- AgBioData-LIST - Main Bioinformatics Lab

collaborations opportunities with the Midwest Big Data Innovation Hub and USDA NIFA

by Annarita Marrano

Hi AgBioData members, Please see below the collaborative activities offered by the MBDH and USDA NIFA. Best regards, Annarita The Midwest Big Data Innovation Hub is participating in the interagency Open Knowledge Network (OKN) Sprint workshop led by NSF. This is a series of collaborative activities between February and June 2022. MBDH is working with USDA NIFA program director Ann Stapleton and others on developing an OKN use case focused on food/ag/nutrition + climate resilience that would look across agencies' award portfolios and identify opportunities for future investments. Please contact John MacMullen (wjohn(a)illinois.edu) if you have interest in participating on this working group. More information: https://apply.hub.ki/okn/ <https://urldefense.com/v3/__https:/apply.hub.ki/okn/__;!!PvXuogZ4sRB2p-tU!R…> Jennifer Clarke on behalf of the MBDH Digital Agriculture Community

3 years, 9 months

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Call for nomination for new members of the AgBioData steering committee!

by Annarita Marrano

Dear AgBioData community, AgBioData is looking for candidates to serve as members of the AgBioData steering committee <https://www.agbiodata.org/steering-committee-members> (SC) for a term of 3 years. The SC is a vibrant, collaborative, and inclusive environment that offers plenty of opportunities to expand leadership skills, network with agricultural research community stakeholders, and help achieve a FAIR agricultural data ecosystem. *If you are interested or want to nominate someone else that you think will fit the position, please submit your application here <https://docs.google.com/forms/d/1e1o8SVA2zklg-_hZ_V_y2Yjlj0iKa9pKJOpB07qb19…>. * *Applications are due by April 1st.* You can find more details about the election process and the general duties of an SC member in the application form. Best regards, Annarita

3 years, 9 months

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AG2PI Field Day: National Institute of Food and Agriculture

by Scott, Nicole M [AGRON]

Dear AgBioData community members, The next AG2PI Field Day is on Wednesday, March 16 from 10:30 AM to 12:00 PM (Central Time, UTC-5). This event will feature the USDA NIFA national program leaders for the agricultural genome to phenome initiative, Frank Siewerdt and Christian Tobias. Dr. Siewerdt will describe some of the current funding opportunities in animal breeding offered by NIFA while Dr. Tobias will describe opportunities in plant breeding. Each will also discuss what makes for a good proposal and provide some "best practices" for submitting proposals in these spaces. We invite you to register for this Zoom event at https://tinyurl.com/AG2PI-FD16, 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). Please 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 ***

3 years, 9 months

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2022 AgBioData Community Workshop

by Annarita Marrano

Dear AgBioData community members, We’d like to invite you to join the “2022 AgBioData Community Workshop: Facilitating crosstalk and network building across working groups” on March 15–17 (7-9 AM Pacific Time). Anyone who uses, generates, or manages agricultural biological data is encouraged to attend. Hearing about the issues that you encounter when searching for, accessing, and reusing data in your research is very important for developing standards and best practices for FAIR data. Even if you can’t make it all three days, we hope that you can participate. As part of our NSF RCN grant <https://www.agbiodata.org/node/472>, we currently have nine working groups (WGs) focusing on different aspects of data sharing and management in agriculture (more information about the WGs here <https://www.agbiodata.org/all-working-groups>). The goals of this community workshop are: - providing a forum for the individual WGs to communicate what they are working on; - gathering detailed, impactful community feedback on specific questions that the WGs have about data curation, archiving, and management in agriculture. Each day will start with short presentations from selected working groups, followed by breakout sessions, where WG and non-WG members can meet and discuss relevant topics, and a brief reporting period at the end. Register for our community workshop here <https://us06web.zoom.us/meeting/register/tZYtduqqqjsrGdfRHdV8yKhUNHUQBbAeLI…>and for more information on the schedule visit our website <https://www.agbiodata.org/node/475>. Please email us with any questions. Best regards, Annarita

