Cloud Labs Tutorial

Litmus integrates with automated cloud laboratories for hands-off experiment execution. This tutorial covers submitting experiments to cloud labs like Enko Cloud Lab (ECL) and Strateos.

What Are Cloud Labs?

Cloud labs are automated facilities where robotic systems execute experiments. Benefits include:

Consistency — Robotic precision reduces variability
Speed — 24/7 operation with no scheduling delays
Scalability — Run many experiments in parallel
Documentation — Automatic logging of all steps

Supported Providers

Provider	Protocol Format	Best For
Enko Cloud Lab (ECL)	SLL	Cell-based assays, qPCR
Strateos	Autoprotocol	High-throughput screening

Checking Provider Capabilities

List Providers

curl https://api.litmus.science/cloud-labs/providers \
  -H "Authorization: Bearer YOUR_TOKEN"

Get Provider Details

curl https://api.litmus.science/cloud-labs/providers/ecl \
  -H "Authorization: Bearer YOUR_TOKEN"

Response:

{
  "id": "ecl",
  "name": "Enko Cloud Lab",
  "supported_experiment_types": [
    "CELL_VIABILITY_IC50",
    "MIC_MBC_ASSAY",
    "QPCR_EXPRESSION"
  ],
  "capabilities": {
    "cell_lines": ["HeLa", "HEK293", "A549"],
    "plate_formats": ["96-well", "384-well"]
  },
  "turnaround_days": {"min": 3, "max": 7}
}

The Translation Process

Cloud labs require experiments in specific protocol formats. Litmus handles translation automatically:

Your Experiment → Interpretation → Translation → Cloud Lab Protocol

Step 1: Validate Compatibility

Before translating, check if your experiment is compatible:

curl -X POST https://api.litmus.science/cloud-labs/validate \
  -H "Authorization: Bearer YOUR_TOKEN" \
  -H "Content-Type: application/json" \
  -d '{
    "intake": {
      "experiment_type": "MIC_MBC_ASSAY",
      "mic_mbc_assay": {
        "target_organisms": ["Escherichia coli"],
        "test_compounds": [
          {"name": "Compound X", "concentrations_ug_ml": [0.5, 1, 2, 4, 8, 16, 32]}
        ]
      }
    },
    "provider_id": "ecl"
  }'

Response:

{
  "valid": true,
  "provider_id": "ecl",
  "warnings": [],
  "estimated_cost_usd": 250,
  "estimated_turnaround_days": 5
}

Step 2: Translate to Protocol

curl -X POST https://api.litmus.science/cloud-labs/translate \
  -H "Authorization: Bearer YOUR_TOKEN" \
  -H "Content-Type: application/json" \
  -d '{
    "intake": {...},
    "provider_id": "ecl"
  }'

Response (ECL/SLL format):

{
  "provider_id": "ecl",
  "protocol_format": "sll",
  "protocol": {
    "name": "MIC Assay - Compound X",
    "steps": [
      {"operation": "dispense", "source": "media", "destination": "plate", "volume": "100uL"},
      {"operation": "serial_dilution", "compound": "Compound X", "factor": 2, "steps": 7},
      {"operation": "inoculate", "organism": "E. coli", "density": "5e5 CFU/mL"},
      {"operation": "incubate", "temperature": "37C", "duration": "18h"},
      {"operation": "measure", "method": "absorbance_600nm"}
    ]
  },
  "estimated_cost_usd": 250
}

Step 3: Submit Experiment

Submit your experiment to Litmus first:

curl -X POST https://api.litmus.science/experiments \
  -H "Authorization: Bearer YOUR_TOKEN" \
  -H "Content-Type: application/json" \
  -d '{
    "experiment_type": "MIC_MBC_ASSAY",
    "hypothesis": {
      "statement": "Compound X inhibits E. coli growth"
    },
    "compliance": {"bsl": "BSL1"},
    "mic_mbc_assay": {...}
  }'

Step 4: Trigger Cloud Lab Translation

curl -X POST https://api.litmus.science/cloud-labs/experiments/exp_abc123/translate \
  -H "Authorization: Bearer YOUR_TOKEN" \
  -H "Content-Type: application/json" \
  -d '{
    "provider_id": "ecl"
  }'

This creates a CloudLabSubmission record tracking the execution.

