchy, and exclusion* The field of plant science has grown dramatically in the past two decades, but global disparities and systemic inequalities persist. We analyzed ~300,000 papers published over the past two decades to quantify global, gender, and taxonomic disparities in plant science. Our analyses reveal striking geographical biases that are correlated with national affluence. Gender imbalances were also evident, with far more papers led by authors with masculine names than those by authors with feminine names. Lastly, we identified substantial taxonomic sampling gaps. The vast majority of surveyed studies focused on major crop and model species, and the remaining biodiversity accounted for only a fraction of publications. Taken together, our analyses reveal a problematic system of publication, with persistent imbalances that poorly capture the global wealth of scientific knowledge and biological diversity. We conclude by highlighting disparities that can be addressed immediately and offer suggestions for long-term solutions to improve equity in the plant sciences. Zoom link: https://us06web.zoom.us/j/89060768261?pwd=TC9EOWR3UVdQS3UxNGZWQTEvWDFaZz09 <https://us06web.zoom.us/j/89060768261?pwd=TC9EOWR3UVdQS3UxNGZWQTEvWDFaZz09>

3 years

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REMINDER - tomorrow's AgBioData webinar at 12 PM CT!!

by Annarita Marrano

Hi everybody, This is a friendly reminder of our monthly webinar tomorrow, *July 12th*, at *12 PM CET*. We will have *Sarah Lippincott *from *DRYAD* talking about how to integrate generalist and specialist repositories to promote agricultural data sharing and reuse. 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: Sarah Lippincott, Dryad <https://datadryad.org/stash> Abstract: *Companion planting: How generalist and specialist repositories can work together to promote agricultural data sharing and reuse.* This conversation explores strategies for enhancing open sharing and reuse of agricultural data through collaboration between disciplinary and generalist repositories, specifically Dryad, an open data publishing platform and community. Generalist and specialist repositories bring distinct strengths to data sharing and reuse. Generalist repositories offer a home for a wide range of data types and support serendipitous discovery, while discipline-specific repositories offer granular metadata, specialized tools, and deep understanding of community needs. Agricultural data creators, and future data re-users, can benefit from collaboration between these different solutions, including building connections with complementary datasets stored in multiple repositories; consistency in metadata standards; and federated discovery systems. In this conversation, Dryad’s Head of Community Engagement, Sarah Lippincott, will describe Dryad’s stewardship of agricultural data and engage attendees in an exploration of how Dryad’s can work with the agricultural research community to improve data sharing, discovery, and reuse. *| 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

3 years

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AG2PI upcoming virtual events: Training Workshop + Field Day + other opportunities

by Scott, Nicole M [AGRON]

Hello AgBioData community members, Friendly reminder that AG2PI will be hosting two virtual events next week: 1. Reminder: the next AG2PI virtual Training Workshop, "CartograPlant Workshop: Integrating, Visualizing and Analyzing Genotype, Phenotype, and Environmental Data from Geo-Referenced Plants" is July 12 from 10 AM to 12:30 PM m CDT (UTC-5). In this workshop, Dr. This event is an outcome of an AG2PI seed grant award to Dr. Cobo. For additional details and to register for this virtual event go to https://www.ag2pi.org/workshops-and-activities/workshop-2023-07-12/. 2. The next AG2PI virtual Field Day, "Public-Private Partnerships in Education and Commercialization" will be July 19, 10:30 AM to 12 PM (CDT, UTC-5). In this field day, Drs. Addie Thompson (Michigan State University) and Nadilia Gomez (Iowa State University) will describe their endeavors in public-private partnerships with regards to opportunities in incorporating these into educational modules and commercialization of research outcomes. For additional details and to register for this virtual event go to https://www.ag2pi.org/workshops-and-activities/field-day-2023-07-19/. 3. Recordings from the AG2PI Conference, "Mapping the Future of Agricultural Genome to Phenome Research", cohosted with USDA NIFA can be found at https://www.ag2pi.org/workshops-and-activities/conference-2023-06-15/#agenda. Each recording link is embedded within the agenda, next to its respective session. 4. An opportunity from University of Florida and ARC Centre of Excellence for Plant Success in Nature and Agriculture. This is a symposium to share understanding and approaches to predict crop performance, accounting for Genotype by Environment by Management(GxExM) Interactions: Considering Breeder, Agronomist and Farmer Perspectives. Please direct any questions to Charlie Messina (cmessina(a)ufl.edu<mailto:cmessina@ufl.edu>). See attached GxExM flyer attached. Please share with your colleagues and students. 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 ***

