AgBioData-LIST November 2023

agbiodata-list@bioinfo.wsu.edu

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2 discussions

REMINDER - Monthly Webinar Next Wed, Nov 1st, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wed, Dec. 6th, at 12 PM CT for our monthly webinar. This webinar will focus on single-cell data and metadata management in livestock and plants Benjamin Cole <https://jgi.doe.gov/our-science/scientists-jgi/benjamin-cole-genomics-of-pl…> , Christopher Tuggle <https://faculty.sites.iastate.edu/cktuggle/>, and Muskan Kapoorand <https://github.com/kapoormuskan>. I have included below more details about the webinar and the Zoom link to attend the webinar. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Abstracts:* *Benjamin Cole (Joint Genome Institute) on "Data management considerations for plant single-cell genomics."* While plants have arrived on the single-cell scene relatively late, the number and complexity of plant single-cell datasets have exploded over the past four years. With that massive increase in data has come a pressing need to ensure accurate documentation of the experimental provenance of plant single-cell datasets, not only for reproducibility but also for reusability in meta-analyses. During this presentation, I will discuss the current state of plant single-cell research as well as the most common practices for data storage. I will also argue for the need for better standards in the field, and what that could potentially enable. *Christopher Tuggle (Iowa State University) & Muskan Kapoor (Iowa State University) on "Single-Cell genomics data incorporation into agricultural G2P research by building a FAIR data ecosystem."* We will describe a pilot-scale project to determine if our current metadata standards for livestock and crops can be used to ingest scRNAseq datasets in a manner consistent with HCA DCP standards and if established resources (e.g., Terra) can be used to analyze the ingested data. Currently, the most comprehensive data ingestion portal for high throughput sequencing datasets from plants, fungi, protists, and animals/humans is Annotare (located at EMBL-European Bioinformatics Institute). For agricultural animal datasets, another EMBL-EBI portal, the FAANG portal, has been developed. scRNAseq data/metadata can be submitted to FAANG using a semi-automated process. We have extended this tool for scRNAseq data so that files can be validated using the HCA DCP metadata and data validation service. These files are incorporated using EMBL-EBI’s HCA DCP ingestion service and transferred to Terra for further analysis. We will also describe a Shiny-based web application, implemented in R and called Shiny-PIGGI, for the single cell-level transcriptomic study of pig immune tissues and peripheral blood mononuclear cells, which will be an important resource for improved annotation of porcine immune genes and cell types ( https://shinypiggi.ansci.iastate.edu). We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem to facilitate single cell-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural 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 Meet anytime 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) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

11 months, 3 weeks

Sign-Up for New AgBioData Working Groups OPEN!!!

by Annarita Marrano

Hello AgBioData community, We are happy to announce that the sign-up for AgBioData working groups is now OPEN! *Please complete this form <https://forms.gle/MeZZrCeSvUywxkQo6> by November 22 at 12 p.m. ET to join one or more of our working groups.* We will have two new working groups starting from January 2023, which are the "*Phenotypic Data Standardization and Management*" and the "*scRNAseq BIOCURATION*" working groups. Two current working groups (i.e., the *DEI Recruiting* and *FAIR Scientific Literature WGs*) are also recruiting new members to join their incredible efforts. You can find more details about them in the form. *We anticipate the commitment will generally be between 2-6 hours per month*, including meeting attendance and offline work (e.g., literature, writing, etc.). This is your opportunity to shape the future of our research community by contributing to developing best practices of data archiving and management that can benefit you and all the other stakeholders. Participating in the AgBioData working groups will also offer you opportunities for - professional networking - leadership skill development - authorship in impactful manuscripts Please share the registration link with anybody that you think can be interested. Thanks, Annarita

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AgBioData-LIST November 2023