OpenLab

A Python platform for controlling an Opentrons liquid handler + a robotic arm to run automated in-vitro wet-lab experiments: pipetting, vortexing, incubation, temperature control, magnetic separation, rocking, tube tightening/inverting, and centrifugation.

Goal

Given a protocol as input, the system:

• generates a materials list, consumables list, and risk assessment
• drives the Opentrons + robotic arm to execute the protocol end to end

Layout

• src/core — orchestration/scheduling
• src/equipment — device drivers (Opentrons, robotic arm, relay board for mag separator/rocker)
• src/safety — risk assessment
• src/inventory — consumables/materials tracking
• src/diagnostics, src/audit — run diagnostics and audit trail
• src/nlp — protocol parsing
• src/notify — run notifications
• src/ui — user interface
• src/data, src/calibration — data handling and instrument calibration
• protocols/ — example protocols (DNA extraction, plasmid miniprep 96-well, sandwich ELISA 384-well, VHH expression + Ni purification 96-well)
• config/hardware_config.yaml — hardware setup (Opentrons IP/port, robotic arm, relay backend); defaults to simulation_mode: true
• docs/BOM.md — recommended hardware bill of materials
• docs/hardware_guide.md — hardware setup guide

Setup

./setup.sh          # creates venv, installs requirements
python main.py       # run

Sensitive values (IPs, credentials) go in a local .env (not committed); config/hardware_config.yaml holds non-sensitive hardware layout and defaults to simulation mode until real hardware is configured.