- AgBioData-LIST - Main Bioinformatics Lab

AgBioData monthly webinar - Next Wed, October 5th

by Annarita Marrano

Hi everybody, Next Wed, *October 5th*, we will have *Chris Mungall <https://bids.berkeley.edu/people/chris-mungall>* from the Lawrence Berkeley National Laboratory talking about Gene Ontology <http://geneontology.org/> and how to use it for functional annotation of plants and animals. 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. Chris Mungall, Lawrence Berkeley National Laboratory Host: Dr. Tanya Berardini Abstract: *The Gene Ontology: Making functional annotation of plants and animals FAIR.* The Gene Ontology is one of the most widely used databases in the biosciences, covering functional annotation of genes and gene products across a wide range of species. The GO is ubiquitously used to analyse a variety of types of high-throughput experimental data. Originally created to unify functional annotation across a handful of model organism databases, the GO has grown to encompass more species, and the structure of the GO has been extended to integrate with other ontologies such as CHEBI and the Plant Ontology. The structure of annotations has also evolved, and the GO now includes more expressive pathway-oriented annotations in the form of GO-CAMs (Causal Activity Models). In this talk I will give a practical guide to the structure of GO, how to find and request terms, how to search and create annotations, and how to use GO tools. I will also talk about how the broader AgBioData can contribute to the GO consortium to help seed functional annotation efforts in a more diverse range of organisms, and in particular with agriculturally relevant species. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+webinar…> 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 +13017158592,,82038356125#,,,,*160683# US (Washington DC) +13092053325,,82038356125#,,,,*160683# US Dial by your location +1 301 715 8592 US (Washington DC) +1 309 205 3325 US +1 312 626 6799 US (Chicago) +1 646 931 3860 US +1 929 205 6099 US (New York) +1 386 347 5053 US +1 564 217 2000 US +1 669 444 9171 US +1 669 900 6833 US (San Jose) +1 719 359 4580 US +1 253 215 8782 US (Tacoma) +1 346 248 7799 US (Houston) Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

3 days, 15 hours

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AG2PI Field Day: Seed Grant Project Lightning Talks

by Scott, Nicole M [AGRON]

Dear AgBioData community members, The next Agricultural Genome to Phenome Initiative (AG2PI) Field Day is on Wednesday, September 21 from 10:30 AM to 12:00 PM (Central Time, UTC-5). In this field day, we will hear from a selection of seed grant recipients regarding the work they are doing to further develop the AG2PI community and advance AG2P science and technology. Talks have been pre-recorded and are in a three-minute thesis format so we can hear from eight project principal investigators in total. Each talk will be played and followed by an open Q&A session. Please note: these talks were recorded during the AG2PI "Thinking Big: Visualizing the Future of AG2PI" conference, which was co-hosted by USDA NIFA. Other recordings from this event are available on the AG2PI website at https://www.ag2pi.org/workshops-and-activities/conference-2022-09-09/. We invite you to register for this Zoom event at https://www.ag2pi.org/workshops-and-activities/field-day-2022-09-21/, 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). 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 weeks, 2 days

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Nick Provart @ AgBioData webinar - TOMORROW!

by Annarita Marrano

Hi everybody, This is a gentle reminder of *tomorrow's *webinar (*Sept. 7th*) with *Nicholas J. Provart* from the University of Toronto. He will talk about the visual analytic tools for transcriptomic and genomics data (e.g., *ePlant*) developed by his lab and available at the Bio-Analytic <http://bar.utoronto.ca/> Resource <http://bar.utoronto.ca/>. 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. Nicholas J. Provart, the University of Toronto Host: Dr. Sunita Kumari Abstract: *Raising the BAR for Hypothesis Generation in Plant Biology Using Open Big Data.* We have developed tools, available as part of the Bio-Analytic Resource at http://bar.utoronto.ca, for exploring large data sets from plants, to allow deeper insights into biological questions. My lab’s three visual analytic tools for transcriptomic data (eFP Browser, ePlant, and eFP-Seq Browser) allow for rapid access to comprehensive gene expression compendia we have curated for identifying tissues, cell-types, or perturbations in which a gene is active or alternatively spliced. Interactions, be they protein-protein or regulatory, create networks. We have developed new tools for exploring such data, either from large collections of experimentally-supported protein-protein or protein-DNA interactions or from predicted interactions, including protein-protein interactions inferred from molecular docking studies. We are currently working on integrating large-scale phenotype data from field trials monitored by drone-based sensors into ePlants we have developed for several agronomically-important species to improve understanding of links between genotype and phenotype. *| 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 +13017158592,,82038356125#,,,,*160683# US (Washington DC) +13092053325,,82038356125#,,,,*160683# US Dial by your location +1 301 715 8592 US (Washington DC) +1 309 205 3325 US +1 312 626 6799 US (Chicago) +1 646 931 3860 US +1 929 205 6099 US (New York) +1 386 347 5053 US +1 564 217 2000 US +1 669 444 9171 US +1 669 900 6833 US (San Jose) +1 719 359 4580 US +1 253 215 8782 US (Tacoma) +1 346 248 7799 US (Houston) Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

