Manual Protocol Designer
Build a protocol step by step from scratch.
Last updated July 2026
The Manual Protocol Designer is the metadata-and-overview side of the Step Designer. It lets you set a protocol's title, field, objective, and hypothesis, and add or edit steps from scratch with full control over every parameter. It complements AI generation for protocols that require proprietary methods, established SOPs, or highly customized workflows.
Accessing the Designer
Open Designer from the sidebar (or ⌘K command palette). You can start a new protocol or load an existing one with ?protocol=<id>. The page combines protocol metadata, the drag-and-drop step canvas, and one-click access to a simulation and a test run.
Protocol Metadata
Before adding steps, fill in the Protocol Overview at the top of the Design tab:
- Protocol title: a descriptive name for your protocol (editable in the toolbar).
- Scientific field: select from the field dropdown in the toolbar.
- Objective: what does this protocol aim to demonstrate?
- Hypothesis: what do you predict will happen, and why?
Step Types
Each step has a type that defines its role in the workflow:
| Type | Use Case | Special Fields |
|---|---|---|
| Action | A discrete lab procedure (pipetting, spinning, staining) | Duration, temperature, equipment |
| Wait / Incubate | A timed pause (incubation, overnight, equilibration) | Duration, temperature |
| Measurement | Recording a quantitative or qualitative output | Expected output, equipment |
| Decision Gate | Branch point based on a result or criterion | Branch labels and descriptions |
| Parallel Block | Steps that run simultaneously | Duration |
| Safety Check | Required biosafety or compliance verification | Notes, critical flag |
| Note | Contextual annotation or important tip | Description only |
Step Fields
Click any step to expand its edit panel. Available fields per step:
- Title (required): a brief, action-oriented name. e.g. "Wash cells with PBS × 3"
- Detailed Instructions: full procedural text including volumes, concentrations, and technique notes.
- Duration: a numeric value with unit (seconds, minutes, hours, days). Used for timeline estimation and simulation.
- Temperature: in degrees Celsius. Leave blank if ambient.
- Expected Output: what should be visually or measurably observable after this step? e.g. "Cell pellet visible" or "OD600 = 0.6–0.8".
- Equipment: select all instruments required for this step.
- Decision Branches (Decision Gate steps only): add labeled branches for each possible outcome and the corresponding next action.
- Step Notes: tips, warnings, or context that do not belong in the procedure text.
- Critical Step: toggle to flag steps where an error would invalidate the entire experiment. Critical steps are highlighted in red and emphasized during test runs.
Reordering Steps
Use the up/down arrow buttons on each step card to reorder. Steps are automatically re-indexed. You can also delete any step using the trash icon. You will not be prompted to confirm unless the step has significant detail filled in.
Saving to Library
Click Save to Library in the toolbar. Your protocol is saved with:
- All steps persisted to the database with full detail
- Auto-calculated quality scores based on step completeness, critical step count, and metadata richness
- Tagged as "manual-design" in your library for filtering