Meeting notes¶

A collection of meeting notes.

August 19, 2024
1 min read

Meeting on 2024-08-19

Data Updates

GBIF: plant dataset that we looked at during summit INSDC Host Organism Database
- scraped genetic data from NCBI, Japanese and European nucleotide archives
- Viruses with associated host taxa information
- Lizzie's exploration of a subset of the data: https://github.com/EMLgit/GBIF-viruses
NEON data: sequencing files not well organized: download zipfiles of fasta files. But sampling is well setup for tick disease and tickborn disease in rodents.

Potential collaborators

Colin Carlson https://ghss.georgetown.edu/people/carlson/
Timothee Poisot https://poisotlab.io/
Tad Dallas https://taddallas.github.io/
Shannon Lynch @ UC Davis host shifts due to climate change: https://www.lynchforestpathology.com/about-us
Rachel Penczykowski St. Louis: https://penczykowskilab.com/

Tasks

Rob: List of key questions, data, and outcomes
by the 26^th.
Send example code for downloading

June 10, 2024
1 min read

Meeting on 2024-06-10

Action Items

Rob will work on NEON / reach out to Lizzie
Marie-Josee will check with colleagues on other promising datasets.
Aaron will do a quick review of the literature
- Focus on tightly coupled molecular data, gut/roots/ect on obligates.

Next meeting is on 2024-07-09 at 12:00 Eastern.

May 14, 2024
2 min read

We ultimately landed on a bunch of different possibilites. Probably we want to use genomic data or metagenomic data to look at interactions over time and space, with particular interest in how (a)synchronous interactions are/may be in the future

Day 2: getting into it

INSDC host organism dataset accessible through GBIF

maybe useful virus data records: https://www.gbif.org/dataset/393b8c26-e4e0-4dd0-a218-93fc074ebf4e#description. - The download for 5/15/2024 is on cyverse datastore. (Community Data/iplant_esiil_summit/2024/GBIF/GBIF_0016186-240506114902167.zip)