3 weeks, 4 days

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AgBiodata monthly webinar - Next Wed, Sept. 7th!

by Annarita Marrano

Hi everybody, Next Wed, *Sept. 7th*, we will have *Nicholas J. Provart* from the University of Toronto talking about the tools recently developed by his lab and available at the Bio-Analytic <http://bar.utoronto.ca/>Resource <http://bar.utoronto.ca> for analyzing large plant data sets. 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. Nicholas J. Provart, the University of Toronto Host: Dr. Sunita Kumari Abstract: *Raising the BAR for Hypothesis Generation in Plant Biology Using Open Big Data.* We have developed tools, available as part of the Bio-Analytic Resource at http://bar.utoronto.ca, for exploring large data sets from plants, to allow deeper insights into biological questions. My lab’s three visual analytic tools for transcriptomic data (eFP Browser, ePlant, and eFP-Seq Browser) allow for rapid access to comprehensive gene expression compendia we have curated for identifying tissues, cell-types, or perturbations in which a gene is active or alternatively spliced. Interactions, be they protein-protein or regulatory, create networks. We have developed new tools for exploring such data, either from large collections of experimentally-supported protein-protein or protein-DNA interactions or from predicted interactions, including protein-protein interactions inferred from molecular docking studies. We are currently working on integrating large-scale phenotype data from field trials monitored by drone-based sensors into ePlants we have developed for several agronomically-important species to improve understanding of links between genotype and phenotype. *| 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 +13017158592,,82038356125#,,,,*160683# US (Washington DC) +13092053325,,82038356125#,,,,*160683# US Dial by your location +1 301 715 8592 US (Washington DC) +1 309 205 3325 US +1 312 626 6799 US (Chicago) +1 646 931 3860 US +1 929 205 6099 US (New York) +1 386 347 5053 US +1 564 217 2000 US +1 669 444 9171 US +1 669 900 6833 US (San Jose) +1 719 359 4580 US +1 253 215 8782 US (Tacoma) +1 346 248 7799 US (Houston) Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

1 month

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AgBiodata monthly webinar - TOMORROW!

by Annarita Marrano

Hi everybody, This is a gentle reminder of our webinar tomorrow (August 3rd). We will have *ThankGod Ebenezer* from EMBL-EBI (UK) talking about the African BioGenome Project (AfricaBP) project and the applications of genomic approaches for food security and biodiversity conservation in Africa. I have included below more details about the webinar and the zoom link to attend the webinar. We hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: Presenters: Dr. ThankGod Ebenezer, EMBL-EBI (UK). AfricanBP <https://africanbiogenome.org/> Host: Dr. Jacqueline Campbell Abstract: *The African BioGenome Project (AfricaBP): Genomics in the service of African biological diversity.* Food security and biodiversity conservation represents a substantial issue worldwide, and requires local solutions, as highlighted in the UN’s Sustainable Development Goals. I will discuss the progress and process of establishing a pan-African network to address this challenge through genomic science and how this could inform and influence policy across Africa. *| 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 +15642172000,,82038356125#,,,,*160683# US +16469313860,,82038356125#,,,,*160683# US Dial by your location +1 564 217 2000 US +1 646 931 3860 US +1 669 444 9171 US +1 669 900 6833 US (San Jose) +1 929 205 6099 US (New York) +1 253 215 8782 US (Tacoma) +1 301 715 8592 US (Washington DC) +1 312 626 6799 US (Chicago) +1 346 248 7799 US (Houston) +1 386 347 5053 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

2 months

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AG2PI Field Day: Industry Showcase of G2P solutions

by Scott, Nicole M [AGRON]

