Biodiversity and Occurrences for Molecular Ecology

BiOME is a self-hostable platform (specifically a LIMS) 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 to handle hot-reloading of the server:

   go install github.com/cosmtrek/air@latest

5. Database setup

• install Gel CLI
• run gel project init in the project directory

6. Client setup

• Install nodejs >= 23
• Install pnpm
• run pnpm i in the /client directory

Running the local server

• run air in the /server directory
• run pnpm dev in the /client directory

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