PASDE Researcher Onboarding

Documentation for researchers joining the Purdue Animal Science Data Ecosystem (PASDE) — the research computing platform maintained by Purdue IT and CoARS (College of Agriculture Research Services) on RCAC's Geddes infrastructure.

This repository collects what a new researcher needs to get productive: how to reach the system, where the data lives, what each dataset contains, and how to analyze it.

Start here

Precision-Dairy-Data-Ecosystem-Researcher-Onboarding.md — the main onboarding document.

It is organized in three parts:

Part	What it covers
1 — Introduction and Contacts	What PASDE is, and who to ask for help
2 — The Geddes JupyterLab Environment	VPN, logging in, notebooks and the terminal, Python 3.11, DuckDB, symbolic links
3 — The Data on Data Depot	What data exists, the `Reference` tree by farm and dataset, Parquet, metadata, transfers, archiving

The short version

Two halves. The data lives on the RCAC Data Depot under /depot/agpasde. The analysis environment is a JupyterLab service on Purdue's Geddes cluster.
You can skip Geddes and mount the depot on your own computer — fine for browsing and smaller datasets.
But use Geddes for the big ones. It has far more compute and memory and reads the depot at high speed. Do your filtering and joining there, then take away only your final dataset.
Access — connect to the Purdue VPN if you are off campus, then log in with your Career Account credentials.
Data — read-only Parquet under /depot/agpasde/data/Reference, generally organized as <farm>/<location>/<vendor>/<dataset>.
Analysis — Python 3.11 with DuckDB, querying Parquet in place. Start from DuckDB-Example.ipynb in ~/sharednotes. R and Apache Spark have been removed.
Joining datasets — use animal_global_id from 00_Animal-Database where it exists; farm-assigned IDs get reused and mistyped.
Read the READMEs — most depot directories carry a README.md with date coverage, provenance, and known gaps. They are more current than any document here.

Contributing

This documentation is expected to drift out of date — vendor systems change, datasets are superseded, and Purdue IT services get renamed. If you hit something wrong or missing, open an issue or a pull request rather than keeping the correction to yourself.

When adding a document, note in this README what it covers and who it is for.

Repository contents

Path	Contents
`Precision-Dairy-Data-Ecosystem-Researcher-Onboarding.md`	Main onboarding document
`media/`	Images referenced by the documentation
`.archive/`	Source documents these files were derived from, kept for reference. Outdated in several respects — verify against the live filesystem.

Questions

Post in the Geddes Jupyter Hub — Q and A and Troubleshooting Teams channel — it reaches fellow researchers, CoARS, and Purdue IT. For data use questions, contact Kirby Kalbaugh (kkalbaug@purdue.edu).

For Data Depot issues specifically — access, permissions, mounting, file recovery — contact RCAC at rcac-help@purdue.edu or https://www.rcac.purdue.edu/help.

PASDE/PASDE-Researcher-Onboarding

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