- AgBioData-LIST - Main Bioinformatics Lab

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

3 years, 6 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 ***

3 years, 6 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

3 years, 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 ***

3 years, 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

3 years, 7 months

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Invitation to participate to 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

3 years, 7 months

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AgBioData monthly webinar - Next Wed, April 5th

by Annarita Marrano

Hi everybody, Join us next Wed, *April 5th, *at 12 PM CT for our monthly webinar. We will have Krystal Tsosie <https://search.asu.edu/profile/535281> from Arizona State University talking about 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

3 years, 7 months

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REMINDER - TOMORROW AgBioData monthly webinar

by Annarita Marrano

Hi everybody, This is a friendly reminder of *tomorrow's* monthly webinar (*March 1st*)*. *We will have *Irene Cobo Simón* from the Institute of Forest Science (ICIFOR-INIA, CSIC; Spain) talking about the CartograPlant <https://treegenesdb.org/ct/about>, a web-based application that integrates, visualizes, and analyzes genotypic, phenotypic, environmental data, and their associated metadata, from georeferenced plants. 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. Irene Cobo Simón, Institute of Forest Science (ICIFOR-INIA, CSIC; Spain) Abstract: *CartograPlant: Cyberinfrastructure to improve plant health and productivity in the context of a changing climate.* Climate change is threatening plant health and productivity at all spatial scales. To date, it remains largely unknown whether plant breeding and agricultural management practices can keep pace with the rate and direction of environmental change, as well as species’ rate of adaptation to rapid environmental change. In addition, the incidence of invasive pests and pathogens is increasing as a consequence of globalization. This trend is being exacerbated by climate change. Thus, future plant health and productivity will depend on the match between genotypes (and their resulting phenotypes) and new environments. However, these analyses are challenging since they require the integration of diverse data types, usually decentralized and lacking in standardization: genotypic, phenotypic and environmental. Hence, centralized and up-to-date platforms which integrate, visualize and analyze high-throughput biological data are key, especially in the current big data era in plant biology. CartograPlant ( https://cartograplant.org/) is a web-based application that integrates, visualizes, and analyzes genotypic, phenotypic, environmental data, and their associated metadata, from georeferenced plants. Environmental data is available through advanced integration of global and regional layers. The genotype and phenotype metrics are collected through direct submission of studies at the time of publication or through the biocuration efforts of the affiliated databases and applications (TreeGenes, BIEN, TreeSnap). Data analysis is enabled by accessing the metadata associated with the public studies and providing appropriate workflows through Galaxy ( https://galaxyproject.org/). This metadata collection, using ontologies and standards, allows data integration and analysis coming from different studies, which is key to perform both mega and meta-analysis. Mega-analysis and meta-analysis of GWAS (GxP association) and landscape genomics (GxE association) studies can improve the power to detect association signals by increasing sample size and by examining more variants throughout the genome than each dataset alone. Thus, they allow users to answer unprecedented and ambitious adaptive questions, taking advantage of the potential of high-throughput biological data. This talk will describe the recent updates in data sources, functionalities, and analytic workflows offered by CartograPlant. *| 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

3 years, 8 months

1
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AgBioData monthly webinar - Next Wed, March. 1st

