- AgBioData-LIST - Main Bioinformatics Lab

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, 4 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, 5 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, 5 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, 5 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, 5 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, 5 months

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Open call: AG2PI Industry Field Days

by Scott, Nicole M [AGRON]

Dear AgBioData members, Agricultural Genome to Phenome Initiative is sending out this open call for two upcoming field days that focus on private industry (includes NGOs and scientific societies) and their collaborations with researchers outside of their organizations. The first call is to businesses looking to exhibit how their technologies provide a solution to an agricultural genomes-to-phenomes adjacent or data pipeline problem by demonstrating the science behind it. The second is a call for industry partnerships, particularly with academic researchers, and how these have led to advances in genomes-to-phenomes research or other related work. Details for each field day are below: 1. AG2PI field day: industry showcase AG2PI invites companies to submit a proposal for an upcoming industry showcase field day scheduled for October 20, 2021 from 10:30 am - 12:00 pm Central Time (GMT -5). This field day will serve as an exhibition of available technologies designed for the AG2P community; selected presenters will demonstrate the science behind their products or services. These presentations may not be used to sell or promote products beyond explaining their use and innovation. This call is open to all companies that wish to apply; however, it should be acknowledged that participation in this event, if selected, is in no way an endorsement from AG2PI. Selected presentations will be limited to 15 minutes, including time for questions. Presentations should focus on the science behind the product or service, how these products or services help advance AG2P research and should include a real-world example of the product or service in use. To apply, fill out this form in Smartsheets: https://app.smartsheet.com/b/form/6eb06e83cba74146a9707ffd453ee867 Applications are due September 1, 2021 1. AG2PI field day: industry-academic collaborations AG2PI invites companies to submit a proposal for an upcoming industry-academic collaborators field day scheduled for November 17, 2021 from 10:30 am - 12:00 pm Central Time (GMT -5). This field day will serve as an exhibition of current collaborations as well as an opportunity for companies to describe the types of collaborations they would like to create. AG2PI recognizes the need to bridge industry and academic needs and pipelines; however, selection to participate in this event is not equivalent to an endorsement from AG2PI. The purpose of this event is to bring together potential collaborators to accelerate the innovation companies and academics are already achieving. Companies seeking collaborators to improve or expand their product lines and/or workforce will have a platform for describing their needs while companies currently with collaborators will have the opportunity to share their successes with the community. This event will also present a network of education partners and pipelines. To apply, fill out this form in Smartsheets: https://app.smartsheet.com/b/form/6eb06e83cba74146a9707ffd453ee867 Deadline for applications is October 1, 2021. Please reach out with any questions by responding to this email or going to our Contact Us page at https://www.ag2pi.org/contact-us/. ------------------------ 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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Fwd: Reminder: AG2PI Field Day on breeding challenges in G2P, 7/21 @ 10:30 CDT!

by Darwin Campbell

---------- Forwarded message --------- From: Scott, Nicole M [AGRON] <nmscott(a)iastate.edu> Date: Mon, Jul 19, 2021 at 11:58 AM Subject: Reminder: AG2PI Field Day on breeding challenges in G2P, 7/21 @ 10:30 CDT! To: Scott, Nicole M [AGRON] <nmscott(a)iastate.edu> Dear AG2PI member, This is a reminder that the next AG2PI Field Day is on Wednesday, July 21 from 10:30 AM to 12:00 PM (Central Time, -5 GMT). In this field day, Dr. Amit Dhingra will share two case studies in G2P that focus on the breeding challenges in fruiting trees. During this event, he will describe how his group is working to rapidly generate novel traits and perform wide crosses in species across different ecological adaptations. Challenges include mutation breeding and the limitations of breeding in a controlled environment. We invite you to register for this Zoom event at https://tinyurl.com/AG2PI-FD9. Upon registration, you will receive a confirmation email with information about joining the meeting. A link to join the meeting will also be provided the day of the event on the AG2PI website <http://ag2pi.org>. 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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Fwd: AG2PI seed grant applications open!

by Darwin Campbell

Greetings! I hope you are doing well and enjoying your summer. Here's a small seed grant opportunity that might be of interest to you. All the best, Darwin AgBioData Program Coordinator ---------- Forwarded message --------- From: Scott, Nicole M [AGRON] <nmscott(a)iastate.edu> Date: Mon, Jul 19, 2021 at 3:23 PM Subject: AG2PI seed grant applications open! To: Scott, Nicole M [AGRON] <nmscott(a)iastate.edu> Dear Colleagues and AG2PI 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 have launched 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 second round of the AG2PI seed grant program aims to fund around twelve (12) awards across three levels of support: Emerging (funds up to $20,000), Enabling (up to $50,000), and Establishing (up to $75,000). Applications will be due by 11:59pm CDT on Sunday, September 19th. The anticipated start date for funded projects is November 29, 2021 and each project may be 6-15 months in duration, depending on the funding level. Further details regarding the request for proposals, application and review can be found at the AG2PI website (https://www.ag2pi.org/seed-grants/). AG2PI will be, again, hosting a Seed Grant Conference on August 12. This conference will provide an overview of our revised seed grant mechanism, examples of projects from the *three* *new focus areas* and will provide an opportunity to ask questions regarding the seed grants. Additionally, there will be 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. Additional details will be available on our “Workshops & Activities” page as we continue to plan this event. 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. 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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Fwd: AG2PI training workshop: Plant Phenotyping Pipeline

by Darwin Campbell

Good morning. Passing this training opportunity along. I hope your day goes well. Darwin AgBioData Program Coordinator <><><><><><><><><><><><><><><><><><><><><><><><><><><><> Dear AG2PI member, Agricultural Genome to Phenome Initiative (AG2PI <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ag2pi.org_&d=DwMFA…>) invites you to register for our next training workshop, “Phenomic Data Processing Using Machine Learning, Distributed Computing & Container Technology”, to be held July 22, 2021, from 1 PM to 3 PM (CDT; GMT -5). In this CyVerse-hosted workshop, the PhytoOracle team will show how to leverage their pipelines to process proximal and remote-sensing data for plant phenotyping. They will showcase two pipelines that leverage distributed computing, machine learning, and container technology. First, they will run through their thermal pipeline, which detects individual plants in thermal images and runs Kmeans clustering to collect individual plant temperature values. Then, they will run through their hyperspectral pipeline, which detects Spectralon reflectance reference targets and calculates plot-level reflectance values. You can access registration information for the workshop through the AG2PI website: https://www.ag2pi.org/workshops-and-activities/workshop-2021-07/ but you will need to register through CyVerse (if you don’t already have a free CyVerse account, you can create one here <https://cyverse.org/discovery-environment>). A recording will be made available on the AG2PI workshop webpage soon after the conclusion of the event. *This workshop will be limited to 50 participants*. Please share the attached flyer with your colleagues or students and encourage them to attend. 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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AgBioData-LIST