- AgBioData-LIST - Main Bioinformatics Lab

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, 5 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, 5 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, 5 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, 6 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, 6 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, 6 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, 6 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, 7 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, 7 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, 7 months

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