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
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Topic: AgBioData Monthly Webinar
Time: This is a recurring meeting Meet anytime
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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