3 years, 9 months

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FW: Book now: Sharing Data Better – The Rise of Data Institutions

by Daureen Nesdill

Hi all, Something tells me AgBioData is an Open Data Institution. See below Daureen Daureen Nesdill MS MLIS Research Data Management Librarian University of Utah Campus Administrator for Labarchives https://campusguides.lib.utah.edu/labarchives/home From: The ODI<mailto:info@theodi.org> Sent: Thursday, February 17, 2022 4:02 PM To: Fox, Mercury - (ceds)<mailto:ceds@arizona.edu> Subject: [EXT]Book now: Sharing Data Better – The Rise of Data Institutions External Email Join us on 30 March online to learn how data institutions are driving us towards a future where data is used for positive impact. [Social media banner image - Sharing Data Better]<https://c4MJj04.na1.hubspotlinks.com/Btc/T5+113/c4MJj04/VV-D4h1llW_PN7Qwvr6…> If we’re to tackle society’s biggest challenges, we need to collect, maintain and share data better. But how can we make this happen? In our free interactive online event<https://c4MJj04.na1.hubspotlinks.com/Btc/T5+113/c4MJj04/VV-D4h1llW_PN7Qwvr6…>, we reveal the role that data institutions can play in driving us towards a future where data is used for positive economic, societal and environmental impact. Join us on 30 March online <https://c4MJj04.na1.hubspotlinks.com/Btc/T5+113/c4MJj04/VV-D4h1llW_PN7Qwvr6…> Event details 🗣️ Sharing Data Better: The Rise of Data Institutions 📅 Wednesday 30 March 2022 ⏰ 14:00-18:00 BST (online) * Sir Nigel Shadbolt<https://c4MJj04.na1.hubspotlinks.com/Btc/T5+113/c4MJj04/VV-D4h1llW_PN7Qwvr6…>, co-founder of the Open Data Institute, will give the opening keynote speech, setting out his vision for data institutions in 2022 * The event will be hosted by Jack Hardinges<https://c4MJj04.na1.hubspotlinks.com/Btc/T5+113/c4MJj04/VV-D4h1llW_PN7Qwvr6…>, the ODI's programme lead for data institutions. Book your free place now <https://c4MJj04.na1.hubspotlinks.com/Btc/T5+113/c4MJj04/VV-D4h1llW_PN7Qwvr6…> What are data institutions? At the ODI, we recognise data institutions as organisations who collect, maintain and share (or steward) data towards public, educational or charitable aims – we've been researching, advocating for and working with data institutions over the past two years. Learn more about what data institutions are and why they’re so important<https://c4MJj04.na1.hubspotlinks.com/Btc/T5+113/c4MJj04/VV-D4h1llW_PN7Qwvr6…>. [Facebook]<https://c4MJj04.na1.hubspotlinks.com/Btc/T5+113/c4MJj04/VV-D4h1llW_PN7Qwvr6…> [LinkedIn]<https://c4MJj04.na1.hubspotlinks.com/Btc/T5+113/c4MJj04/VV-D4h1llW_PN7Qwvr6…> [Twitter]<https://c4MJj04.na1.hubspotlinks.com/Btc/T5+113/c4MJj04/VV-D4h1llW_PN7Qwvr6…> [Instagram]<https://c4MJj04.na1.hubspotlinks.com/Btc/T5+113/c4MJj04/VV-D4h1llW_PN7Qwvr6…> The Open Data Institute, 5th Floor, Kings Place, 90 York Way, London, N1 9AG, United Kingdom Unsubscribe<https://hs-748510.s.hubspotemail.net/hs/manage-preferences/unsubscribe-all?…>

3 years, 10 months

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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

3 years, 10 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 ***

3 years, 11 months

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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 ***

3 years, 11 months

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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 ***

4 years

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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 ***

4 years

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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.

4 years, 1 month

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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

4 years, 1 month

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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 ***

4 years, 1 month

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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

4 years, 1 month

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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

4 years, 2 months

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Provide new Working Group ideas for the AgBioData RCN!

by Campbell, Darwin A [AGRON]

Last week, the Steering Committee shared with you the goals and objectives of the recently funded NSF-RCN. The recording of the meeting is available on YouTube at https://youtu.be/Sx3mZENaTro and the slides are available at the AgBioData website: https://www.agbiodata.org/meetings This is your opportunity to propose additional Working Groups and their objectives or goals. You will find the form to make suggestions here (best viewed in Firefox, Chrome, or Opera browsers): https://iastate.qualtrics.com/jfe/form/SV_0HhG7VCjFYBqUyW Do not delay! This form will remain open through September 15th. Please expect a second and final survey on working group participation and membership in mid-September. These Working Groups were presented by the Steering Committee: Nomenclature, Metadata Standards, Data federation, Emerging data types, Recruiting, Implementation, Education, Sustainability You can review the kickoff meeting slides for more information: https://www.agbiodata.org/sites/default/files/files/September_1_2021_RCN.pdf. During the RCN kickoff meeting, these additional Working Groups were suggested: Data collection accuracy and precision Ontologies Incorporation of data from precision sensing technologies Pan-genomes Phenology Pan-transcriptome Molecular genotype-phenotype links; such as GTEx Thank you once again for your interest and support of AgBioData! The AgBioData Steering Committee: Jacqueline Campbell, Darwin Campbell (coordinator), Ethy Cannon, Laurel Cooper, Lisa Harper, Eva Huala, Sook Jung, Monica Poelchau, Leonore Reiser, Meg Staton, Marcela Tello-Ruiz