3 years

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AgBioData monthly webinar - Next Wed, July 12th

by Annarita Marrano

Hi everybody, Join us next Wed, *July 12th, *at 12 PM CT for our monthly webinar. We will have *Sarah Lippincott *from *DRYAD* talking about how to integrate generalist and specialist repositories to promote agricultural data sharing and reuse. 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: Sarah Lippincott, Dryad <https://datadryad.org/stash> Abstract: *Companion planting: How generalist and specialist repositories can work together to promote agricultural data sharing and reuse.* This conversation explores strategies for enhancing open sharing and reuse of agricultural data through collaboration between disciplinary and generalist repositories, specifically Dryad, an open data publishing platform and community. Generalist and specialist repositories bring distinct strengths to data sharing and reuse. Generalist repositories offer a home for a wide range of data types and support serendipitous discovery, while discipline-specific repositories offer granular metadata, specialized tools, and deep understanding of community needs. Agricultural data creators, and future data re-users, can benefit from collaboration between these different solutions, including building connections with complementary datasets stored in multiple repositories; consistency in metadata standards; and federated discovery systems. In this conversation, Dryad’s Head of Community Engagement, Sarah Lippincott, will describe Dryad’s stewardship of agricultural data and engage attendees in an exploration of how Dryad’s can work with the agricultural research community to improve data sharing, discovery, and reuse. *| 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

3 years

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AgBioData monthly webinar - TOMORROW!!

by Annarita Marrano

Hi everybody, This is a friendly reminder of our monthly webinar tomorrow, *June 7th, *at 12 PM CT. We will have *Peter Selby *from Cornell University talking about the *BrAPI project and its applications in plant breeding*. 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: Dr. Peter Selby, Cornell University Abstract: *Applications and impacts of the BrAPI project on plant breeding* Modern genomic breeding methods rely heavily on very large amounts of phenotypic and genotypic data, presenting new challenges in effective data management and integration. The datasets are often large and complex, and the data is often stored on multiple systems, sometimes separated by country and organization. As the common analysis methods increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. This webinar will be an introduction to The Breeding API (BrAPI) Project. The BrAPI Project began in 2014 when a small group of plant breeding and technology experts came together to try to standardize their data. Since then, BrAPI has become internationally accepted as one of the primary data exchange standards in the plant breeding domain. This webinar will give an overview of what BrAPI is, how it works, what it is capable of, and the impact the project has had so far on the community. *| 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

3 years, 1 month

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AG2PI training workshop: Enhancing Discoverability and Accessibility of UAV-Based Forage Phenotyping Hyperspectral Data

by Scott, Nicole M [AGRON]

Dear AgBioData members, The next Agricultural Genome to Phenome Initiative training workshop, "Enhancing Discoverability and Accessibility of UAV-Based Forage Phenotyping Hyperspectral Data on CyVerse: A Tutorial", will be held June 20, from 10 AM to 11 AM (CDT; UTC -5). In this workshop, Dr. Zhou Zhang will demonstrate how to publish agricultural geospatial data on the data sharing platform, CyVerse. You can access registration information for the workshop through the AG2PI website: https://www.ag2pi.org/workshops-and-activities/workshop-2023-06-20/. A recording will be made available on this webpage soon after the conclusion of the event. You do not need to register in order to access the recording - it will be publicly available. Please share this message and flyer with your colleagues. 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 ***

3 years, 1 month

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AgBioData monthly webinar - Next Wed, June 7th

by Annarita Marrano

Hi everybody, Join us next Wed, *June 7th, *at 12 PM CT for our monthly webinar. We will have *Peter Selby *from Cornell University talking about the *BrAPI project and its applications in plant breeding*. 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: Dr. Peter Selby, Cornell University Abstract: *Applications and impacts of the BrAPI project on plant breeding* Modern genomic breeding methods rely heavily on very large amounts of phenotypic and genotypic data, presenting new challenges in effective data management and integration. The datasets are often large and complex, and the data is often stored on multiple systems, sometimes separated by country and organization. As the common analysis methods increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. This webinar will be an introduction to The Breeding API (BrAPI) Project. The BrAPI Project began in 2014 when a small group of plant breeding and technology experts came together to try to standardize their data. Since then, BrAPI has become internationally accepted as one of the primary data exchange standards in the plant breeding domain. This webinar will give an overview of what BrAPI is, how it works, what it is capable of, and the impact the project has had so far on the community. *| 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

