lab-workflow

I need to connect protocols, records, and lab automation platforms

Connect protocols.io, Benchling, Opentrons, Pylabrobot, and experiment logs into one traceable execution chain.

Who it helps

Wet-lab groupsAutomation platform usersResearchers standardizing experiment logs

Bring these materials

Protocol or SOPSample, reagent, or plate layout informationInstrument platform or API notesExperiment log template

Skills used

sa.protocolsio-integrationsa.benchling-integrationsa.opentrons-integrationsa.pylabrobotns.nature-experiment-log

Before you start

Install the Skills for this workflow

Choose your system and agent, then run the command in your terminal. After installation, send the prompts below to your agent.

System
Agent
curl -sSL https://paperskills.com/scripts/paperskills-install.sh | bash -s -- \
  --tool codex \
  --skills sa.protocolsio-integration,sa.benchling-integration,sa.opentrons-integration,sa.pylabrobot,ns.nature-experiment-log \
  --registry https://paperskills.com/api/registry

Recommended workflow

Step 1 · sa.protocolsio-integration

Organize protocol and materials

View skill

Task for your agent

Use protocolsio-integration to split the SOP into steps, materials, parameters, cautions, and version history, flagging fields that need human confirmation.

Expected outputs

Structured protocolMaterials listConfirmation list

Step 2 · sa.benchling-integration

Connect the lab data platform

View skill

Task for your agent

Use benchling-integration to design mappings for entities, inventory, ELN entries, and query fields so results flow back into project records.

Expected outputs

Benchling mappingData fieldsReturn-flow rules

Step 3 · sa.opentrons-integration

Draft automation execution

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Task for your agent

Use opentrons-integration or pylabrobot to turn key steps into a robot protocol draft with deck layout, liquid transfers, checkpoints, and simulation checklist.

Expected outputs

Robot protocol draftDeck layoutSimulation checklist

protocolsio-integration

Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.

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benchling-integration

Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with benchling-sdk or the v2 API.

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opentrons-integration

Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons protocols, official API compatibility. For multi-vendor automation or broader equipment control use pylabrobot.

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pylabrobot

Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation. For Opentrons-only protocols with official API, opentrons-integration may be simpler.

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nature-experiment-log

标准化实验日志记录——接收原始材料（图/语音/文字），产出带 YAML frontmatter 的标准日志到 Obsidian vault。需配合飞书 CLI 或手动输入使用。

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Life science dataCustom research agents