Configure Notebook templates and Template Collections

The Notebook streamlines documentation of observations, data, and SOPs ensuring your team remains in compliance with established protocols. These benefits can be further realized through the use of Notebook Templates and Sub-templates stored in Template Collections, which standardize the layout of Notebook entries for well-defined experimental data capture in your organization. 

Notebook templates are pre-formatted entries that an admin configures to ensure consistency, completeness, and compliance across an organization. While sub-templates enable you to create reusable content that can be used in multiple entries and Notebook templates.

This guide will walk you through creating and managing Template Collections, Notebook templates, and sub-templates. 

Create a Template Collection

Template Collections act as folders that store Notebook templates. To create a Template Collection: 

1. Click on your avatar at the bottom of the navigation bar
2. Navigate to Feature Settings and select Template Collections
3. Click New Collection to open a modal from which you can specify attributes of the Template collection including:
   • Collection name
   • Owner
   • Description
   • Permissions
4. Click Create Template Collection to finalize creating the new collection 

Once created, you may manage settings for the collection by clicking the gear icon in the upper right corner. Depending on your Benchling license, your template collection might host Notebook Templates, Sub-templates, Request templates, Forms, and Recipes. Notebook Templates and Sub-templates are the focus of this article, but to learn more about the other features, see the linked articles.

Template publishing 

Template publishing is an opt-in feature that allows you to create and store templates and sub-templates that are under development in a draft format in your Template Collection, only making it available to the relevant end-users upon finalization by publishing it. 

If you would like to turn this feature on, please reach out to support@benchling.com. 

Template state overview

Templates are labeled with a version state to indicate their status. There are four version states that are used to designate where a template is in its lifecycle. The table below summarizes each version state, permissions, and if a version state can be used by end-users. 

Create and publish a new draft

If you are ready to iterate on a template and update it, you must create a new draft as you cannot make changes to the effective version of a template. To create and publish a new draft: 

1. Click on the Version dropdown and click create new draft
2. Make updates and changes in the draft
3. When ready to publish, click the Version draft dropdown
4. Optionally update the display name and description if necessary
5. Confirm that you would like to publish the new version by clicking Publish

When a new version is published for an existing version, the published version will supersede the prior effective version. However, this does not affect entries already created from the superseded version. All new entries will be made from the newly published effective version.

If you are publishing for the first time, you will need to provide a display name. For each update, Benchling will auto-increment the display name (ex. Version 1 to Version 2).

Note: you can opt out of the default auto-incrementing of display names, but this will require you to input a custom name each time you publish a new draft. 

Withdraw a template

If you want to withdraw a template, for instance if it contains errors, you will remove it from circulation and there will be no effective version of that template for users. To withdraw a template: 

1. Click on the Version dropdown and click Withdraw version
2. Confirm that you would like to withdraw the version by clicking the Withdraw button 

Template version history

The version history panel is designed to display the template’s history and primary metadata. You can view the version history of a template in the template history panel at the right side. The panel will display all effective versions with the newest version at the top. If any new drafts exist, they will be displayed above the latest effective version.

Version metadata is available in the Warehouse and can be used to provide deeper operational insights to different processes. 

Updates to version history via publishing are tracked in audit logs. For every publish action, at least four audit events are generated: 

• created publishing record
• update version name
• update version description
• update publishing status

If a version is superseded by a publishing action, an additional audit event is generated: updated publishing status. 

Template Collection permissions and access

Access to the Notebook templates within the collection is controlled by permissions set at the Template Collection level. These permissions determine the actions a user can take. The table below summarizes the permissions users have to take various actions in the collection. 

Note: it is not possible to set None permissions for individual users 

Template permissions are not impacted by using versions states associated with template publishing. 

