- AgBioData-LIST - Main Bioinformatics Lab

Fwd: AgBiodata monthly webinar February 2nd

by Annarita Marrano

Hi everybody, It's that time of the month to advertise our monthly webinar! We will have our first webinar of the year this Wed, February 2nd, with *Baron Koylass* and *Timothee Cezard* from EMBL-EBI. They are going to talk about the European Variation Archive, a primary open repository for archiving and accessioning genetic variation. Below you can find more details about the webinar and the *NEW zoom link* to attend the webinar. We hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: Presenters: Dr. Baron Koylass and Dr. Timothe Cezard, EVA/EGA Team, European Bioinformatics Institute (EMBL-EBI) <https://www.ebi.ac.uk/about/teams/ega-eva-archive/> Host: Marcela Karey Tello-Ruiz Abstract: *The European Variation Archive: Genetic variation archiving and accessioning* The European Variation Archive (EVA) is a primary open repository for archiving, accessioning, and distributing genetic variation, including single nucleotide variants, short insertions and deletions (indels), and larger structural variants (SVs) in any species. Created in 2014 to provide FAIR access to genetic variation data, it has since grown to be a primary resource for genomic variants hosting >3 billion records and now maintains and provides the permanent variant locus identifiers (rs IDs) for all non-human species. *| 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 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) +1 312 626 6799 US (Chicago) +1 669 900 6833 US (San Jose) +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

5 months

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AG2PI Field Day: 2020 AI Institutes

by Scott, Nicole M [AGRON]

Dear AgBioData community members, The next AG2PI Field Day is on Wednesday, February 16 from 10:30 AM to 12:00 PM (Central Time, UTC-6). This event will feature the directors of the 2020 Artificial Intelligence Research Institutes, Dr. Vikram Adve and Ilias Tagkopoulos, funded by USDA National Institute of Food and Agriculture (NIFA). These AI institutes are part of a network of AI institutes established by USDA NIFA and the National Science Foundation to pursue transformational advances in a range of economic sectors, science and engineering fields. Dr. Adve will describe the work of AIFARMS to address major challenges across the agriculture sector, including efficiency and welfare in animal agriculture, environmental resilience in crops and soil health. Dr. Tagkopoulos will discuss the AIFS goal of accelerating critical solutions to the entire food system: from farm to consumer. This discussion will hit themes that are relevant to engineering as well as animal and plant sciences, so we hope you join us for an engaging conversation! We invite you to register for this Zoom event at https://tinyurl.com/AG2PI-FD15, 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. Please note: 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 ***

5 months, 2 weeks

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AG2PI seed grant RFP and informational conference

by Scott, Nicole M [AGRON]

Dear AgBioData community members, A major goal of the Agricultural Genome to Phenome Initiative (AG2PI<https://ag2pi.org/>) is to bring together agricultural scientists from multiple disciplines to work together in addressing shared challenges in genome-to-phenome research and related endeavors. As such, we provide a seed grant program to foster first steps towards the development of community solutions to research needs and opportunities, as well as gaps in physical infrastructure and the data management pipeline. This third round of the AG2PI seed grant program aims to fund around twelve (12) awards across three levels of support: Emerging (funds up to $50,000), Enabling (up to $75,000), and Establishing (up to $100,000). Applications will be due by 11:59pm CST (UTC-6) on Tuesday, March 8th. The anticipated start date for funded projects is June 1, 2022 and each project may be 6-12 months in duration. Further details regarding the request for proposals, application and review process can be found at the AG2PI website (https://www.ag2pi.org/seed-grants/2022-01-05/). AG2PI will host a Seed Grant Mini-Conference on January 19 from 10:30 AM to 12:00 PM (CST, UTC-6). This conference will provide an overview of our revised seed grant mechanism and review process, examples of projects that have been funded in previous rounds and will provide an opportunity to ask questions regarding the seed grants. We are excited to also feature a short session on best practices of team science. The conference will finish with a "teaming" event, which will provide a virtual space to discuss your seed grant idea with like-minded researchers with whom you may want to work. Registration is now open (https://www.ag2pi.org/workshops-and-activities/conference-2022-01-19/) and additional details will be available on that webpage soon. Feel free to share this message and opportunity with colleagues at your institution. If you have any questions regarding the mini-conference or seed grants, please direct them to Nicole Scott at nmscott(a)iastate.edu<mailto:nmscott@iastate.edu>. 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 ***

5 months, 2 weeks

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AG2PI Field Day: Leveraging Microbiomes in Agriculture

by Scott, Nicole M [AGRON]

Dear AgBioData community members, The next AG2PI Field Day is on Wednesday, December 15 from 10:30 AM to 12:00 PM (Central Time, -6 GMT). In this field day, Dr. Ben Holt, AgBiome, Inc., will discuss the challenges of putting microbes to work for human benefit, particularly with respect to plants. Then, Dr. Katie Summers, USDA ABBL, will describe the inter-kingdom communications that occur between the weanling pig's gut bacteriome and mycobiome and how these affect piglet performance. This discussion will hit themes that are relevant to both animal and plant sciences, so we hope you join us for an engaging conversation! We invite you to register for this Zoom event at https://tinyurl.com/AG2PI-FD14, 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. Please note: 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 ***

7 months

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Final reminder: AG2PI survey to advance efforts in G2P

by Scott, Nicole M [AGRON]

