https://github.com/lsdch/biome
Biodiversity and Occurrences for Molecular Ecology
https://github.com/lsdch/biome
biodiversity conservation database ecology lims molecular occurrences platform taxonomy
Last synced: 3 months ago
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Biodiversity and Occurrences for Molecular Ecology
- Host: GitHub
- URL: https://github.com/lsdch/biome
- Owner: lsdch
- Created: 2025-01-18T09:41:23.000Z (9 months ago)
- Default Branch: main
- Last Pushed: 2025-07-11T09:09:47.000Z (3 months ago)
- Last Synced: 2025-07-11T12:33:50.896Z (3 months ago)
- Topics: biodiversity, conservation, database, ecology, lims, molecular, occurrences, platform, taxonomy
- Language: TypeScript
- Homepage:
- Size: 4.81 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# BiOME : Biodiversity and Occurrences for Molecular Ecology
BiOME is a self-hostable platform (specifically a [LIMS](https://en.wikipedia.org/wiki/Laboratory_information_management_system)) for managing and analyzing taxonomic occurrence data supporting research in ecology and biodiversity.
In ecology, an occurrence is defined as the reported presence of a specific taxon in one location, at a specific time. Generating occurrences typically involves sampling specimens on the field and sorting the specimen by assigning them a taxonomic identification, either using morphological criteria or molecular barcoding.
## Dev environment
### Setup
1. Install golang >= 1.24
2. Setup `GOBIN` environment variable in your shell profile
3. Add it to your `PATH` environment variable
4. Install [air](github.com/cosmtrek/air@latest) to handle hot-reloading of the server:
```bash
go install github.com/cosmtrek/air@latest
```
5. Database setup
- install [Gel CLI](https://docs.geldata.com/reference/cli)
- run `gel project init` in the project directory
6. Client setup
- Install `nodejs >= 23`
- Install [pnpm](https://pnpm.io/installation)
- run `pnpm i` in the `/client` directory
### Running the local server
- run `air` in the `/server` directory
- run `pnpm dev` in the `/client` directory
## Built with
