- AgBioData-LIST - Main Bioinformatics Lab

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

1 year, 5 months

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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 ***

1 year, 6 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.

1 year, 6 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

1 year, 6 months

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Data Curator and Outreach Specialist Position at Clemson University

by Annarita Marrano

Dear everyone, The Gasic Lab at Clemson University is looking for a *Data Curation/outreach specialist* to support research activities on an exciting new SCRI project. This highly collaborative project includes a diverse team of researchers working on crop breeding, genomics, genetics, curation, and bioinformatics. The successful applicant will be working on data curation for the Genome Database for Rosaceae (https://www.rosaceae.org/). The *full job description* and *application link* are attached. Best, Annarita

1 year, 7 months

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Registration is OPEN! --- VIRTUAL 2023 AgBioData community workshop

by Annarita Marrano

Dear AgBioData community, We are excited to announce that the registration for *VIRTUAL* participation in the* 2023 AgBioData community workshop* (May 1-2, 2023) is now *OPEN*! This workshop will bring together the working group (WG) members and member database resources to share the progress and achievements made by the WGs and discuss the future directions of the consortium. You can find a draft of the workshop here <https://www.agbiodata.org/meetings/AGB_community_2023> . If you are interested in participating virtually and providing valuable insights as a data generator and manager, *please register by completing this short form <https://forms.gle/LaYcyh4Z12yZ9Pa19> by April 26th*. I hope you will be able to join us! Please let me know if you have any questions. Have a nice week. Annarita

1 year, 7 months

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FY2023 NIFA Agricultural Genomes to Phenomes Initiative RFA

by Scott, Nicole M [AGRON]

Dear AgBioData community members, We'd like to announce, on behalf of USDA NIFA, that the newest Agricultural Genomes to Phenomes Initiative program RFA was published today. Here's the link<https://www.nifa.usda.gov/grants/funding-opportunities/agricultural-genome-…> to the RFA on the USDA NIFA website. ------------------------ 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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REMINDER - Tomorrow AgBioData Monthly Webinar

by Annarita Marrano

Hi everybody, This is a friendly reminder of tomorrow's webinar at 12 PM CT with Krystal Tsosie <https://search.asu.edu/profile/535281> from Arizona State University. She will present digital data tools and machine learning approaches to protect indigenous knowledge and biodiversity. 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. Krystal Tsosie, Arizona State University Abstract: *From Green Revolution to “Rescue” Indigeneity: Using Digital Data Tools and Machine Learning Approaches to Protect Indigenous Knowledge and Biodiversity.* Comprising less than 5% of the world's population, Indigenous people protect 80% of global biodiversity. The next genomic ”discoveries” in industry and academia may co-opt Indigenous knowledge or disenfranchise Indigenous peoples, who are often last to benefit and are least protected from intellectual property claims. Ethical and sustainable research necessitates new digital data approaches as grounded in machine learning and Indigenous stewardship models to operationalize CARE data governance principles, direct benefit sharing, and equitable engagement and partnerships with Indigenous communities. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Annarita Marrano is inviting you to a scheduled Zoom meeting. 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

1 year, 7 months

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Upcoming AG2PI events: Field day + Training workshops + conference

by Scott, Nicole M [AGRON]

Hello AgBioData community members, There are four upcoming events we'd like to share with you: 1. The next AG2PI Field Day, "CENSA - A circular economy approach for reducing nitrogen use inefficiencies in integrated livestock production systems", is April 19 from 10:30 am to noon CDT (UTC-5). Drs. Edward Buckler and Mark Boggess will Describe a vision for more sustainable integrated crop and livestock production systems. See flyer attached. Register for this virtual event at https://www.ag2pi.org/workshops-and-activities/field-day-2023-04-19/. 1. The next AG2PI training workshop will be April 25 from 12pm to 2pm CDT (UTC-5) titled, "Water dynamics from molecular structure to phenotype". In this workshop, Drs. Carmela Rosaria Guadagno and Marilyn Gunner, along with graduate students Benjamin Romanjenko and Jose Ortiz-Soto, will introduce how to utilize protein structural information and sequencing data to predict hydration phenotype in different organisms. This workshop is an outcome of an AG2PI seed grant award<https://www.ag2pi.org/resources/ag2pi-funded-seed-grants/#round-2> to Dr. Guadagno. See flyer attached. Register for this virtual event at https://www.ag2pi.org/workshops-and-activities/workshop-2023-04-25/. 1. An additional AG2PI training workshop, will be April 28 from 10am to 11:30am CDT (UTC-5) titled, "Homomorphic encryption to enable sharing of confidential data in agricultural genome to phenome". In this workshop, Drs. Hao Cheng and Jack Dekkers will demonstrate a new method of encrypting data that preserves privacy of proprietary information. See flyer attached. This workshop is an outcome of an AG2PI seed grant award<https://www.ag2pi.org/resources/ag2pi-funded-seed-grants/#round-3> to Dr. Cheng. Register for this virtual event at https://www.ag2pi.org/workshops-and-activities/workshop-2023-04-28/. 1. Registration is now open for the AG2PI conference, cohosted with USDA NIFA: Mapping the Future of Agricultural Genome to Phenome Research, June 15-16! Registration is free (go to https://www.ag2pi.org/workshops-and-activities/conference-2023-06-15/) but limited to 150 attendees. Some travel support is available for those who request it but is contingent upon attendance and the availability of funds. This event will include talks by community thought leaders, stakeholder roundtables, small group discussions, and networking opportunities, all designed to map the future of AG2P research and develop recommendations concerning the research investments needed to achieve that future. These recommendations have been requested by USDA-NIFA. 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 ***

1 year, 7 months

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REMINDER: Register for the 2023 AgBioData in-person community workshop

by Annarita Marrano

Dear AgBioData member, We are excited to announce that AgBioData will have a *two-day in-person workshop in Chicago (IL)* on *May 1-2, 2023*. This meeting is meant to bring together working group (WG) members and member database resources to share the progress and achievements made by the WGs and discuss the future directions of the consortium (more details and a draft meeting agenda here <https://www.agbiodata.org/meetings/AGB_community_2023>). We have *funds to cover travel expenses*, in detail, a two-ways flight ticket, a two-night hotel room (nights: 04/30-05/01), and meals onsite during the event for about 50 participants. *We have a few spots still available *and are opening the invitation to anybody from the AgBioData community interested in learning more about our WGs and willing to contribute to our mission of FAIR data in agriculture research. *We can support ONLY members located in the US.* *Please complete this form <https://forms.gle/nj12dgafaB2F9Rc67> to secure a spot. * If you can't attend in person but are interested in participating virtually, we assure you that the meeting will be hybrid and will soon send more details and a Zoom registration link. Please let me know if you have any questions. Annarita

1 year, 7 months

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