Manage permissions in the Template Collection

1. Click the gear icon in the top-right corner
2. You can directly change the name, owner, and description. To change who has access to the collection, click Manage access

3. To add access
   • Use the search bar to search for a user, team, or organization
   • Use the dropdown to the right to select the permission level, then click Add 

4. To change access
   • Use the dropdown next to the user, team, or organization’s name to change the level of access they have to the template collection

5. To remove access
   • Click the … icon to the right of the user, team, or organization’s name
   • Click Remove 

6. Click Done to return to the Template Collection Settings menu and click Save 

Proper permission settings ensure that only authorized users can modify templates. 

Notebook templates can be modifiable or fill-in

Benchling offers two types of Notebook templates: 

• Modifiable templates: pre-made content in entries made from modifiable templates can be added to, modified, or removed
  • They are typically used to standardize format and encourage consistency across a team while preserving flexibility for users to modify sections as needed
• Fill-in templates: pre-made content in entries made from fill-in templates cannot be changed. The only edits a user can make are attaching files into placeholders, checking checkboxes, entering text into text boxes, and filling in tables
  • They are typically used to ensure data stays compliant with organization protocols 

Fill-in templates are especially useful when your team needs to follow strict documentation practices—such as in GxP or QA environments. They help ensure only intended fields are editable, reducing the chance of accidental changes to protocol text or structural elements.

Create a Notebook template

To create either a modifiable or fill-in template: 

1. Create a new Template Collection, or enter an existing one and click Create
2. From the dropdown menu, select Entry template
3. In the Create template modal, define the template attributes including:
   • Template name
   • Template Collection (which allows you to move the template before it is created)
   • Schema
   • If it is fill-in or modifiable (which can be changed in the template itself)
4. Then click Create so you can be brought to the Notes tab of the entry where you can configure the template 

Note: if you have enabled template publishing, you will need to publish the draft before it is available for use. 

Once created, you can convert between a fill-in and modifiable template by using the dropdown at the top right of the template and selecting the desired option. You can also clone existing templates by accessing the template's version history and selecting Duplicate from version. 

If you would like to define metadata or a review process for your Notebook template, navigate to those tabs in the template editor and fill out the relevant information. 

Configure your template

In your Notebook template, you have extensive flexibility to configure something that fits your organization’s needs. In your template, you can make use of: 

• Formatting options available in the Notebook
• Plain and structured tables
  • That can be pre-filled with starting values or formulas to help guide users on what data to enter, automate calculations, or provide a consistent starting structure for common workflows. This can be particularly useful for tasks like master mix calculations or sample tracking
• Sub-templates 

The sections below discuss other options for configuring your templates. 

Formulas in templates 

Click on the cell of the plain or unstructured table you wish to add an equation to. Use the built-in Benchling formulas to create your custom equations. You can also add rows if you will have formulas that calculate over multiple rows.

Note: You can combine equations as needed. For example, if you wanted to calculate the range you can write the equation =Max()-Min()

Lock a column for fill-in templates

To limit editing within tables, you can display table columns as read-only in an entry created from a template and prevent users from modifying its content. This is done by locking table columns.

To lock a table column:

1. In the template, click the top of the column you want locked
2. Select Lock column

In the Column Header Context menu, you can also:

• Delete column
• Unlock column (if locked)
• Insert column left
• Insert column right

Insert a text box in a fill-in table

You can add text boxes to templates, enabling users to enter free text directly in an entry and format their text. With text boxes, users can capture observation notes and summaries, @-mention users, link entities, and more.

To insert a text box into a template, select Text box from the Insert menu in the entry header.

Create Sub-templates 

Sub-templates let you maintain consistent blocks of content—like headers, safety reminders, or shared tables—across many templates or Notebook entries. By centralizing reusable content, Sub-templates save time and promote consistency. To create a sub-template:

1. Create a new Template Collection, or enter an existing one and click Create
2. From the dropdown menu, select Sub-template
3. In the Create template modal, define the template attributes including:
   1. Template name
   2. Template Collection (which allows you to move the template before it is created)
4. Then click Create so you can configure the template 

Like Notebook templates, you can create a new Sub-template by cloning an existing Sub-template, and leverage tables and other formatting options. You can do anything in a Sub-template that you can do in a template, except: 

• Add date inserts
• Assign Entry schemas
• Configure review criteria or assign review processes
• Use the fill-in feature 

If you have enabled template publishing, you will need to publish the draft before it is available for use. 

