Example Protocols

Examples live in the OS source snapshot. Use each program with its matching deck configuration. Run the first transfer before trying a complete protocol.

Purpose	Program	Configuration
Two liquid transfers	examples/transfer/transfer.culs	examples/transfer/deck.json
PCR thermal cycling	examples/pcr-benchmark/protocol.culs	examples/pcr-benchmark/deck.json
Static bead-buffer exchange on OT-2	examples/magnetic-buffer-exchange/protocol.culs	examples/magnetic-buffer-exchange/deck.json
Bead-buffer exchange with Flex plate movement	Same bead program	examples/magnetic-buffer-exchange/deck-flex.json
Mixed PCR and bead programs on one resident station	Both programs above	examples/resident-station/deck.json and workspaces.json

PCR

culsma-os run examples/pcr-benchmark/protocol.culs \
  --station-id pcr-demo \
  --host-db run-artifacts/pcr/os.sqlite3 \
  --driver-config examples/pcr-benchmark/deck.json \
  --artifacts-dir run-artifacts/pcr

The example retains 30 cycles and 92 temperature holds. Precision and carryover constraints map to explicitly configured liquid methods and fresh tips. Missing required method settings reject execution; these constraints are not silently discarded.

Magnetic Bead Washing

culsma-os run examples/magnetic-buffer-exchange/protocol.culs \
  --station-id beads-demo \
  --host-db run-artifacts/beads/os.sqlite3 \
  --driver-config examples/magnetic-buffer-exchange/deck.json \
  --artifacts-dir run-artifacts/beads

This is a reduced capture-and-wash workflow with two static washes, including magnetic release, refill and recapture. It is not the full language Module05 benchmark. The Flex configuration adds supported gripper docking/removal operations. Confirmed magnetic commands do not measure bead recovery or assay yield.

See Station Configuration for the shared resident station. Submitted runs retain independent simulated material inputs while station resources continue between jobs.