3 years, 1 month

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AG2PI upcoming virtual events: Training Workshop + Field Day

by Scott, Nicole M [AGRON]

Hello AgBioData community members, We are excited to share the following two virtual events with you: 1. The next AG2PI virtual Training Workshop, "Using Remote Sensing to Monitor Nitrogen Stress and Yield in Alfalfa (Medicago sativa L.)" is May 23 from 10am to 12pm CDT (UTC-5). In this workshop, Drs. Anju Biswas and Esteban Rios will demonstrate an image processing pipeline for nitrogen/abiotic stress detection in crops. For additional details and to register for this virtual event go to https://www.ag2pi.org/workshops-and-activities/workshop-2023-05-23/. See flyer attached. 1. The next AG2PI virtual Field Day, "Homomorphic Encryption to Enable Sharing of Confidential Data in Agricultural Genome to Phenome" is June 21 from 10:30am to 12pm CDT (UTC-5). Note: this was previously Workshop #20. In this field day, Drs. Hao Cheng and Jack Dekkers will demonstrate a new method of encrypting data that preserves privacy of proprietary information. This workshop is an outcome of an AG2PI seed grant award to Dr. Cheng. For additional details and to register for this virtual event go to https://www.ag2pi.org/workshops-and-activities/field-day-2023-06-21/. See flyer attached. Please share with your colleagues and students. 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 ***

3 years, 2 months

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Job opportunities for graduate students @ University of Arizona

by Annarita Marrano

Hi everybody, Please see below the details and the application form for *paid opportunities for graduate students interested in the analysis of agricultural genomics data sets* at the University of Arizona. Best, Annarita ____________________________ Funding is available to support students interested in analysis of agricultural genomics data sets. We will provide $8,000 per student for graduate students to work on analyzing publicly available sequencing data either over Summer or Fall of 2023. Graduate students need to be currently enrolled in a US graduate program and located at a US institution. In particular we are interested in graduate students who will work with either • short-read Illumina data analysis against a reference genome; OR • long-read data sets generated from PacBio; OR • long-read data sets generated from Oxford Nanopore. Analysis will require the use of open-source software and publicly available data sets from agricultural species. The student’s advisor or mentor should have demonstrated expertise in the required analysis methods and in timely submission of sequence data to public archives. Students will be required to provide comprehensive documentation of their analysis methods using readthedocs or protocol.io and be available in the following semester to answer questions about their workflow and documentation (no more than 3 one-hour online sessions). Applications are due on May 23 and can be submitted via this link: https://uarizona.co1.qualtrics.com/jfe/form/SV_0rh6csLi7mAx3ZY Applications should include: 1. A statement of up to 250 words briefly outlining experiment design, detailing which samples will be analyzed and what software will be used. Note that the emphasis should be on troubleshooting and optimizing data analysis rather than completing a large number of samples. 2. A statement of up to 300 words outlining evidence of their commitment to documentation and public release of computational workflows (e.g., the research group’s best practice, github contributions, publications). 3. A letter of support from their mentor or advisor briefly describing lab expertise in the analysis method and confirming that that the data set is publicly available. 4. Select if they are requesting support for Summer 2023 or Fall 2023. Successful applicants and their mentors will be required confirm that the student will be available in the semester following their funding on this project to answer questions about their workflow and documentation. Applications will be reviewed based upon the following criteria: 1) Student preparedness for completing the analysis workflow (e.g., understanding of software and analysis optimization). 2) Evidence of the research groups’ commitment to documentation and public release of workflows. 3) The mentor’s history of public data release and well documented analysis pipelines. 4) Feasibility of completing analysis of the samples in the time frame of the project. Please contact Fiona McCarthy (fionamcc(a)arizona.edu) with any questions.

3 years, 2 months

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REMINDER: No Monthly webinar next week!

by Annarita Marrano

Dear all, I want to remind everyone that there *will be NO monthly webinar *next Wednesday. There will be, instead, *the 2023 AgBioData community workshop on May 1-2. *(agenda available here <https://www.agbiodata.org/meetings/AGB_community_2023>). If you haven't done it yet and would like to attend virtually, *today is the last day for registration* (registration link here <https://forms.gle/kdeLq8XvJgfeDSwj7>). Best, Annarita

3 years, 2 months

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AgBioData-LIST