How to Use Improved PD Studies

Introduction

Improved PD Studies enhances how Process Development (PD) teams design, execute, and analyze complex experimental workflows in Benchling. With this feature, users can manage multiple recipe runs within a single PD study and link unit operation instances across those runs, without requiring custom entity schemas.

This release improves support for split/join use cases across recipes, simplifies data tracking, and supports integrated study-level analysis. It empowers scientific teams to conduct multi-step PD workflows within one cohesive system.

Key use cases:

Conducting PD experiments involving multiple related recipes
Linking unit operations across recipe runs (e.g., output from a unit operation is split across multiple downstream unit operation or an output from many unit operations is joined into a single unit operation)
Study-wide data analysis and tracking

How to Use

Creating a PD Study

Navigate to Studies
Select the + Create button
Choose a study schema configured for Process Development
Enter a study name, select a folder, and add a description
Click Create

This will now create a PD study which you can add recipe runs to!

Adding a Recipe Run

Open your PD Study
Click + Add Recipe Run
Enter a recipe run name (if not using a naming template).
Select a recipe and data entry mode.
Customize condition settings (e.g., add conditions, set planned values).
Click Add Recipe Run.
1. The study overview auto-refreshes to show the new recipe run.

Viewing a Recipe Run

Click on a recipe run in the study overview to access two tabs:

Overview Tab: Displays unit operation instances grouped by status. Click a status (e.g., Planned, In Progress) to filter the list. Each row represents a unique Unit Operation × Condition × Replicate. Click any row to open the corresponding worksheet.
Design Tab: Displays a read-only view of the run’s structure across unit operations and conditions.

Linking Unit Operation Instances

Open the recipe run you want to link from.
Click Link to existing.
Select one or more unit operation instances. You can hold shift to select multiple unit operations instances.
Once you select a unit operation instance, a sidebar on the right will appear. In the sidebar, choose the unit operations you want to link to within the same study.
Once you select a unit operation instance to link to, a line will display the link created between the two unit operations you are linking.
You can continue to add additional links by selecting any unit operation instance, and repeating step 5 for it.
The unit operation instances you are linking from are known as your targets, and the unit op instances you are linking to are known as your sources. This is especially relevant when you are working with analyses or attempting to query the warehouse for these links.
Once you’ve added all your necessary links, select confirm to set the links.
After confirming the links you’ll return to the recipe run page where you will be able to find the links you just set in the unit operation instances table, under the column “Previous unit operations”.

Viewing and Editing Unit Operation Links

There are two ways to view unit operation links, both from a recipe run’s page:
1. The unit operation instances table, under the column “Previous unit operations” as explained above
2. By selecting “Link to existing”
To view links by selecting “Link to existing”, select “Link to existing”
This will display a visual graph of all unit operation links for the given recipe run

Editing existing unit operation links

You can edit existing unit operation links from a recipe run page by selecting “Link to existing”
After selecting “link to existing” you will see a visual graph of all unit operation links for the given recipe run
Select any unit operation instance that is part of the given recipe run to display the right side panel
Deselect the link you want to remove, and press confirm. This will remove between the source unit operation instance and the target unit operation instance and will update everywhere a unit operation instance link is surfaced (i.e. previous unit operations column in a recipe run, datasets, warehouse, etc)

Analyzing a Recipe Run

Go to a recipe run page.

Click Analyze. This will generate a new analysis that will be automatically associated with your PD study.

The analysis will create datasets based on the recipe, unit operation links, as well as any entities and results that were submitted within the procedure run.
1. Planned Conditions
2. Parameter values
3. Material input values
4. Material output values
5. Equipment values
6. Unit operation links
7. Entities registered
8. Results registered

The unit operation links dataset includes the following information:
1. Source Unit Operation ID: Unique identifier for the upstream unit operation instance
2. Source Unit Operation Name: Name of the upstream unit operation
3. Source Recipe Name: Name of the recipe that contains the source unit operation
4. Source Study Name: Name of the study containing the source unit operation
5. Source Study ID: Unique identifier for the source study
6. Target Unit Operation ID: Unique identifier for the downstream unit operation instance
7. Target Unit Operation Name: Name of the downstream unit operation
8. Target Recipe Name: Name of the recipe that contains the target unit operation
9. Target Study Name: Name of the study containing the target unit operation
10. Target Study ID: Unique identifier for the target study

Analyzing an Entire PD Study

Go to the PD Study page.
Click Analyze to create an analysis with all the datasets for all recipe runs in a given PD study. This will generate a new analysis, that will be automatically associated with your PD study.
The analysis will create datasets based on the recipe, unit operation links, as well as any entities and results that were submitted within the procedure run.
1. The details of the datasets are the same as the details listed above for the recipe run analysis

Default and Custom Run Name Templates

PD studies use a default recipe run naming template: DATE - RECIPE NAME - RUN ID (e.g., 20250618-mAB29X-RR981)
To edit the run name template:
- Open the Study Schema.
- Hover over the name template field and click the pencil icon.
- Customize the format (note: RUN ID is required and cannot be removed).

Viewing Link History and Audit Logs

You download recipe run audit logs from a recipe run page. Select the ellipsis and then select ‘export audit log’.
Choose CSV or PDF format.
Audit logs include:
1. Link creations (marked as “added to associations”)
2. Link removals (marked as “removed from associations”)

Accessing Link Data via Warehouse

If using the Benchling Warehouse, links are recorded in the table: procedure_method_exec_instance_assoc

FAQ and Troubleshooting

Why doesn’t material automatically transfer between linked unit ops?

This is a known limitation at launch. Linking does not move material outputs across recipes.

Workaround: Manually copy/paste materials from source to target operations.

Can I view a visualization of links across the entire study?

Not yet. Link visualizations are only accessible from individual recipe runs.

Coming Soon: A read-only, study-level graph is planned for post-GA.

My analysis isn’t working—what should I check?

Ensure recipe runs are saved and complete.
Confirm that links were created and confirmed.
Verify access to related entities and results.

Are run names required to be unique?

Yes. Run names must be unique and are enforced via the naming template. This helps avoid downstream errors in analyses and tracking.

Can I use this with existing studies?

Improved PD Studies is additive and compatible with existing schemas that are configured for Process Development. For best results, use newly created PD Studies.