4 years, 2 months

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AG2PI Field Day: Industry Showcase of G2P solutions

by Scott, Nicole M [AGRON]

Dear AgBioData members, The next AG2PI Field Day is on Wednesday, October 20 from 10:30 AM to 12:00 PM (Central Time, -5 GMT). In this field day, we will hear from scientists at two companies that develop tools for genomic and phenomic research and analysis. First, Dr. Katrin Jakob, from Plant Di-Tech, will discuss how their PlantArray functional phenotyping technology captures plant-water balance in tomato plants, which allows for customized and precise set-up of drought stress conditions. Then, Matt Bechdol and Evan Flatt, from GRYFN, will discuss the multi-modal UAS sensing solutions they develop for multi-sensor integration design, calibration, processing, and operations. This discussion will hit themes that are relevant to the animal, plant 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-FD12, 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 ***

4 years, 2 months

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Survey for cloud-based computational needs

by Meg Staton

A group of investigators including Alex Feltus is seeking information to develop an NSF CSSI grant. It will support some genome database software (Tripal) but also basic computational research needs for scientists. If you have a moment to answer a few questions, they would appreciate it: https://tntech.co1.qualtrics.com/jfe/form/SV_0rEroKTEqUW1MSG Meg -- Margaret Staton Associate Professor Department of Entomology and Plant Pathology Office: 154 PBB Mail: 370 PBB, 2505 EJ Chapman Drive Knoxville, TN 37996-4560 she/her/hers 864-506-4515 Mobile mstaton1(a)utk.edu *Advanced Out of Office Notice* *October 11-15, 2021*

4 years, 3 months

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AG2PI Field Day: Precision Livestock Management on Extensive Rangelands

by Scott, Nicole M [AGRON]

Dear AgBioData members, The next AG2PI Field Day is on Wednesday, September 15 from 10:30 AM to 12:00 PM (Central Time, -5 GMT). In this field day, Drs. Hector Menendez and Jameson Brennan will discuss the challenges and opportunities that exist in precision livestock management on extensive rangelands. This discussion will hit themes that are relevant to the animal, plant 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-FD11, 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.. 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 ***

4 years, 3 months

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Help us chart the future of agricultural data! - Sept 1st seminar

by Campbell, Darwin A [AGRON]

Greetings. If you have not yet signed up for the RCN kick-off meeting next Wednesday, it’s not too late, links are below. Also, if you know a person that would be a good fit for the Program Coordinator position, encourage them to apply. All the best, Darwin .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. Dear Researchers, Breeders, Database Providers, Funders, Editors, Students, Software Engineers, and other Scientists, Do you want easy access to better quality data? We are THRILLED to announce that AgBioData (https://www.agbiodata.org/) has received a three-year NSF RCN award to expand our community committed to improving quality and access to agricultural data. New activities will include organizing workshops, establishing new working groups, and developing FAIR curriculum for scientists. We are expanding the consortium and welcome new members, especially students, post-docs, big-data scientists, funding agency scientists, and members of the scientific publishing community interested in solving common FAIR data issues. We invite all of you to an important kickoff All-Hands Meeting on Sept 1st at 10 am PDT (find your local time - https://bit.ly/389VeJA). At this meeting, you will hear about our RCN objectives, the benefits of joining AgBioData, and how YOU can make a difference in the biological data environment for years to come. Please pre-register for this meeting at: https://iastate.zoom.us/meeting/register/tJcld-iqqD4vE9awJKcFGnmHwxtCNc_a7U… We are also hiring a scientist to coordinate AgBioData activities, outreach and curriculum development. Please help us publicize this opportunity! Applications should be submitted by August 31 to https://phoenix-bioinformatics.hirehive.com/job/83452/scientific-program-co…. Thank you! The AgBioData Steering Committee: Jacqueline Campbell, Darwin Campbell (coordinator),Ethy Cannon,Laurel Cooper,Lisa Harper,Eva Huala,Sook Jung,Monica Poelchau,Leonore Reiser,Meg Staton,Marcela Tello-Ruiz

4 years, 3 months

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Job Opening for Agricultural Data Curator

by Piaskowski, Julia (jpiaskowski＠uidaho.edu)

