{"id":29491074,"url":"https://github.com/lsdch/biome","last_synced_at":"2026-05-16T22:32:37.395Z","repository":{"id":304141809,"uuid":"918574939","full_name":"lsdch/BiOME","owner":"lsdch","description":"Biodiversity and Occurrences for Molecular Ecology","archived":false,"fork":false,"pushed_at":"2025-07-11T09:09:47.000Z","size":5040,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-07-11T12:33:50.896Z","etag":null,"topics":["biodiversity","conservation","database","ecology","lims","molecular","occurrences","platform","taxonomy"],"latest_commit_sha":null,"homepage":"","language":"TypeScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lsdch.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2025-01-18T09:41:23.000Z","updated_at":"2025-07-11T09:09:50.000Z","dependencies_parsed_at":"2025-07-11T12:45:04.370Z","dependency_job_id":null,"html_url":"https://github.com/lsdch/BiOME","commit_stats":null,"previous_names":["lsdch/biome"],"tags_count":null,"template":false,"template_full_name":null,"purl":"pkg:github/lsdch/BiOME","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lsdch%2FBiOME","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lsdch%2FBiOME/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lsdch%2FBiOME/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lsdch%2FBiOME/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lsdch","download_url":"https://codeload.github.com/lsdch/BiOME/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lsdch%2FBiOME/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":265437663,"owners_count":23765126,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["biodiversity","conservation","database","ecology","lims","molecular","occurrences","platform","taxonomy"],"created_at":"2025-07-15T13:26:00.816Z","updated_at":"2026-05-16T22:32:37.389Z","avatar_url":"https://github.com/lsdch.png","language":"TypeScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cdiv style=\"display:flex; justify-content: center;\"\u003e\n\u003cimg src=\"./biome_logo.svg\" height=\"100\"/\u003e\n\u003c/div\u003e\n\n# Biodiversity and Occurrences for Molecular Ecology\n\n![Status badge](https://img.shields.io/badge/status-in%20development-orange)\n\n\nBiOME 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.\n\nIn 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.\n\n## Dev environment\n\n### Setup\n\n1. Install golang \u003e= 1.24\n2. Setup `GOBIN` environment variable in your shell profile\n3. Add it to your `PATH` environment variable\n4. Install [air](github.com/cosmtrek/air@latest) to handle hot-reloading of the server:\n\n   ```bash\n   go install github.com/cosmtrek/air@latest\n   ```\n5. Database setup\n  - install [Gel CLI](https://docs.geldata.com/reference/cli)\n  - run `gel project init` in the project directory\n\n6. Client setup\n- Install `nodejs \u003e= 23`\n- Install [pnpm](https://pnpm.io/installation)\n- run `pnpm i` in the `/client` directory\n\n### Running the local server\n\n- run `air` in the `/server` directory\n- run `pnpm dev` in the `/client` directory\n\n## Built with\n\n\u003cdiv style=\"display:flex\"\u003e\n\u003ca href=\"https://vuejs.org/\"\u003e\n\u003cimg src=\"docs/assets/images/vue-js.png\" height=50/\u003e\n\u003c/a\u003e\n\n\u003ca href=\"https://vuetifyjs.com/\"\u003e\n\u003cimg src=\"docs/assets/images/vuetify.png\" height=50/\u003e\n\u003c/a\u003e\n\n\n\u003ca href=\"https://huma.rocks/\"\u003e\n\u003cimg src=\"docs/assets/images/huma.png\" height=50/\u003e\n\u003c/a\u003e\n\n\u003ca href=\"https://www.geldata.com/\"\u003e\n\u003cimg src=\"docs/assets/images/gel.svg\" height=50/\u003e\n\u003c/a\u003e\n\n\n\u003c/div\u003e","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flsdch%2Fbiome","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flsdch%2Fbiome","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flsdch%2Fbiome/lists"}