A lightweight, high-performance Laboratory Information Management System (LIMS) for synthetic biology and automated high-throughput labs. It tracks projects, strains, samples, plates and experimental results in one place, and exposes a REST API so both humans (via the web UI) and lab automation can work with the same data.

The backend is written in OCaml for type safety, with a minimal Vanilla JS frontend and PostgreSQL for storage.

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Quick start (how to use it)

Option A: Docker (fastest)

docker compose up --build

This starts the app (port 8080), PostgreSQL (port 5433) and Adminer (port 8090). Open http://localhost:8080 and log in.

Option B: Local install

Prerequisites: OCaml 5.x (via opam), dune, PostgreSQL 15+.

git clone https://github.com/exfab/exlab.git
cd exlab
opam install . --deps-only
export DATABASE_URL=postgresql://user:password@localhost:5433/exlab_dev
dune exec exlab

Then open http://localhost:8080 and log in.

Logging in

On first run the database is migrated automatically. If no users exist, a default administrator account is created:

• Email: admin@exlab.com
• Password: admin123

Override these with the DEFAULT_ADMIN_EMAIL and DEFAULT_ADMIN_PASSWORD environment variables. To start with example projects, strains and plates, set AUTO_POPULATE_TEST_DATA=true (Docker Compose enables this by default).

Trying it with sample data: point your browser at the /docs page for an interactive API reference, and see examples/ for CSV files you can bulk import through the UI.

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What it can do

Core data model

• Projects – top-level grouping for experiments and team management; each project can have its own team of users and a dashboard.
• Strains – organism records with lineage and cross-references to external databases (e.g. NCBI).
• Samples – physical or virtual biological materials, linked to projects and strains, with optional parent/child (lineage) relationships.
• Plates & Wells – multi-well plates (24, 48, 96, 384-well) with well-coordinate mapping and dashboard views.
• Results – extensible experimental measurements built from categories and definitions (e.g. an "OD600" definition), recorded against samples or plates.
• Products – a catalog of standard labware and reagents.

Working with plates

• Create plates and assign/unassign samples to wells, by coordinate or by bulk operations.
• Layouts: upload a plate layout as an alphanumeric list (A1 → sample), a numeric list, or a visual matrix grid (see examples/plate_layout*.csv).
• Plate planner and multi-plate planner: plan new plates / transfers and generate a transfer map in a few steps.
• Auto-fill wells, bulk-create multiple plates at once, and export a plate's data.

Recording results

• Define result categories and result definitions (with a short_id used in bulk uploads).
• Add results against individual samples or entire plates.
• Bulk-import results from CSV (see examples/example_results*.csv).
• Export results for a project.

Bulk import & export

ExLab supports CSV (and some JSON) for high-throughput workflows. Ready-made templates live in examples/:

File	Purpose
example_products.csv	Bulk-import labware and reagents
example_strains.csv	Bulk-import strains
example_strains.json	Bulk-import strains with external DB links
example_samples.csv	Bulk-create samples within a project
example_results.csv	Bulk-import results against samples
example_results_plate.csv	Bulk-import results against plates
plate_layout*.csv	Set plate layouts (list, numeric, or matrix)
bulk_plate_creation.csv	Generate multiple plates + assign samples in one upload

Access control

Role-based access control (RBAC) with four roles — Admin, Lab Manager, Project Manager, Project User — enforced through encrypted cookie sessions and email/password authentication (Argon2 hashing).

API

The server exposes a versioned REST API under /api/v1 covering all resources above. An interactive reference is served at /docs (OpenAPI/Scalar), and the spec is available at /openapi.yaml.

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Project layout

src/core/      Domain types, pure logic, serialization
src/storage/   PostgreSQL access (Caqti) and code-based migrations
src/server/    Dream web framework, REST routes, auth middleware
bin/           Executable entry point (DB wait → migrate → seed → serve)
test/          Unit and integration test suites
examples/      CSV/JSON templates for bulk import

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Development

dune build                 # build everything
dune exec exlab            # run the server
dune runtest -f            # run all tests (needs PostgreSQL on localhost:5433)
dune fmt                   # format with ocamlformat
dune build @fmt            # check formatting without writing

Environment variables (with defaults) are documented in AGENTS.md.

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Documentation

The API is documented with an OpenAPI specification, served as an interactive reference inside the running app. Start the server, then visit http://localhost:8080/docs (or the /docs link in the frontend navigation) to browse and try every endpoint. The raw spec is available at /openapi.yaml. Sample data and CSV templates for bulk import live in examples/.

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Funding

This material is based on work performed at the NSF ExFAB BioFoundry and supported by the National Science Foundation under Award No. DBI-2400327. ExLab is developed in collaboration between UC Santa Barbara and UC Riverside.