Hello, Would it be possible to send this to the AgBioData listserve? Thank you, Julia Job Opening for Data Curator Statistical Programs in the College of Agricultural and Life Sciences at the University of Idaho is looking to hire a full-time technician to clean and curate a large collection of agricultural data sets for inclusion in a database. The successful candidate will primarily work independently with supervision as needed. Funding is available to support this position for one year and may be extended. Remote candidates will be considered. The pay is $20.33 per hour or higher depending on experience. Job Duties: Curate, clean and prepare agronomic data from crop variety trials conducted across the Pacific Northwest for inclusion into a database. These data sets are drawn from different research programs located across the Pacific Northwestern U.S. The work will involve extensive data validation: checking for data entry errors, resolving naming and spelling discrepancies and defining data validation guidelines for variables. Basic data manipulation steps will compose a large part of the work: bulk import of tables, merging tables and set operations. The successful candidate will work largely independently and will communicate with research programs to resolve data discrepancies and other collaborators regarding best practices. The candidate will also need to coordinate and collaborate with other project members via git for code development supporting data curation. Communicate with project participants about progress and information needs. Participate in regular meetings with collaborators. Develop training materials focused on training collaborators on storage and management of their annual trial data using an existing industry-focused database solution and other relevant tools. Work with the database user community as needed to acquire and/or further develop content that supports routine usage of these tools for data management. As needed, build resources for print and web delivery including written tutorials, live workshops, quick reference pages (“cheat sheets”), and possibly short instructional videos. Required Qualifications: * Experience in working with tabular data. * Experience with spreadsheet software. * Experience with written communications such as reports, manuscripts, conference abstracts, and grant applications. * Experience using git for version control. * Experience in bulk import of files, merging data sets, automated error checking using command line software such as R, bash, python, or OpenRefine. * Experience in R Programming with R base commands and the R Tidyverse. * Experience collaborating with others. To learn more about this position and apply, please visit the University of Idaho job openings website: https://uidaho.peopleadmin.com/postings/32752 __________________________________ Julia Piaskowski, PhD Consulting Statistician Statistical Programs College of Agricultural and Life Sciences 875 Perimeter Dr MS 2337 University of Idaho Moscow, ID 83844-2337 jpiaskowski(a)uidaho.edu<mailto:jpiaskowski@uidaho.edu> julia.piask(a)gmail.com<mailto:julia.piask@gmail.com>

4 years, 3 months

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Help us chart the future of agricultural data!

by Campbell, Darwin A [AGRON]

Dear Researchers, Breeders, Database Providers, Funders, Editors, Students, Software Engineers, and other Scientists, Do you want easy access to better quality data? We are THRILLED to announce that AgBioData (https://www.agbiodata.org/) has received a three-year NSF RCN award to expand our community committed to improving quality and access to agricultural data. New activities will include organizing workshops, establishing new working groups, and developing FAIR curriculum for scientists. We are expanding the consortium and welcome new members, especially students, post-docs, big-data scientists, funding agency scientists, and members of the scientific publishing community interested in solving common FAIR data issues. We invite all of you to an important kickoff All-Hands Meeting on Sept 1st at 10 am PDT (find your local time - https://bit.ly/389VeJA). At this meeting, you will hear about our RCN objectives, the benefits of joining AgBioData, and how YOU can make a difference in the biological data environment for years to come. Please pre-register for this meeting at: https://iastate.zoom.us/meeting/register/tJcld-iqqD4vE9awJKcFGnmHwxtCNc_a7U… We are also hiring a scientist to coordinate AgBioData activities, outreach and curriculum development. Please help us publicize this opportunity! Applications should be submitted by August 31 to https://phoenix-bioinformatics.hirehive.com/job/83452/scientific-program-co…. Thank you! The AgBioData Steering Committee: Jacqueline Campbell, Darwin Campbell (coordinator),Ethy Cannon,Laurel Cooper,Lisa Harper,Eva Huala,Sook Jung,Monica Poelchau,Leonore Reiser,Meg Staton,Marcela Tello-Ruiz

