# Build Opentrons Protocols for Flex and OT-2

Designing reliable robot protocols requires precise API, labware, pipette, and module details. This skill provides focused guidance and templates for Opentrons Flex and OT-2 workflows.

## Install

```bash
npx skillstore add davila7/opentrons-integration
```

## Metadata

- Status: approved
- Slug: davila7-opentrons-integration
- Skillstore revision: r2
- Version status: missing
- Tree hash: 6e7760b4ed7f83b06368f901d7e722895abdd324372b4548e80be44bd50287ff
- Author: davila7
- GitHub username: davila7
- License: MIT
- Repository: https://github.com/davila7/claude-code-templates/tree/main/cli-tool/components/skills/scientific/opentrons-integration
- Ref: c43861a65bb95efcae259cd161c9d6f4dc7eec6f
- Supported tools: Claude, Codex, Claude Code
- Audit status: complete
- Agent install advisory: allowed
- Manual install advisory: allowed
- Artifact signature: available
- Audit attestation: unavailable
- Human verification: not\_verified
- Risk factors: external\_commands
- Quality score: 80
- Quality tier: silver
- Public page: https://skillstore.pages.dev/skills/davila7-opentrons-integration
- Manifest: https://skillstore.pages.dev/api/skills/davila7-opentrons-integration/manifest

## Capabilities

- Creates standard Python protocol structures with metadata, requirements, and run functions.
- Configures Flex and OT-2 pipettes, labware, adapters, deck slots, and tip racks.
- Guides transfer, distribute, consolidate, mix, air-gap, and flow-rate operations.
- Supports temperature, magnetic, heater-shaker, thermocycler, and plate-reader modules.
- Provides templates for basic transfers, serial dilution, plate replication, and PCR setup.

## Use Cases

- Automate Routine Pipetting: Create a protocol for transfers, dilutions, or plate replication with explicit labware and tip handling.
- Prepare PCR Reactions: Design a PCR setup and thermocycler workflow with reagent distribution, sample addition, and cycling stages.
- Standardize Protocol Code: Turn an experimental procedure into a structured Protocol API v2 implementation for simulation and review.

## Prompt Templates

### Create a Basic Transfer

```
Create an Opentrons {robot} protocol that transfers {volume} microliters from {source wells} to {destination wells}. Use {pipette} and replace tips {tip policy}.
```

### Design a Serial Dilution

```
Design a {dilution factor} serial dilution across {plate rows}. Specify diluent volume, transfer volume, mixing, tip policy, labware, and deck layout.
```

### Build a PCR Workflow

```
Build a Flex PCR protocol for {sample count} samples. Include master mix distribution, sample transfer, thermocycler temperatures, cycle count, controls, and final hold.
```

### Optimize a Complex Protocol

```
Review this Opentrons procedure: {procedure}. Propose a collision-aware deck layout, pipette allocation, tip strategy, flow rates, module sequence, pauses, and simulation checks.
```

## Limitations

- The skill does not connect to a robot or execute protocols.
- Examples use Protocol API 2.19 and may require updates for other software versions.
- Users must supply validated labware, volumes, deck positions, and experiment parameters.
- Simulation, calibration, contamination review, and physical run validation remain required.

## Best Practices

- Simulate every protocol and resolve deck, labware, volume, and tip errors before robot execution.
- Use verified labware definitions, explicit API versions, meaningful labels, and documented liquid volumes.
- Review contamination boundaries, pipette limits, module states, pauses, and final deactivation steps.

## Anti Patterns

- Do not run generated protocols on hardware without simulation and human review.
- Do not reuse tips across samples when contamination or carryover would invalidate results.
- Do not assume example deck positions, labware, temperatures, or volumes match a specific experiment.

## Security Audit

- Audited at: 2026-07-23T14:42:19.286\+00:00
- Summary: All 100 static findings are false positives caused by laboratory terms, Markdown code fences, and inline Python identifiers. The reviewed content uses documented Opentrons APIs and contains no shell execution, host reconnaissance, prompt injection, or hidden data access.

## Stats

- Views: 466
- Downloads: 9
- Favorites: 0
- Popularity score: 0