Choosing the Right Protocol

You have a hypothesis. Now you need a way to test it. This tutorial covers how to select from Litmus standard templates, customize them, or design a custom protocol.

The Protocol Decision Tree

Do you know exactly what assay you need?
├── YES → Is it a common, standardized assay?
│         ├── YES → Use a Litmus template
│         └── NO  → Submit a custom protocol
└── NO  → Request protocol design assistance

Most users fall into one of three categories:

Expert in the field: Knows the exact protocol, submits custom
Knows the assay type: Uses a template with parameters
Has hypothesis, needs guidance: Requests protocol design

Option 1: Standard Templates

Litmus maintains validated templates for common experiment types. Using a template means:

Faster matching with qualified operators
Predictable pricing
Known turnaround times
Quality-controlled protocols

Example: Enzyme Inhibition Assay

If your hypothesis is "Compound X inhibits Enzyme Y," you'd use the enzyme inhibition template:

{
  "protocol": {
    "type": "standard_template",
    "template_id": "enzyme-inhibition-colorimetric-v1",
    "template_parameters": {
      "enzyme": "β-galactosidase",
      "enzyme_source": "E. coli, Sigma G4155",
      "enzyme_concentration": "0.5 U/mL",
      "substrate": "ONPG",
      "substrate_concentration": "4 mM",
      "compound_concentrations_uM": [0, 0.1, 1, 10, 100, 1000],
      "incubation_time_minutes": 30,
      "incubation_temperature_C": 37,
      "detection_wavelength_nm": 420,
      "buffer": "Z-buffer, pH 7.0",
      "replicates": 3
    },
    "materials": [
      {
        "name": "Test compound",
        "specification": "≥95% purity, dissolved in DMSO",
        "quantity": { "value": 10, "unit": "mg" },
        "provided_by_requester": true
      }
    ]
  }
}

The template defines the protocol steps. You just fill in the parameters.

Browsing Available Templates

Use the API to find templates:

GET /templates?category=biochemistry&bsl_level=BSL-1

Or browse by common experiment types:

Enzyme assays: inhibition, kinetics, activity
Microbiology: MIC/MBC, growth curves, zone of inhibition
Cell biology: viability, proliferation, cytotoxicity
Molecular biology: PCR, gel electrophoresis, cloning verification
Analytical: HPLC, mass spec, spectroscopy

Option 2: Custom Protocol

If you have a specific protocol that's not templated, submit it in full:

{
  "protocol": {
    "type": "custom",
    "custom_protocol": {
      "title": "Modified Kirby-Bauer Disk Diffusion",
      "version": "1.0",
      "steps": [
        {
          "step_number": 1,
          "action": "Prepare Mueller-Hinton agar plates. Pour 25mL of molten MH agar into 100mm Petri dishes. Allow to solidify at room temperature for 30 minutes.",
          "duration": { "value": 30, "unit": "minutes" },
          "temperature": { "value": 25, "unit": "C", "tolerance": 5 },
          "expected_outcome": "Solid, even agar surface with no bubbles"
        },
        {
          "step_number": 2,
          "action": "Prepare bacterial inoculum. Suspend colonies from overnight culture in sterile saline to 0.5 McFarland standard (~1.5 × 10^8 CFU/mL).",
          "critical_parameters": ["McFarland standard must be 0.5 ± 0.05"],
          "expected_outcome": "Turbid suspension matching 0.5 McFarland"
        }
      ],
      "safety_notes": [
        "BSL-2 practices required for handling bacterial cultures",
        "Dispose of all materials in biohazard waste"
      ]
    }
  }
}

Custom Protocol Requirements

Your protocol must include:

Numbered steps with clear actions
Critical parameters that must be followed exactly
Expected outcomes so the operator knows if it's working
Materials list with enough specificity to source correctly
Equipment list so we can match you with capable operators

Option 3: Protocol Design Requested

Don't know the exact protocol? That's fine. Describe what you need to accomplish:

{
  "protocol": {
    "type": "protocol_design_requested",
    "protocol_design_brief": "I need to test whether my compound (a small molecule, MW ~350, soluble in DMSO up to 10mM) has antibacterial activity against E. coli and S. aureus. I want to determine the minimum inhibitory concentration (MIC) if there is activity. I have about 50mg of compound available. Budget is flexible up to $800.",
    "materials": [
      {
        "name": "Test compound",
        "specification": "Small molecule, MW 350, >95% purity",
        "quantity": { "value": 50, "unit": "mg" },
        "provided_by_requester": true
      }
    ]
  }
}

When you request protocol design:

Litmus reviews your hypothesis and brief
We propose a protocol (usually within 48 hours)
You review and approve before execution begins
Price is confirmed with the protocol proposal

Materials: Who Provides What?

Materials can be:

Provided by requester: You ship them to the operator
Sourced by operator: Included in the quoted price

When to Provide Materials

Provide materials when:

It's your proprietary compound
It's a specific lot you need tested
It's not commercially available
You already have it and it's cheaper than buying new

Material Shipping Requirements

If you're providing materials:

{
  "name": "Test compound ABC-123",
  "specification": "≥95% purity by HPLC, lot #2024-001",
  "quantity": { "value": 25, "unit": "mg" },
  "provided_by_requester": true,
  "storage_requirements": "-20°C, protected from light",
  "cas_number": "123456-78-9"
}

You'll receive shipping instructions after an operator claims your job.

Replicates: How Many Do You Need?

Technical Replicates

Same sample measured multiple times. Controls for measurement variability.

Minimum: 3 (allows outlier detection)
Typical: 3-6

Biological Replicates

Independent samples (different cell passages, different bacterial colonies, etc.). Controls for biological variability.

Minimum: 1 (if you just need a preliminary answer)
Recommended: 3 (for publishable results)

{
  "replicates": {
    "technical_replicates": 3,
    "biological_replicates": 3
  }
}

Cost implication: More replicates = more materials, time, and cost. Start with fewer for preliminary experiments, increase for definitive tests.

Exercise Answers (from Previous Tutorial)

1. "Is green tea extract good for cells?" Better: "Does 100μg/mL green tea extract (EGCG-standardized) increase HeLa cell viability by ≥20% after 24-hour exposure to 100μM hydrogen peroxide?"

2. "Does temperature matter for enzyme activity?" Better: "Does increasing temperature from 25°C to 37°C increase the Vmax of purified alkaline phosphatase by ≥50% when measured with pNPP substrate?"

3. "Can bacteria grow in salt water?" Better: "Can E. coli K-12 maintain >10^6 CFU/mL viability after 24 hours in LB medium supplemented with 5% NaCl at 37°C?"

Next Steps

You have a hypothesis and a protocol. The next tutorial covers acceptance criteria, constraints, and actually submitting your experiment.

Quick Reference: Protocol Checklist

Protocol type selected (template, custom, or design requested)
All required parameters filled (for templates)
Steps are clear and numbered (for custom)
Materials list complete with specifications
Equipment requirements specified
Replicate numbers defined
Materials shipping requirements clear (if providing)
Safety requirements within BSL-1/2

Hypothesis Formulation Submission & Results