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Create and Add Protocol Steps

Once a protocol has been created, the workflow itself is built by adding protocol steps.

A protocol may contain a single step or hundreds of individual steps. Each step represents a discrete laboratory operation and can define:

Together these steps become the executable workflow used by batches and samples.

Adding a Step

Select Add Step from the Protocol Steps section.

Each new step becomes part of the protocol execution order.

Steps may be reordered or configured to depend on previous steps.

Every step contains several independent sections that can be expanded and edited.

Step Configuration

Every protocol step begins with its core configuration.

Depends on Step

A step may optionally depend on another step.

Dependent steps cannot begin until their prerequisite has completed.

This allows construction of complex workflows while preventing operators from performing work out of sequence.

Step Title

Provide a concise title describing the laboratory operation.

Examples include:

The title appears throughout protocol execution, reports, audit logs, and dashboards.

Step Action

Step actions allow individual steps to update the workflow state of batches and samples on step completion while a protocol is still in progress.

Protocols are designed to represent reusable laboratory procedures that are assembled into larger workflows. A workflow typically consists of many protocols executed in sequence, with each protocol performing one portion of the laboratory process.

Most protocols contain multiple laboratory operations. Some of those operations represent meaningful workflow milestones that should be reflected immediately in the sample or batch status rather than waiting until the protocol has finished.

For example, a tissue culture workflow might contain separate protocols for:

Within the Culture Initiation protocol, the workflow state may change several times:

Step Action
Prepare media None
Sterilize explants Sterilize
Transfer explants Transfer
Inspect cultures Inspection

Although the protocol is still executing, the sample's workflow state is updated as each milestone is reached.

This provides more accurate laboratory reporting, allows dashboards to display current progress, and enables workflow automations to react immediately to important laboratory events.

Step actions are entirely optional. They should generally be assigned only to steps that represent meaningful workflow state transitions rather than every laboratory instruction.

Available actions include:

Instructions

Instructions describe exactly what the operator should perform.

These should be written as clear laboratory procedures.

Include:

Good instructions reduce operator variation and improve reproducibility.

Expected Outcome

Every step should define the expected result.

Examples:

Expected outcomes provide operators with a simple way to determine whether a step has been completed successfully.

Step Criticality

Steps may be marked as Critical.

Critical steps identify operations that have significant impact on quality, safety, compliance, or experimental success.

Examples include:

Critical steps are prominently highlighted during execution and reporting.

Required Materials

Each protocol step may define the materials required for execution.

Unlike traditional protocol systems, FlaskTrack links requirements directly to centralized catalog items.

Supported requirement types include:

Each requirement is independently tracked for inventory, procurement, costing, and reporting.

Ingredients

Ingredients represent consumable laboratory materials.

Examples include:

Each ingredient can define:

Ingredient quantities are automatically scaled using the protocol reference batch.

Tools

Tools represent reusable laboratory equipment.

Examples include:

Tools do not consume inventory but document equipment required to complete the step.

Species / Agrobacterium Strains

Certain workflows require additional biological materials.

Examples include:

Associating these materials with a step improves documentation and execution consistency.

Plasmids

Transformation workflows may require one or more plasmids.

Each plasmid can specify:

Plasmids remain linked to the laboratory catalog for traceability.

Step Usage Overrides

Every required material can optionally override its default catalog values.

Overrides are useful when a particular protocol uses:

Overrides affect only the current protocol step and never modify the catalog itself.

Data Collection

Each protocol step controls the information operators must record during execution.

FlaskTrack supports three approaches.

No Form

No information is collected.

Operators simply complete the step.

Prompt System Form

FlaskTrack automatically presents the standard data collection form associated with the workflow action.

This is useful for standardized laboratory operations.

Custom Form

Custom forms allow completely tailored operator input.

Fields may include:

Fields can be marked as required.

Custom forms make it possible to collect exactly the information required by the protocol.

Validation Rules

Custom forms may include validation rules.

Validation ensures submitted data satisfies laboratory requirements before the step can be completed.

Examples include:

Validation improves data quality while reducing transcription errors.

Timing

Timing controls how long a laboratory step is expected to take and when it should be scheduled.

These values help operators plan work, estimate completion times, and monitor overdue tasks.

Scheduled Offset

A scheduled offset delays when a step becomes available relative to the previous step or protocol schedule.

This is useful for workflows that require incubation, recovery, waiting periods, or delayed processing.

Timing Type

FlaskTrack supports four timing modes.

Fixed

The step requires one expected duration.

Example:

Incubate for exactly 30 minutes.

Minimum

Only a minimum execution time is required.

Operators may continue once the minimum duration has elapsed.

Example:

Sterilize for at least 20 minutes.

Range

Specify both minimum and maximum acceptable durations.

This is useful when laboratory procedures have an acceptable operating window.

Example:

Incubate for 18–24 hours.

Until Condition Met

The step has no predefined completion time.

Instead, operators continue until a biological or laboratory condition has been satisfied.

Examples include:

This timing mode is particularly useful for tissue culture and microbiology workflows where biological progress determines completion.

Rest Window

Steps may also define acceptable rest periods between workflow stages.

This is useful for incubation, recovery, acclimatization, rooting, or waiting periods.

Environmental Conditions

Environmental conditions document the expected environment required while performing a protocol step.

These values serve as laboratory guidance and improve reproducibility across operators and facilities.

Temperature

Specify the acceptable operating temperature range.

Both minimum and maximum temperatures may be defined.

Example:

Agitation

Specify how materials should be handled during the step.

Available options include:

Setting Typical Use
Static No movement
Gentle Agitation Slow mixing or orbital movement
Stirred Continuous magnetic or mechanical stirring
Shaking Orbital or reciprocal shaking
Rocking Platform rocking motion

Light

Specify lighting conditions for the step.

Available options include:

Setting Typical Use
Ambient Light Standard laboratory lighting
Dark Protected from light
Light / Dark Cycle Alternating light and dark periods
Constant Light Continuous illumination
Photoperiod Cycle Controlled day/night schedule

Light requirements are especially important for tissue culture, plant growth, fungal development, and photosensitive compounds.

Environmental Notes

Each environmental parameter may include notes documenting laboratory-specific requirements, observations, or special handling instructions.

Examples include:

Saving Changes

Each section of a protocol step can be saved independently.

This allows complex protocols to be developed incrementally without requiring the entire workflow to be completed before saving.

Procurement Preview

As materials are added, FlaskTrack continuously calculates protocol requirements.

The procurement preview estimates:

All calculations automatically scale using the protocol reference batch.

Building Complete Workflows

Most protocols consist of multiple connected steps.

A typical workflow might include:

  1. Prepare materials
  2. Sterilize equipment
  3. Prepare media
  4. Inoculate cultures
  5. Incubate
  6. Inspect
  7. Subculture
  8. Harvest
  9. Complete

Because every step records instructions, materials, environmental requirements, and operator data, FlaskTrack creates fully reproducible laboratory workflows that can be executed consistently across experiments, operators, and facilities.