BioDex is a terminal-native species atlas: part field guide, part taxonomy browser, part cached research notebook.
It opens into a fast three-pane TUI with species portraits, range maps, lineage history, compact biological stats, and two ways to browse: a curated A-Z species list or a taxonomy tree.
Click the preview to open the full demo clip.
- Browse a curated 100-species starter pack with local cached data
- Move through species alphabetically, with auto-loading as you pause on entries
- Switch into taxonomy mode when you want to explore by kingdom, phylum, class, order, family, genus, and species
- View portraits, range maps, lineage, genome metadata, conservation status, and life-history stats in one terminal screen
- Reuse cached SQLite data so repeat browsing stays fast and mostly offline
BioDex is currently built from source.
git clone https://github.com/Jakeelamb/BioDex.git
cd BioDex
cargo build --releaseRun the optimized binary:
./target/release/biodexOptionally install it locally so biodex is available on your PATH:
cargo install --path .Open a specific species:
./target/release/biodex "Homo sapiens"Run from source without keeping a release binary:
cargo run --release -- "Panthera leo"- Rust toolchain
- A modern terminal
- An image-capable terminal for portraits and raster range maps; otherwise BioDex falls back to text placeholders
The examples below assume biodex is on your PATH. If not, use ./target/release/biodex from the repo root.
biodex: open the TUI atAnimaliabiodex "Ailuropoda melanoleuca": open a species directlybiodex --text "Homo sapiens": print species data without launching the TUIbiodex --prefetch: seed the default 100-species hot cachebiodex --prefetch-animals: refresh curated Animalia candidates and cache mediabiodex --import-backbone: import the GBIF backbone for offline taxonomy search, roughly 200 MBbiodex --cache-all-rich: run a long resumable sweep for richer cached species rowsbiodex --stats: show local cache statistics
↑/↓orj/k: move through the active navigatort: switch between the A-Z species list and taxonomy browserEnter/l/→: open the selected entryh/←: move up a taxonomy level/: searchr: refresh from live sourcesf: toggle saved status?: helpq/Esc: quit or close the active panel
BioDex merges public data from several sources and caches the result locally:
| Source | Used for |
|---|---|
| GBIF | Taxonomy matching, backbone import, occurrence counts, continent/range data, and raster map overlays |
| NCBI | Taxonomy IDs, lineage, and genome metadata when available |
| iNaturalist | Preferred species portraits when available |
| Wikipedia | Summaries, descriptions, and fallback life-history extraction |
| Wikidata | Conservation status, aliases, rank hints, and structured life-history fields |
| Ensembl | Supplementary genome statistics when available |
| Ollama | Optional local pass to fill missing life-history fields from cached article text |
| Local curated pack | Starter metadata for the 100-species browsing set |
BioDex stores its local database and media cache under biodex app directories. Species rows, portraits, and range maps are cached after fetch, and the curated browser is designed to feel instant after biodex --prefetch.
Offline taxonomy search depends on the GBIF backbone import:
biodex --import-backboneThat import is larger than the normal starter cache, but it makes search and taxonomy navigation much more useful without repeated network calls.
BioDex is early but usable. The current focus is a fast, polished terminal atlas with strong cached browsing. Future directions include broader curated packs, better offline packaging, and an optional nostalgic desktop/window-shell presentation.
BioDex source code is licensed under the MIT License. See LICENSE.
Species data, images, range maps, and other third-party content fetched or cached by BioDex are not relicensed by this repository and remain subject to the terms of their original sources.