4 years, 3 months

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An opportunity to serve as a panelist in EDI workshop organized by ISB

by Sushma Naithani

Greetings to you all on behalf of the ISB EDI committee! *In mid-April, the Equity, Diversity, and Inclusion (EDI) committee of the International Society for Biocuration (ISB) hosted a screening of the film 'Picture a Scientist'. Sponsored by the Executive Committee, this 90-minute film is an acclaimed documentary that addresses systemic gender bias and racism in the world of science (available on Netflix). We are following this with a workshop on 17 August 2021 entitled “Picture a Scientist”. This workshop will be of great interest to those who were able to view the film, as well as those with an interest in EDI issues. Please let me know if you would like to serve as a Panelist for this workshop in the next two days.EDI workshop aims at a discussion on how to make science more diverse, equitable, and open to all”. The requirements for serving as a panelist are: i) someone who has experience of working as a biocurator and is familiar with the ISB; would like to bring some of the articulation from their work experience as a biocurator to the panel discussion; ii) someone who has watched the movie “Picture a Scientist” and is able to reflect on the movie itself, specific challenges and unique aspects of Biocurators job, and what a society like ISB has done or how it could help in improving the work environment and offering professional opportunities/ mentoring to biocurators from minority and under-represented background. If you have someone else in mind, please forward their names and emails. We prefer to fill this last spot with someone working on plants, but others are also welcome.Best regardsSushma (On behalf of ISB EDI committee)* -- *Sushma Naithani* (she/her) Associate Professor Senior Research Editor-in-chief, Current Plant Biology Dept. of Botany and Plant Pathology Center for Genome Research & Biocomputing *Oregon State University*, Corvallis, OR, 97331 Phone: +1-541-737-8022 Fax: +1-541-737-3573 e-mail: sushma.naithani(a)oregonstate.edu <sushma.naithani(a)oregonstate.edu> e-mail: naithans(a)science.oregonstate.edu <naithans(a)science.oregonstate.edu> webpage: https://agsci.oregonstate.edu/users/sushma-naithani “*He is an emissary of pity, and science, and progress, and devil knows what else.”— Heart of Darkness, Joseph Conrad*

4 years, 4 months

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Next AG2PI Field Day on newly funded AI Institutes

by Scott, Nicole M [AGRON]

Dear AgBioData members, The next AG2PI Field Day is on Wednesday, August 18 from 10:30 AM to 12:00 PM (Central Time, -5 GMT). In this field day, Drs. Baskar Ganapathysubramanian and Ananth Kalyanaraman will discuss their respective, newly funded AI Institutes. These AI institutes were established by USDA National Institute of Food and Agriculture and the National Science Foundation to pursue transformational advances in a range of economic sectors, science and engineering fields. Dr. Ganapathysubramanian will describe the work the AI Institute for Resilient Agriculture (AIIRA<https://aiira.iastate.edu/>) will pursue in the development of digital twins of individual crops and whole fields. Dr. Kalyanaraman will describe the work the Agricultural AI for Transforming Workforce and Decision Support (AgAID<https://agaid.wsu.edu/>) Institute will conduct related to labor, water, weather and climate change. We invite you to register for this Zoom event at https://tinyurl.com/AG2PI-FD10. 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. Space IS limited, so register soon. 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 ***

4 years, 4 months

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AgBioData Webinar - May 5th

by Darwin Campbell

Greetings! I hope you are doing well. Below are the details of the *May 5th AgBioData webinar*, we look forward to seeing you and hope your schedule allows you to join us *next* Wednesday! Darwin Campbell, AgBioData coordinator on behalf of the AgBioData steering committee Jacqueline Campbell Ethalinda Cannon Laurel Cooper Lisa Harper Sook Jung Dorrie Main Monica Poelchau Meg Staton Leonore Reiser Marcela K. Tello-Ruiz •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• *Wednesday, May 5th, 2021*Hosted by Monica Poelchau 1 hour | 1P ET | 12P CT | 11A MT | 10A PT Find your local time: http://bit.ly/3856d6Y 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 *Recommendations from the AgBioData GFF3 working group* Over a year ago, AgBioData convened a discussion on GFF3 formatting issues, led by Scott Cain. This discussion led us to form the AgBioData GFF3 working group. Our goals are to 1) identify common problems with the GFF3 format; 2) recommend solutions for these problems; and 3) promote community adoption of these recommendations, so that data can be formatted in standard ways across databases. Members of AgBioData, the Alliance of Genome Resources, and NCBI have been working on these goals for the past year. We are now ready to receive feedback from the AgBioData community on our recommendations, in order to get traction on the final goal – community adoption of these solutions. In this webinar, we will give an overview of our recommendations and will open up the floor for a stimulating discussion. If possible, please review our recommendations prior to the webinar: https://docs.google.com/document/d/180g1rfC5n_cR6sioG_LFGaUPNmQyDqTsPafVu4g… •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• •• Past webinars can be found here. <https://www.youtube.com/channel/UCwMIJWOX7n_ZFoFpOsmCzgw/videos>

4 years, 4 months

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5
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