Dear AG2PI Partner Organization leaders and community members, Please share the below message with your members: We need your help to gather feedback on the USDA-funded Agricultural Genomes to Phenomes Initiative (AG2PI<https://www.ag2pi.org/>) and to help direct future funding opportunities in agriculture. Your responses will be used to inform USDA NIFA about access and barriers to resources in the area of G2P research, training, connections and other efforts. The below URL is reusable and not unique; anyone with this link will have the ability to participate. We ask that you finish the survey in one session, which should take around 10 minutes. This survey will remain open until December 3, 2021: https://iastate.qualtrics.com/jfe/form/SV_bm95xi3GFELb2xE 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. Importantly, this is an opportunity for the community to create a vision that may be used to guide future funding opportunities in this space. 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. General results of this survey will be made available to the public on the AG2PI website, on our Community Survey<https://www.ag2pi.org/community-surveys/> page (you can review results of our 2020 survey there now). We appreciate your help with this survey and telling us how the AG2PI project can be used to better your own agricultural endeavors and inform funding agencies of your needs. ------------------------ 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 ***

7 months

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AgBioData monthly seminar October 6th

by Campbell, Darwin A [AGRON]

Greetings! I hope your fall is off to a great start, not sure about you, but it is one of favorite seasons of the year. The upcoming October seminar is amazingly timely, and the neat thing is that the topic was set up early this spring, prior to the RCN announcement/kickoff last month (https://youtu.be/Sx3mZENaTro). If you were online or have watched the video, you will recall a significant amount of time was spent on making data FAIR and is a core objective of the RCN. Dr. Allyson Lister from Oxford e-Research Centre at the University of Oxford is a Knowledge Engineer, and FAIRsharing advocate that will challenge us on how we do our work AND make our data FAIR. Read more in the abstract below. I hope your schedule will allow you to join us. As usual we will record and publish the content after the meeting. All the best! Darwin :-: :-: :-: :-: :-: :-: :-: :-: :-: :-: :-: :-: :-: FAIRsharing: promoting the discovery of data standards, policies and databases across all research domains. Presenter: Dr. Allyson Lister from Oxford e-Research Centre, University of Oxford Host: Jacqueline Campbell | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time: https://bit.ly/3qQcgES https://iastate.zoom.us/j/91906292999?pwd=NlZrK0lUNjlPRVZxZ0JBSlB4ZXF0QT09 Or, go to https://iastate.zoom.us/join and enter meeting ID: 919 0629 2999 and password: 294711 Join from dial-in phone line: Dial: +1 312 626 6799 or +1 646 876 9923 Meeting ID: 919 0629 2999 +13126266799,,91906292999,,,,,,0#,,294711 +16468769923,,91906292999,,,,,,0#,,294711 Participant ID: Shown after joining the meeting International numbers available: https://iastate.zoom.us/u/aJkMOd9A Abstract: FAIRsharing is an informative and educational resource on interlinked standards, repositories and policies, three key elements of the FAIR ecosystem. FAIRsharing promotes the existence and value of these standards, repositories and policies, fostering a culture change within the research community into one where the use of these resources for FAIRer data is pervasive and seamless. This is achieved by guiding consumers to discover, select and use these resources with confidence, and helping producers to make their resources more visible, more widely adopted and cited. This presentation will highlight key collaborative, successful activities as well as next steps within FAIRsharing. It will also provide information on how to become a recommended repository in FAIRsharing and how to use FAIRsharing to engage with your stakeholders as well as with journal publishers and their data policies.

8 months

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PAG 2022 Tripal Workshop - Extended Deadline

by Buehler, Sean

Hi folks, We are still accepting abstracts for the Tripal Session at PAG 2022 (https://www.intlpag.org/2022/). If you are planning to give a talk (either in person or virtually) in the Tripal session, please submit your abstract via this Google Form: https://forms.gle/jZVeEDDQKzXFMHRs6 There are spots available for in person talks and and a limited number of spots for virtual presentations. The deadline is for abstract submission has been extended again until November 5. Thanks

8 months

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AG2PI Field Day: Institutional Collaborations

by Scott, Nicole M [AGRON]

Dear AgBioData members, The next AG2PI Field Day is on Wednesday, November 17 from 10:30 AM to 12:00 PM (Central Time, -6 GMT). In this field day, we will hear from scientists at two institutions that are developing tools for genomic and phenomic research and analysis. First, Drs. Anthony Hearst and Edwin Reidel, from Progeny Drone, will describe how their software can help with phenotyping in small plot field trials with small unmanned aerial systems. Then, Dr. Dugan Um, from Texas A&M University Corpus Christi, will describe the development of an AI system for predicting yield using plant images and two AI agents. This discussion will hit themes that are relevant to engineering and data sciences, so we hope you join us for an engaging conversation! We invite you to register for this Zoom event at https://tinyurl.com/AG2PI-FD13, 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. 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. 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 ***

8 months

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November Seminar - postponed 1 week, now on 11/10/21

by Campbell, Darwin A [AGRON]

Greetings. Normally about this time I would be sending you the information about the upcoming monthly AgBioData seminar. However, due to scheduling difficulties, this month’s seminar will be pushed back one week to Wednesday, November 10th, when Marcela Tello-Ruiz will host Dr. Silvie Fexova who will present on the Plant Expression Atlas. Thank you for understanding and I hope your schedule will allow you to attend. If it does not, the recording will be posted on the AgBioData YouTube channel<https://www.youtube.com/channel/UCwMIJWOX7n_ZFoFpOsmCzgw/videos?view=0&sort…> along with all previous seminars. Wishing you all the best, Darwin AgBioData Program Coordinator

8 months, 1 week

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PAG 2022 Tripal Workshop

by Buehler, Sean

Hi folks, PAG 2022 is just around the corner. If you are planning to give a talk (either in person or virtually) in the Tripal session, please submit your abstract via this Google Form: https://forms.gle/jZVeEDDQKzXFMHRs6 There are spots available for in person talks and and a limited number of spots for virtual presentations. The deadline is for abstract submission is October 25. Thanks

8 months, 3 weeks

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