Make updates to templates after schema changes

If your template includes structured tables that reference Registry or Result schemas (e.g., registry-linked columns), those templates may need updating if you make changes to schemas. A template is relevant to a schema if the template depends on the way a schema is configured. As a result, the template must contain at least one of the following:

• Registration table for the schema
• Results table for the schema
• Structured table with a lookup column that references a field on the schema

An entity link field in a structured table is not considered relevant to the Entity schema because the field isn’t dependent on the schema’s configuration.

After a schema is updated, existing templates will not automatically reflect those changes. You’ll need to review and update templates manually. When entity or result schemas are updated, templates referencing them may require adjustments. To identify affected templates:

1. Navigate to the updated schema
2. Click the Relevant Templates tab
3. Review the list of templates that may need updates
4. Click the template link to go to the template configuration page where you can update the relevant table(s) accordingly

This ensures that structured tables within templates remain accurate and functional. 

Permissions

You can access the Relevant Templates tabs of Result and Entity schemas you have permissions on. In the tab itself, you can view the templates you have Read or Write permissions on.

If you don’t have permissions to a relevant template, a banner at the bottom of the page indicates how many templates you don’t have access to and provides a link to the Members tab on the relevant Organization page to help you determine the org admins they can contact about updating the templates.

Archive templates

If you have Admin or Write permissions in a Template Collection, you can archive its templates and sub-templates or the Template Collection itself. 

Archiving templates removes them from active use without deleting them, preserving historical data. To archive a template:

1. Navigate to the template collection
2. Hover over the template and click Archive
3. Select a reason for archiving and confirm

Archived templates can be unarchived if needed. If you have Template publishing enabled, you can choose to withdraw a template instead of archive it. 

Manage Notebook template size

When working with notebook entries, your team may encounter performance slowdowns as their entries grow, use these considerations to help you structure your Notebook templates 

One of the main factors affecting the performance when using a notebook entry is the total number of table cells. 

• Warning threshold (17,500 cells): When the total count of table cells in an entry exceeds 17,500, we recommend that you break up the entry into smaller parts.
• Maximum limit (35,000 cells): While you will not be blocked from exceeding this 35,000 total table cell limit, Benchling will not be able to assist with performance issues past this scale.

Optimize your entry

• Remove unnecessary columns to reduce the total cell count
• Collapse large tables when not actively using them
• When working on a single large table, open the table in full-screen mode
• Use sections to organize content logically. Collapse the sections when not in use
• Use the table of contents sidebar to jump to content more easily

Maintaining optimal entry sizes ensures smooth performance.

Frequently asked questions 

Q: Can I link a template to a workflow or request?

A: Yes, entry templates can be configured as execution templates for request types or workflow stages. This allows your team to use the same template format when submitting tasks or completing experimental work.

Q: How can I structure large templates to reduce performance risk?

A: Use sub-templates to break out reusable sections, minimize the number of structured tables per entry, and use collapsible sections to manage length. Consider distributing content across multiple entries or workflows if needed.

Q: Can I edit a template after publishing?

A: Yes, create a new draft from the effective version, make your changes, and publish the new version.

Q: Do changes to sub-templates update existing entries?

A: No, updates to sub-templates do not retroactively change content in entries where they have been inserted.

Q: How do I restrict users from editing certain parts of a template?

A: Use the Fill-in only option when creating or editing a template to lock specific sections.

Q: What happens when I archive a template?

A: Archived templates are removed from active use but can be unarchived later if needed.