How to Configure Benchling Bioprocess

Introduction

Benchling Bioprocess supports process design, experiment planning, batch execution, and data visualization in a unified environment.

This guide details how to configure and administer Benchling Bioprocess Recipes, Unit Operations, Steps, Study Schemas, and Equipment Schemas. It also covers key permissions required to properly manage and use Bioprocess in your tenant. For a detailed walkthrough of how Benchling Bioprocess is used—including use cases, experiment execution, and visualization—please refer to How to Use Benchling Bioprocess.

This feature is available for customers with the Bioprocess package enabled in their Benchling tenant. If you're unsure whether your tenant is licensed, please contact your Customer Success representative or reach out to support@benchling.com 

Bioprocess terminology and structure

In Benchling Bioprocess, the core structure follows this hierarchy:
Recipe > Study > Experiment > Unit Operation > Step

• Recipe: The structured process model created within a Template Collection.
  
  
• Unit Operation: A segment of the process, containing definitions like parameters, inputs/outputs, and equipment
  
  
• Step: Discrete tasks within a Unit Operation
  
  
• Study: The object used to execute and manage a series of Experiments
  
  
• Experiment: An execution instance of a Recipe across defined Conditions and Replicates
  
  

How to configure a Recipe

Recipes are configured in template collections, to configure a Recipe, complete the following steps: 

• Click your avatar > Feature Settings > Template Collections
  
  

• In your chosen Template Collection, click Create and select  Recipe from the dropdown

• Name your Recipe and click Create
  

You can also duplicate an existing Recipe to reuse common process frameworks.

• Each Recipe must have at least one Unit Operation. Click the + icon to add a new Unit Operation. Rename it and use the gear icon to edit Definitions and Steps.

Recipe permissions

Recipe permissions are controlled by the Template Collection they belong to, using General Access Policies. You must have Write access to the Template Collection to create or edit Recipes.

Each Access Policy defines what users can do with Recipes—like viewing, editing, executing, or archiving them. See the “Recipes - General Access Policies” table below for a summary. 

Note: Although the “Templates” table in General Access Policies only lists permissions for Notebook Templates, the Template Collection settings apply the same policies to Recipes as well.

Example: If a user has default Write access to a Template Collection, they can fully manage Recipes in that collection—this includes viewing, editing, executing, archiving, and unarchiving them.

Recipes - General Access Policies
Derived from the Template Collection containing the Study

How to configure Unit Operations, Definitions, and Steps

In the Recipe designer, you must create at least one Unit Operation to execute your Recipe. You can also optionally configure Definitions and Steps within each Unit Operation to guide operators during execution.

When you open the Recipe designer, one unnamed Unit Operation is automatically created. 

To edit or add a Unit Operation follow the steps below: 

1. Click the textbox to enter a name
   
   
2. Click the ✔️ icon to save it
3. Create additional Unit Operations if needed by clicking the + icon on either side of a Unit Operation to add a new one. 
   • Repeat the renaming and creation process until all necessary Unit Operations are added
4. To rename a Unit Operation later , double-click the name.

Configure Definitions in a Unit Operation

Definitions include Parameters, Material Inputs, Material Outputs, and Equipment. To configure them, follow the steps below: 

• Click the gear icon on a Unit Operation and select the  Edit details option
  
  
• In the modal, click Edit (top right)
  
  
• Fill in the name and type for each item in the relevant Definition tables
  •  Note: Each item must have a unique name.
• Click Submit when done. Use the Flowchart > Edit dropdown to move to the next Unit Operation or return to the Recipe overview.
  
  

Configure Steps in a Unit Operation

Steps define the actions operators will take. To configure a step: 

• In the Edit modal of the Unit Operation, go to the Step Configuration tab
  
  
• Click + Add step in a Step Group (e.g., Pre-run, Run, Post-run)
  
  
• Enter a title for the Step (required) and add checklists, structured tables, or notes
  
  
• Add more steps as needed within or across groups
  
  
• Use the Flowchart > Edit dropdown to configure Steps for other Unit Operations

Pro Tips

• Drag and drop Unit Operations to reorder them
  
  
• Steps for Parameters, Materials, and Equipment from your Definitions will be auto-generated in Worksheets when you create a Study—no need to add these manually
• Use sub-templates for repeated Step patterns (e.g., cell counts across operations)

