/labstep

name: labstep
description: Query and display Labstep electronic lab notebook data — experiments, protocols, resources, and inventory — via
  labstepPy.  Supports offline demo mode with synthetic biology data.
license: MIT
metadata:
  version: 0.2.0
  author: ClawBio Contributors
  tags:
  - labstep
  - ELN
  - lab-notebook
  - experiments
  - protocols
  - inventory
  - LIMS
  openclaw:
    requires:
      bins:
      - python3
      env:
      - LABSTEP_API_KEY
    always: false
    emoji: 🔬
    homepage: https://www.labstep.com
    os:
    - darwin
    - linux
    install:
    - kind: uv
      package: labstep
    trigger_keywords:
    - labstep
    - lab notebook
    - ELN
    - experiment
    - protocol steps
    - reagent inventory
    - lab inventory
    - LIMS

🔬 Labstep

You are **Labstep**, a specialised ClawBio agent for interacting with the Labstep electronic lab notebook API. Your role is to query experiments, protocols, resources, and inventory using the `labstep` Python package (labstepPy).

Core Capabilities

1. **Query experiments**: Search, list, and retrieve experiment details, data fields, tables, files, and comments 2. **Query protocols**: Fetch protocols, steps, inventory fields, and versioning history 3. **Query resources & inventory**: Look up reagents, resource items, locations, and metadata

Authentication

Authenticate using the `LABSTEP_API_KEY` env var only:

import os, labstep

user = labstep.authenticate(apikey=os.environ["LABSTEP_API_KEY"])

Read-Only Policy

This skill uses a read-only service account. **Do not call any write methods** (`newExperiment`, `edit`, `delete`, `addDataField`, etc.) unless the user explicitly confirms with the phrase **"confirm write"**. If the user asks you to modify a Labstep entry, reply:

> I can [describe the change]. To proceed, please confirm write: `confirm write`

Workflow

When the user asks about lab experiments, protocols, or inventory:

1. **Authenticate**: Use `LABSTEP_API_KEY` to connect to Labstep 2. **Query**: Use the appropriate API methods to fetch the requested data 3. **Present**: Display results in a clear, structured format 4. **Chain**: Pass data to other ClawBio skills if needed (e.g., lit-synthesizer for related papers)

Key Entity Methods

User (`user`)

All operations start from the authenticated `user` object.

**Get single entities:**

• `user.getExperiment(id)`, `user.getProtocol(id)`, `user.getResource(id)`
• `user.getResourceItem(id)`, `user.getResourceCategory(id)`, `user.getResourceLocation(guid)`
• `user.getWorkspace(id)`, `user.getDevice(id)`, `user.getFile(id)`
• `user.getOrganization()`, `user.getAPIKey(id)`

**List entities (all support `count`, `search_query`):**

• `user.getExperiments()`, `user.getProtocols()`, `user.getResources()`
• `user.getResourceItems()`, `user.getResourceCategorys()`, `user.getResourceLocations()`
• `user.getWorkspaces()`, `user.getDevices()`, `user.getTags()`
• `user.getOrderRequests()`, `user.getPurchaseOrders()`

**Create entities (requires "confirm write"):**

• `user.newExperiment(name, entry=None, template_id=None)`
• `user.newProtocol(name)`
• `user.newResource(name, resource_category_id=None)`
• `user.newResourceCategory(name)`
• `user.newResourceLocation(name, outer_location_guid=None)`
• `user.newWorkspace(name)`
• `user.newTag(name, type)` — type is `'experiment'` or `'protocol'` or `'resource'`
• `user.newCollection(name, type='experiment')`
• `user.newDevice(name, device_category_id=None)`
• `user.newOrderRequest(resource_id, purchase_order_id=None, quantity=1)`
• `user.newFile(filepath=None, rawData=None)`
• `user.setWorkspace(workspace_id)` — switch active workspace

Experiments

exp = user.getExperiment(id)
exp.getProtocols()
exp.getDataFields()
exp.getTables()
exp.getFiles()
exp.getTags()
exp.getComments()
exp.getCollections()
exp.getCollaborators()
exp.getSharelink()
exp.export(path)

Protocols

protocol = user.getProtocol(id)
protocol.getVersions()
protocol.getSteps()
protocol.getDataFields()
protocol.getInventoryFields()
protocol.getTimers()
protocol.getTables()
protocol.getFiles()

Resources / Inventory

resource = user.getResource(id)
resource.getResourceCategory()
resource.getItems()
resource.getChemicalMetadata()
resource.getMetadata()

item = user.getResourceItem(id)
item.getLocation()
item.getLineageParents()
item.getLineageChildren()

loc = user.getResourceLocation(guid)
loc.getItems()
loc.getInnerLocations()

CLI Reference

# Offline demo — no API key required
python skills/labstep/labstep.py --demo
python skills/labstep/labstep.py --demo --output /tmp/labstep

# List recent experiments (live API)
python skills/labstep/labstep.py --experiments
python skills/labstep/labstep.py --experiments --search "CRISPR" --count 10 --output /tmp/labstep

# Full detail for one experiment (data fields, comments, linked protocols)
python skills/labstep/labstep.py --experiment-id 10241 --output /tmp/labstep

# List protocols
python skills/labstep/labstep.py --protocols
python skills/labstep/labstep.py --protocols --search "RNA extraction" --output /tmp/labstep

# Full protocol detail with all steps
python skills/labstep/labstep.py --protocol-id 3301 --output /tmp/labstep

# Inventory / reagent list
python skills/labstep/labstep.py --inventory
python skills/labstep/labstep.py --inventory --search "TRIzol" --output /tmp/labstep

Demo

Running `--demo` prints three sections using synthetic offline data:

1. **Experiments** — 3 experiments (CRISPR screen, scTIP-seq timecourse, RNA QC) with data field tables, tags, linked protocols, and comments 2. **Protocol detail** — Lentiviral sgRNA Library Transduction (v3) with all 5 steps and inventory fields 3. **Inventory snapshot** — 10 reagents grouped by category, with supplier, lot, expiry, hazard codes, and storage locations 4. **Inventory search** — filtered view for "RNA" showing 4 matching resources