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lab-automation skill

/skills/lab-automation

This skill helps researchers implement reliable lab automation workflows using open-source Opentrons and commercial platforms for efficient liquid handling and

npx playbooks add skill omer-metin/skills-for-antigravity --skill lab-automation

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Files (4)
SKILL.md
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---
name: lab-automation
description: Patterns for laboratory automation including liquid handling robotics, LIMS integration, protocol development, quality control, and high-throughput workflows. Covers both open-source (Opentrons) and commercial platforms. Use when ", " mentioned. 
---

# Lab Automation

## Identity



## Reference System Usage

You must ground your responses in the provided reference files, treating them as the source of truth for this domain:

* **For Creation:** Always consult **`references/patterns.md`**. This file dictates *how* things should be built. Ignore generic approaches if a specific pattern exists here.
* **For Diagnosis:** Always consult **`references/sharp_edges.md`**. This file lists the critical failures and "why" they happen. Use it to explain risks to the user.
* **For Review:** Always consult **`references/validations.md`**. This contains the strict rules and constraints. Use it to validate user inputs objectively.

**Note:** If a user's request conflicts with the guidance in these files, politely correct them using the information provided in the references.

Overview

This skill provides patterns and practical guidance for laboratory automation, covering liquid-handling robotics, LIMS integration, protocol development, quality control, and high-throughput workflows. It supports both open-source platforms (e.g., Opentrons) and commercial systems, and enforces domain-specific creation, diagnosis, and validation rules from the reference files. The skill is written in Python and designed to produce reproducible, reviewable automation artifacts.

How this skill works

When asked to create an automation pattern, the skill consults references/patterns.md to determine the correct construction approach and preferred building blocks. For diagnosis it inspects failure modes using references/sharp_edges.md to explain likely causes and risks. For reviews and validations it checks constraints and rules in references/validations.md and produces objective validation feedback or remediation steps.

When to use it

  • Designing or implementing liquid-handling protocols for Opentrons or commercial robots
  • Integrating experiments with a LIMS or data-management system
  • Creating or reviewing high-throughput workflows and plate maps
  • Diagnosing recurrent errors, contamination, or timing failures in automation
  • Validating protocols against lab safety and quality constraints

Best practices

  • Always follow patterns/patterns.md as the authoritative construction guide for new protocols
  • Use sharp_edges.md to explain root causes when diagnosing failures or anomalies
  • Run validations from validations.md before executing protocols on robotics hardware
  • Version-control protocol definitions and keep hardware/consumable mappings explicit
  • Start with small-volume dry-runs or simulation before full plate runs to reduce risk

Example use cases

  • Generate an Opentrons protocol that follows established modular patterns and outputs a validated checklist
  • Diagnose a recurring tip-pickup failure by mapping symptoms to causes listed in sharp_edges.md
  • Review a new LIMS integration for metadata mapping and validation rules from validations.md
  • Produce a high-throughput dilution series workflow with explicit QC checks and stop conditions

FAQ

Which file is authoritative when building a new protocol?

Always use references/patterns.md as the primary guide for creation; it defines the supported patterns and block structure.

How do you explain recurring failures?

I map observed symptoms to entries in references/sharp_edges.md to identify likely causes, risk level, and targeted mitigations.

Can you approve a protocol for execution?

I provide objective validation against references/validations.md and recommend remediations, but final execution approval must come from qualified lab personnel.