Quickstart

Install the CLI, connect an instrument data source, and run your first protocol end-to-end. Estimated time: under 10 minutes with instrument data available. The example below uses a western blot protocol; substitute your own assay name in Step 3.

Step 1 — Install the CLI and initialise a project

Install the Cypher CLI via pip, then run cypher init in your project directory.

~/projects/my-lab — bash
$ pip install cypher-ai Successfully installed cypher-ai-0.4.1 $ cypher init Initializing Cypher AI project... Created .cypher/config.yml Project initialized. API key: set via `cypher auth login`

Step 2 — Connect an instrument

Use cypher connect to link an instrument data source. Supported types include plate readers, qPCR thermocyclers, flow cytometers, sequencers, and generic CSV exports.

~/projects/my-lab — bash
$ cypher connect --instrument plate_reader Detecting plate_reader connector... Connector: BioTek Epoch 2 (CSV export) Data path: ./data/plate_reader/ Connection confirmed. Data fabric updated.

Supported instrument types include: plate_reader, qpcr, flow_cytometer, sequencer, generic_csv. More connectors are added with each release.

Step 3 — Run your first protocol

You can write a protocol YAML manually, or generate one with cypher protocol generate "describe your experiment". Then execute with cypher run. The CLI validates steps against connected instruments before starting.

~/projects/my-lab — bash
$ cypher run --protocol western_blot.yml Loading protocol: western_blot.yml (v1.3) Validating steps against connected instruments... [1/5] Sample Prep ✓ complete [2/5] Gel Electrophoresis ✓ complete [3/5] Transfer ✓ complete [4/5] Blocking ⟳ running (42 min remaining) Log: ./runs/2025-11-14/western_blot_run_3.log

Next steps

With your first protocol running, you can explore the full platform:

  • Generate analysis code with the AI Agent: cypher agent "calculate fold-change for conditions A vs B, normalize to control wells"
  • Search your data fabric by natural language: cypher search "plate reader runs from November 2025 with OD above 1.5"
  • Integrate Cypher into an existing pipeline via the REST API

Questions or issues during setup? Reach the team at [email protected].