- AgBioData-LIST - Main Bioinformatics Lab

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, 1 month

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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, 2 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

4 years, 2 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 ***

4 years, 2 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

4 years, 2 months

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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, 3 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, 3 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, 3 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, 4 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, 4 months

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