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Day 2 — Data & Methods

Focus: try a few datasets and analyses. Keep it visual, keep it simple. Update the site to reflect what you test.

1) Explore the Data Library & Analytics Library

  • Browse your Data Library for candidate datasets (portals, STAC catalogs, archives). Capture links and notes.
  • Browse your Analytics Library for example workflows (scripts, notebooks).
  • Make edits on Home → docs/index.md under:
  • Data sources we’re exploring: Add 2-4 promising data sources (links + 1-line notes)
  • Methods / technologies we’re testing: Add 2-4 methods/technologies you're testing (stats, models, viz)

2) Transfer or access data via gocmd (if needed)

Use when moving files to/from institutional storage (e.g., CyVerse Data Store).

Install & initialize gocmd (Linux):

# Download latest gocmd and extract
GOCMD_VER=$(curl -L -s https://raw.githubusercontent.com/cyverse/gocommands/main/VERSION.txt); \
curl -L -s https://github.com/cyverse/gocommands/releases/download/${GOCMD_VER}/gocmd-${GOCMD_VER}-linux-amd64.tar.gz | tar zxvf -

# Configure iRODS (accept defaults for Host/Port/Zone; use your CyVerse username)
./gocmd init

# Quick sanity check: can you list your home?
./gocmd ls i:/iplant/home/YOUR_USER

i: indicates an iRODS remote path. Omit i: for local filesystem paths.

Example transfers:

# Single file download (shared path → local ./data/)
./gocmd get --progress -K --icat \
  i:/iplant/home/shared/earthlab/nfs_career/outputs/SUMMER_2024/Buffalo_creek-BC1-06_20_24/Buffalo_creek-BC1-06_20_24_1_all_layers.tif \
  ./data/

# Folder download (entire collection)
./gocmd get --progress -K --icat -r \
  i:/iplant/home/shared/earthlab/nfs_career/outputs/SUMMER_2024/Buffalo_creek-BC3-06_20_24 \
  ./data/

# Upload a results folder to your home
./gocmd put --progress -K --icat -r \
  ./outputs/run_01 \
  i:/iplant/home/YOUR_USER/projects/myproj/outputs/run_01

# Optional sync-like upload to skip unchanged files
./gocmd put --progress -K --icat --diff -r \
  ./outputs/run_01 \
  i:/iplant/home/YOUR_USER/projects/myproj/outputs/run_01

Troubleshooting:

# If a path "is not found", list upward, then drill down to confirm exact names
./gocmd ls i:/iplant/home/shared/earthlab/nfs_career/outputs/SUMMER_2024
./gocmd ls i:/iplant/home/shared/earthlab/nfs_career/outputs/SUMMER_2024/Buffalo*

# Inspect type and permissions if a collection exists but transfers fail
./gocmd stat i:/iplant/home/shared/earthlab/nfs_career/outputs/SUMMER_2024/<EXACT_NAME>

Keep large data out of GitHub. Store externally, link from the Data page.

3) Show early results (visual-first)

  • Add Visuals on Home → docs/index.md:

  • A static figure (PNG)

  • A small GIF for change over time (if you have one)
  • An iframe map or relevant portal view
  • Add brief captions: what it shows and why it matters.
  • Run at least one workflow and capture a shareable output — a plot, table, map, or other scientific product. Save static outputs (PNG, GIF, JPG) to the site, or embed live results (for example, an iframe for an HTML widget or interactive table).
  • Save all of your scripts and notebooks in the code/ folder. This keeps everyone’s work in one place and makes it easy to find later. Don’t worry if your code isn’t perfect—the important thing is to make it runnable and shareable.
  • After you’ve run your code, take a screenshot or save the result as a file. Then add it to the Code page (docs/code.md) so others can see what your code does. Even a quick plot or table is great!
  • On Code (docs/code.md), add a short entry for each workflow: what it does, required inputs, how to run it, and where to view the output (linked image, iframe, or hosted artifact). Use the template below to get started:
### Corridor overlap analysis
**What this code does:** Calculates where infrastructure corridors intersect areas of high biodiversity value.
**Inputs needed:** `data/biodiversity_occurrences.geojson`, `data/infrastructure_corridors.geojson`
**How to run it:**
```bash
python code/corridor_overlap.py
```
**What to look for:** Weighted overlap metrics, summary table, and annotated map layers.
**Results:** [outputs/corridor_overlap.png](outputs/corridor_overlap.png)

5) Day 2 checklist

  • [ ] 2–4 data sources listed with links on Home.
  • [ ] 1–2 methods listed on Home.
  • [ ] At least one prototype visual added.
  • [ ] Code linked from Code page.
  • [ ] Large files moved via gocmd (or linked externally).