Tracking Submissions

List Submissions

curl https://api.litmus.science/cloud-labs/submissions \
  -H "Authorization: Bearer YOUR_TOKEN"

Get Submission Status

curl https://api.litmus.science/cloud-labs/submissions/sub_abc123 \
  -H "Authorization: Bearer YOUR_TOKEN"

Submission Status Values

Status	Description
`pending`	Created, not yet sent
`submitted`	Sent to cloud lab
`queued`	Waiting in cloud lab queue
`running`	Experiment in progress
`completed`	Results available
`failed`	Execution error
`cancelled`	Cancelled by user

Protocol Formats

SLL (Symbolic Lab Language)

Used by Enko Cloud Lab. Declarative steps:

{
  "steps": [
    {"operation": "dispense", "source": "reservoir", "destination": "plate", "volume": "100uL"},
    {"operation": "incubate", "temperature": "37C", "duration": "24h"}
  ]
}

Autoprotocol

Used by Strateos. JSON with refs and instructions:

{
  "refs": {
    "plate": {"new": "96-pcr", "store": {"where": "cold_4"}}
  },
  "instructions": [
    {"op": "dispense", "object": "plate", "reagent": "media", "volume": "100:microliter"}
  ]
}

Complete Workflow Example

import requests
 
API_URL = "https://api.litmus.science"
headers = {"Authorization": "Bearer YOUR_TOKEN"}
 
# 1. Define experiment
intake = {
    "experiment_type": "MIC_MBC_ASSAY",
    "hypothesis": {
        "statement": "Compound X inhibits E. coli with MIC < 32 μg/mL"
    },
    "compliance": {"bsl": "BSL1"},
    "mic_mbc_assay": {
        "target_organisms": ["Escherichia coli"],
        "test_compounds": [
            {"name": "Compound X", "concentrations_ug_ml": [0.5, 1, 2, 4, 8, 16, 32]}
        ]
    }
}
 
# 2. Validate for cloud lab
validation = requests.post(
    f"{API_URL}/cloud-labs/validate",
    json={"intake": intake, "provider_id": "ecl"},
    headers=headers
).json()
 
if not validation["valid"]:
    print("Validation errors:", validation["errors"])
    exit(1)
 
print(f"Estimated cost: ${validation['estimated_cost_usd']}")
 
# 3. Submit experiment
experiment = requests.post(
    f"{API_URL}/experiments",
    json=intake,
    headers=headers
).json()
 
exp_id = experiment["experiment_id"]
print(f"Created experiment: {exp_id}")
 
# 4. Translate for cloud lab
submission = requests.post(
    f"{API_URL}/cloud-labs/experiments/{exp_id}/translate",
    json={"provider_id": "ecl"},
    headers=headers
).json()
 
print(f"Cloud lab submission: {submission['id']}")
print(f"Protocol format: {submission['protocol_format']}")

Handling Validation Errors

When validation fails:

{
  "valid": false,
  "errors": [
    {
      "field": "mic_mbc_assay.target_organisms",
      "message": "Organism 'Custom strain' not available at ECL"
    }
  ]
}

Common issues:

Unsupported organism/cell line — Check provider capabilities
Invalid concentrations — Must match available stock dilutions
Missing required fields — Fill in all protocol parameters

Best Practices

Validate first — Always validate before submitting
Check costs — Cloud labs may cost more than manual execution
Review translations — Verify the protocol matches your intent
Monitor submissions — Track status for timely results
Use webhooks — Get notified when experiments complete

Next Steps

Edison Integration — Generate hypotheses automatically
API Reference — Full endpoint documentation
AI Integration Guide — Build automated pipelines

Submission & Results Overview