Best Practices for Unit Operations

Use multiple Unit Operations when:

• Equipment changes (e.g., bioreactor to centrifuge)
  
  
• Parameter sets differ significantly
  
  
• Intermediate products are created or stored
  
  
• You want to optimize or track independently
  
  

Keep a single Unit Operation when:

• There are only minor parameter adjustments (e.g., temperature shifts)
  
  
• The process is continuous without major context changes
  
  

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How to configure a Process Development Study schema

A Study schema defines how PD Studies behave in your tenant, including the fields and templates they use. PD Study configuration is largely similar to Custom Study configuration, with the key difference being that the study type must be set to Process Development.

How to Configure

1. Go to Feature Settings
   
2. Click Study schemas
3. Click Create Schema

3. Define schema attributes:
   
   
   • Prefix and name
     
     
   • Owner and Study type (select PD Study)
     
     
   • Optional fields and templates
     
     
   • Whether design approval is required
     
     
4. Set Schema Access Policies to control who can Read, Write, or Create Studies
   
   
   

Study permissions

To execute a Study, users need:

• Read access to the Template Collection containing the Recipe
  
  
• Write access to the Project/Folder where the Study is stored
  
  
• Create access to the Study Schema

Study permissions are controlled by two areas:

1. Project or Folder where the Study is stored — governed by General Access Policies
   
   
2. Study Schema — governed by Schema Access Policies
   
   

Example: If a user has Read access to a Project or Folder, they can also view any Studies saved there.

Permissions for Study schemas are derived from access policies set on the specific Study Schema within feature settings. To create a new Study, users must have Create access to the associated Study Schema.

Note: General Access Policies on Projects and Template Collections can affect multiple objects—not just Studies—so review those settings carefully when managing Bioprocess permissions.

Unit Operation tasks will be stored in the same folder as the Study. If the Study is moved, tasks do not automatically move with it.

Studies – General Access Policies

Derived from the Project / Folder containing the Study

Studies – Schema Access Policies

Derived from the access policies set on the specific Study Schema within feature settings

Schema Objects

How to configure Equipment schemas

To link Equipment in Recipes, equipment must be modeled with specific schemas. To create a model schema follow the steps below:

1. Click your avatar

2. Go to Feature Settings

3. Select Study Schemas

4. Click Create to start a new schema

5. Define the prefix and name of the schema

6. Select Custom for the entity type

7. (Optional) Add any relevant entity fields

8. Click Next when you've finished setting the schema attributes

9. Add users, teams, organizations, or apps and define their access policies

10. Click Create to finalize the schema

Once you have the model schema, you can configure the equipment schema using the steps below: 

1. From the Entity schemas page, click Create Schema
   
   
2. Set entity type to Custom
   
   
3. Check the Configure as Equipment box

4. Click the + icon next to Entity fields to add the required fields. The following fields must be added with exact names and types:
   
   
   • Model (required) — entity link to a specific model schema
     
     
   • Serial number (required) — text
     
     
   • Calibration due date — datetime

Once complete, users can reference equipment entities directly in Definitions tables within Unit Operations.

FAQ and Troubleshooting

Can I “branch” a Recipe?

Recipes in Bioprocess are linear and sequential—Unit Operations cannot branch within a single Recipe. If your process includes different paths or variations, each should be configured as a separate linear Recipe.

However, material outputs from one Unit Operation can be routed to the inputs of multiple subsequent Unit Operations, allowing the material flow itself to branch.

When you create a Study from a Recipe, Benchling generates Unit Operation tasks for each Condition and Replicate, which can be executed in parallel—this creates a form of branching at the task execution level.

What happens to Unit Operation tasks when a Study is moved?

Tasks do not automatically move. Manually move both Study and associated tasks to avoid access issues.

Why aren’t my units appearing in the dropdown?

Ensure that the units have been enabled in your Unit Dictionary. See the Unit Dictionary section of this article for setup.

What if I can’t find my equipment in the dropdown?

Make sure the equipment entity is linked to a properly configured Equipment Schema with required fields.

Permissions FAQs

What are the key access requirements?

For more questions, please contact support@benchling.com or your Benchling representative.