by Annarita Marrano

Hi everybody, Our next monthly webinar is next Wed, *March 1st. *Irene Cobo Simón from the Institute of Forest Science (ICIFOR-INIA, CSIC; Spain) will talk about the CartograPlant <https://treegenesdb.org/ct/about>, a web-based application that integrates, visualizes, and analyzes genotypic, phenotypic, environmental data, and their associated metadata, from georeferenced plants. 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. Irene Cobo Simón, Institute of Forest Science (ICIFOR-INIA, CSIC; Spain) Abstract: *CartograPlant: Cyberinfrastructure to improve plant health and productivity in the context of a changing climate.* Climate change is threatening plant health and productivity at all spatial scales. To date, it remains largely unknown whether plant breeding and agricultural management practices can keep pace with the rate and direction of environmental change, as well as species’ rate of adaptation to rapid environmental change. In addition, the incidence of invasive pests and pathogens is increasing as a consequence of globalization. This trend is being exacerbated by climate change. Thus, future plant health and productivity will depend on the match between genotypes (and their resulting phenotypes) and new environments. However, these analyses are challenging since they require the integration of diverse data types, usually decentralized and lacking in standardization: genotypic, phenotypic and environmental. Hence, centralized and up-to-date platforms which integrate, visualize and analyze high-throughput biological data are key, especially in the current big data era in plant biology. CartograPlant ( https://cartograplant.org/) is a web-based application that integrates, visualizes, and analyzes genotypic, phenotypic, environmental data, and their associated metadata, from georeferenced plants. Environmental data is available through advanced integration of global and regional layers. The genotype and phenotype metrics are collected through direct submission of studies at the time of publication or through the biocuration efforts of the affiliated databases and applications (TreeGenes, BIEN, TreeSnap). Data analysis is enabled by accessing the metadata associated with the public studies and providing appropriate workflows through Galaxy ( https://galaxyproject.org/). This metadata collection, using ontologies and standards, allows data integration and analysis coming from different studies, which is key to perform both mega and meta-analysis. Mega-analysis and meta-analysis of GWAS (GxP association) and landscape genomics (GxE association) studies can improve the power to detect association signals by increasing sample size and by examining more variants throughout the genome than each dataset alone. Thus, they allow users to answer unprecedented and ambitious adaptive questions, taking advantage of the potential of high-throughput biological data. This talk will describe the recent updates in data sources, functionalities, and analytic workflows offered by CartograPlant. *| 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

3 years, 8 months

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AgBioData monthly webinar - Tomorrow!

by Annarita Marrano

Hi everybody, This is a friendly reminder of our webinar tomorrow (*February 1st.). *Monica Munoz-Torres <https://tislab.org/members/monica-munoz-torres.html> from the University of Colorado School of Medicine will talk about the Monarch Initiative <https://monarchinitiative.org/>, a consortium and a set of resources that seeks to bridge the space between basic and applied and clinical research by developing tools that facilitate connecting data across a variety of scientific approaches and disciplines. Below you can find more details about the webinar and the zoom link to attend the webinar. We hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Presenters: *Dr. Monica Munoz-Torres <https://tislab.org/members/monica-munoz-torres.html>, University of Colorado School of Medicine *Host: *Dr. Monica Poelchau Abstract: *The Monarch Initiative: harmonizing cross-species data for disease diagnostics and discovery.* Addressing complex scientific challenges requires weaving together data from diverse sources, organisms, contexts, formats, and granularities, and building a coherent holistic view of this data landscape to address any given problem is non-trivial – much of the relevant information is scattered and not readily accessible for searching or analysis. The Monarch Initiative is a consortium and a set of resources aiming to overcome these limitations by integrating the fragmented data landscape into the most comprehensive open collection of genotype-phenotype data available. Monarch seeks to bridge the space between basic and applied and clinical research, developing tools that facilitate connecting data across a variety of scientific approaches and disciplines including genomics, proteomics, molecular modeling, diagnosis of disease and syndromes, and the organization of patient record data. The Monarch Knowledge Graph (KG) links together clinical, biomedical, and basic science research data spanning multiple species, and it supports reasoning across a wide range of organisms, body systems, and diseases. We founded the Human Phenotype Ontology (HPO), one of the most widely used biomedical ontologies and the gold standard for describing human phenotypes, and are also creators of the Mondo unified disease ontology, the Unified Phenotype Ontology (uPheno), the cross-species anatomy ontology (Uberon), the Environmental Conditions and Treatments Ontology (ECTO), and most recently, the Vertebrate Breed Ontology (VBO), a single source for data standardization and integration of all breed names. We also created the Simple Standard for Sharing Ontology Mappings (SSSOM) to harmonize the ontologies that are used by the sources, and the only ISO-approved standard for exchanging detailed, case-level phenotype data, Phenopackets. Monarch tools and resources are publically available and are designed for both informatics users, as well as clinical and basic research use cases. By making data more interoperable, our widely-used standards for data annotation and exchange help support a wide range of data sharing and reuse by projects and organizations around the world, and reduce the effort they need to devote to data harmonization. During this presentation, we will introduce you to a few of these resources and offer you the information to find and implement the ones that best serve your scientific needs. *| 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

3 years, 9 months

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AgBioData-LIST