Dear AgBioData community members, The next Agricultural Genome to Phenome Initiative (AG2PI) Field Day is on Wednesday, August 17 from 10:30 AM to 12:00 PM (Central Time, UTC-5). In this field day, we will hear from scientists at two companies that develop tools for genomic and phenomic research and analysis. Paul McMahon, from Phenospex, and Andrea Johnstone, from EpiCypher, will describe the work being done at their respective companies to facilitate genome to phenome discoveries. Please note: this field day is a result of an open call for presenters; AG2PI does not endorse or otherwise benefit from the companies presenting at this event. We invite you to register for this Zoom event at https://tinyurl.com/AG2PI-FD20, 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). Feel free to share this message and attached flyer with colleagues at your institution. 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 months

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AgBiodata monthly webinar - Next Wed, August 3rd!

by Annarita Marrano

Hi everybody, Next Wed, *August 3rd*, we will have *ThankGod Ebenezer* from EMBL-EBI (UK) talking about the African BioGenome Project (AfricaBP) project and the applications of genomic approaches for food security and biodiversity conservation in Africa. 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. ThankGod Ebenezer, EMBL-EBI (UK). AfricanBP <https://africanbiogenome.org/> Host: Dr. Jacqueline Campbell Abstract: *The African BioGenome Project (AfricaBP): Genomics in the service of African biological diversity.* Food security and biodiversity conservation represents a substantial issue worldwide, and requires local solutions, as highlighted in the UN’s Sustainable Development Goals. I will discuss the progress and process of establishing a pan-African network to address this challenge through genomic science and how this could inform and influence policy across Africa. *| 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 +15642172000,,82038356125#,,,,*160683# US +16469313860,,82038356125#,,,,*160683# US Dial by your location +1 564 217 2000 US +1 646 931 3860 US +1 669 444 9171 US +1 669 900 6833 US (San Jose) +1 929 205 6099 US (New York) +1 253 215 8782 US (Tacoma) +1 301 715 8592 US (Washington DC) +1 312 626 6799 US (Chicago) +1 346 248 7799 US (Houston) +1 386 347 5053 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

2 months

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Attention: AgBioData Ontologies and Data Federation Working Groups Survey

by Laurel Cooper

3 months

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NO AgBioData webinar next week!

by Annarita Marrano

Hi everybody, I just want to inform you that AgBioData will take a short break from the monthly webinar in July. So,* there won't be a webinar next Wed.* We will return in August with ThankGod Ebenezer from the African Biogenome Project. I wish you a wonderful day. Best regards, Annarita

3 months

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AG2PI survey: Priorities for future funding opportunities in G2P

by Scott, Nicole M [AGRON]

Dear AgBioData member, Tell us where future research and development funds should be directed! In this survey, you will tell us which areas of agricultural genomes-to-phenomes (G2P) research you think are most critical for future investment, which are easiest to accomplish and in what areas might cross-kingdom collaborations be most successful. Summarized responses will be shared with USDA NIFA and on the AG2PI Community Survey<https://www.ag2pi.org/community-surveys/> webpage. The below URL is anonymous and does not collect identifying information. We ask that you finish the survey in one session, which should take 10-15 minutes. Follow this link to the Survey: https://iastate.qualtrics.com/jfe/form/SV_6rlzERMQZcxsLmm This survey will close July 1, 2022. Please note: If you have joined an AG2PI mailing list then you will receive a direct email from this project asking you to fill out the survey. You should only fill out the survey once. As a thank you for participating in the survey, we'd like to offer you the opportunity to enter into a random drawing for one of two (2) $50 gift cards and one of eight (8) AG2PI 20 oz aluminum water bottles. A link to a Google Form can be found at the end of the survey for you to enter the drawing. This opportunity is only open to individuals currently living in the U.S. and who are 18 years or older. As a reminder, the focus of the AG2PI project is to build cross-kingdom research communities to address the challenges of genome to phenome (G2P) research and find opportunities to work together to identify shared critical research gaps. AG2PI is not, itself, a research producing project. Importantly, this survey is an opportunity for the community to share with the USDA a vision that may be used to guide future requests for proposals in this space as Congress continues to appropriate money for the general AG2PI program authorized in the 2018 Farm Bill. We appreciate your input on how the AG2PI project can be used to better your own agricultural endeavors and inform USDA of your needs. Kind regards, Nicole Scott ------------------------ 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 months, 3 weeks

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