SampleTown: an open-source, MIxS-native laboratory information management system for environmental DNA, from field collection to sequence archive

Environmental DNA (eDNA) studies produce a chain of physical and digital records—sites, water samples, filters, extracts, PCR plates, libraries, sequencing runs and analyses—that must stay linked from the field to a public sequence archive. In practice that chain is kept in spreadsheets and notebooks, and contextual metadata are lost or reformatted at each hand-off, which limits reuse of archived sequences. We present SampleTown, a web-based laboratory information management system (LIMS) that stores sample metadata under Minimum Information about any (x) Sequence (MIxS) slot names directly, rather than mapping to the standard at submission time. The MIxS 6.3 LinkML schema (786 slots, 12 checklists, 23 extensions, 276 checklist–extension combination classes) is compiled into runtime indices that drive required-field grouping and highlighting on data-entry forms, row-level validation on import, and column selection on export. SampleTown imports NCBI BioSample templates, spreadsheets and public archive accessions (BioProject, BioSample, experiment, run or GenBank record), reconciling ENA and NCBI records, and exports MIxS/BioSample and SRA submission sheets. Field and bench workflows include plate-based PCR and library entry, QR-code labels printed to sheet or thermal printers, a camera or handheld scanner, an offline sample-capture wizard, and a server mode for ship or field-station networks without internet access. Permits and community agreements are first-class records scoped to sites and date ranges, sensitive locations are coarsened on export, and permit identifiers travel with exported records, supporting FAIR, CARE and OCAP® commitments. One installation serves many isolated labs with per-lab roles, and each lab can keep versioned backups in, and synchronize across installations through, a GitHub repository. SampleTown is written in TypeScript (SvelteKit, SQLite), released under the MIT License, and available at https://github.com/SampleTown-org/eDNA-SampleTown, with a hosted instance at https://edna.sampletown.org.