IMRS Biodiversity Explorer

Live Deployment

The Challenge

For years, the biodiversity records of the Indio Mountains Research Station (IMRS), a 40,000-acre research facility in the Chihuahuan Desert managed by UTEP, were locked away in a static PDF handbook: Natural Resources and Physical Environment of Indio Mountains Research Station.

While authoritative, this format made it difficult for students, researchers, and visitors to quickly identify species, cross-reference data, or prepare for their upcoming trip to IMRS.

The Solution

The IMRS Biodiversity Explorer turns that handbook into a living, interactive website. Anyone such as a student, a researcher, or a curious visitor, can search the station's plants and animals, see where recent sightings have been reported, check how each species is doing conservation-wise, and explore five years of on-site weather. It's the field guide and the data prospective researchers and visitors alike can use to prepare for their trip.

Features

• Species Catalog — search and filter every species ever recorded at the station, in a visual grid or a detailed table.
• Conservation Status — at-a-glance badges show how each species is doing, drawn from NatureServe, the IUCN Red List, and the Texas SGCN (Species of Greatest Conservation Need) list.
• Recent Observations — Real-time integration with the iNaturalist API to display the latest confirmed sightings at IMRS
• Climate & Weather — five years (2020–2024) of the station's weather, charted and filterable by year and season.
• Gazetteer — an interactive map of the named places across the station.

Technology Stack

• Framework: TanStack Start (React) — Router, Query, Table & Virtual
• Styling: Tailwind CSS & ShadCN UI
• Maps: Leaflet / React-Leaflet
• Database: Turso (cloud SQLite) via @libsql/client
• External API: iNaturalist

Also uses Recharts (weather charts), Framer Motion (animation), Zod (validation), and Vercel Analytics / Speed Insights.

Roadmap

• Authentication & Admin Dashboard: Implement secure login for station administrators to manage and update the species index directly (CRUD operations).
• Open Source: The codebase is clean and well-tested; the remaining work is a contribution guide (CONTRIBUTING.md) and setup docs to help other field stations digitize their records.

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Getting Started

Prerequisites

• Node.js (v24, see .nvmrc)
• pnpm (the repo pins a version via the packageManager field)
• SQLite3 (for local database management)

Installation

1. Clone the repository

   git clone https://github.com/missatrox44/imrs.git
   cd imrs

2. Install dependencies

   pnpm install

3. Environment Setup Create a .env file in the root directory:

   cp .env.sample .env

   Note: For local development, you typically only need the DATABASE_URL pointing to your local SQLite file (e.g., file:local.db).

4. Run the development server

   pnpm dev

   Open http://localhost:3001 to view the app.

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Database Setup

The application uses SQLite. In production, we use Turso.

1. Local SQLite Setup (Mac)

Check if SQLite3 is installed:

sqlite3 --version
# If not installed:
brew install sqlite3

Initialize Database:

# Create DB and Table
sqlite3 imrs-species.db

# In SQLite prompt:
CREATE TABLE specimens (
  id INTEGER PRIMARY NOT NULL,
  category TEXT,
  kingdom TEXT,
  phylum TEXT,
  phylum_common_name TEXT,
  sub_phylum TEXT,
  sub_phylum_common_name TEXT,
  class_name TEXT,
  class_common_name TEXT,
  sub_class TEXT,
  sub_class_common_name TEXT,
  order_name TEXT,
  order_common_name TEXT,
  sub_order TEXT,
  sub_order_common_name TEXT,
  family TEXT,
  family_common_name TEXT,
  sub_family TEXT,
  sub_family_common_name TEXT,
  genus TEXT,
  species TEXT,
  authorship TEXT,
  collectors_field_numbers TEXT,
  note TEXT,
  species_common_name TEXT,
  records TEXT,
  iucn_category TEXT,
  natureserve_grank TEXT,
  natureserve_srank_tx TEXT,
  natureserve_id TEXT,
  texas_sgcn TEXT
);

# Import Data (ensure specimens.tsv is in root)
.mode tabs
.headers on
.import specimens.tsv specimens

# Verify
SELECT count(*) FROM specimens;
.exit

2. Migration to Turso (Production)

Turso Migration Guide

Prepare Local DB:

sqlite3 imrs-species.db "PRAGMA journal_mode=WAL;"
sqlite3 imrs-species.db "PRAGMA wal_checkpoint(TRUNCATE);"

Push to Turso:

# Auth
turso auth login
turso config set token "YOUR_TOKEN"

# Import
turso db import imrs-species.db

3. Conservation Status

The iucn_category / natureserve_* columns are populated by a seed script that fetches conservation status from two free sources:

• NatureServe Explorer — no API key. Provides the global G-rank and the Texas subnational S-rank.
• IUCN Red List API v4 — free, but requires a registered token. Set IUCN_API_TOKEN in .env.local. If it's omitted, the script seeds NatureServe only and skips IUCN.

A third source, Texas SGCN (Species of Greatest Conservation Need), comes from the TPWD State Wildlife Action Plan. TPWD has no public API, so you must supply its list as a local CSV at src/data/tpwd-sgcn-list.csv (git-ignored, not committed — a fresh clone won't have it). It's then seeded by a separate script that flags the texas_sgcn column for any specimen whose binomial matches the list. SGCN is binary (listed / not listed), so it renders as a flag badge rather than a 1–5 rank.

These calls happen only at seed time — the app makes no external conservation requests at runtime. The scripts add their columns idempotently (so they're safe on an existing DB); seed-conservation.ts is resumable (it skips species that already have data; pass --force to reprocess all).

# Seed the local DB (NatureServe + IUCN)
IUCN_API_TOKEN=your_token npx tsx scripts/seed-conservation.ts

# Seed the Texas SGCN flag (no token needed)
npx tsx scripts/seed-sgcn.ts

To propagate the seeded data to the existing production Turso DB, update it in place. turso db import only ever creates a new database, so it can't update the live one — instead generate an idempotent migration from the local DB and apply it with turso db shell:

# Generate ALTERs + UPDATEs from the freshly-seeded local DB
{
  echo "ALTER TABLE specimens ADD COLUMN iucn_category TEXT;"
  echo "ALTER TABLE specimens ADD COLUMN natureserve_grank TEXT;"
  echo "ALTER TABLE specimens ADD COLUMN natureserve_srank_tx TEXT;"
  echo "ALTER TABLE specimens ADD COLUMN natureserve_id TEXT;"
  echo "ALTER TABLE specimens ADD COLUMN texas_sgcn TEXT;"
  sqlite3 imrs-species.db "SELECT 'UPDATE specimens SET iucn_category='||quote(iucn_category)||', natureserve_grank='||quote(natureserve_grank)||', natureserve_srank_tx='||quote(natureserve_srank_tx)||', natureserve_id='||quote(natureserve_id)||', texas_sgcn='||quote(texas_sgcn)||' WHERE id='||id||';' FROM specimens WHERE iucn_category IS NOT NULL OR natureserve_grank IS NOT NULL OR natureserve_srank_tx IS NOT NULL OR natureserve_id IS NOT NULL OR texas_sgcn IS NOT NULL;"
} > conservation-updates.sql

# Apply to the production DB (the ALTERs are one-time; ignore "duplicate column" if re-running)
turso db shell <your-db> < conservation-updates.sql
rm conservation-updates.sql

The columns must exist in production for the badges to render. If one is missing the app degrades gracefully (no badge) — it does not error.

Conservation data courtesy of NatureServe Explorer, the IUCN Red List, and the Texas Parks & Wildlife SGCN list.

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iNaturalist Resources

• IMRS Location ID
• API Reference