The Notebook is a digital workspace for documenting experiments, tracking data, and collaborating with your team. It centralizes research activities so you can organize, link, and share scientific information efficiently.

This article outlines how to use the Notebook—from creating your first entry to managing and sharing your scientific records.

Create a Notebook entry

To get started, you'll need to create a Notebook entry. Entries can be created blank or with pre-built templates, depending on your team's workflow.

1. Click on Global Create in the navigation bar and elect Entry from the menu
2. From the menu choose how you’d like to create your entry
   • Blank entry allows you to create an entry with a blank workspace
   • Entry from template allows you to create an entry with content pre-configured by an admin
3. Fill out attributes for the entry by entering a descriptive title for your entry and assigning your entry to a project and folder
4. Click Create to begin editing your new entry

Edit and format entries

Editing Text

Once your entry is created, you can begin writing and organizing your content using built-in rich text editing features. Click directly in the notebook body to begin typing. 

You can then use the top toolbar to apply formatting like:

• Typographical emphasis: bold, italic, underline, and strikethrough
• Additional text elements: superscripts, subscripts, symbols, colored text, highlighting
• Content organization: headers, bulleted lists, numbered lists, check boxes
• Insert: insert plain and structured tables, attachments, code blocks 

These elements can also be inserted by using the /-keyboard shortcut. A list of other shortcuts can be found below. The other sections in this article cover how to add these elements to your entry.

Note: The table of contents automatically compiles date inserts, headers, subheaders, attachments, and Benchling tables to create an outline for your Notebook entry. These sections are all clickable and will take you to that specific section.

Keyboard Shortcuts

Benchling supports a number of keyboard shortcuts to make editing faster and more efficient:

Notebook Shortcuts

Table Shortcuts

Creating Collapsible Sections

Collapsible sections help organize long or complex notebook entries by allowing users to expand or hide specific blocks of content. This reduces visual clutter and makes protocols easier to navigate. To insert collapsible sections:

1. Click Insert in the toolbar at the top of the entry
2. Choose Section
3. Give your section a Name and choose a Date for the section
4. Add content inside the collapsible block
5. Click the directional arrow next to the section’s name to expand or collapse the section

Insert dates, references to people, objects, and attachments

Add a new day

Use date inserts to timestamp actions and provide a clear historical context for experimental work. Mentions notify collaborators directly within the entry, making it easier to assign tasks or request input. Author tags record contributors for each entry, supporting transparency and compliance with research documentation standards.

Date inserts can be done directly in the body of the entry. To insert a date: 

1. Type /New day and press Enter
2. Click on the date and a calendar pops up allowing you to adjust the date

Note: if you want to change the date, you may do so as long as the date follows the entry’s previous date. 

Note: if your have Collapsible Sections enabled on your tenant, inserting dates in the entry is disabled due to the duplicative nature of the feature with Collapsible Sections

You can enrich your entries by embedding file attachments, linking Sequences, or referencing Entries or other Entities.

Link objects

1. Click into the Notebook entry body and type @ symbol
2. Start typing the name of the person or object you’d like to link (e.g. Sequence, Entry, entity, file)
3. Click the item you want to insert

Insert Attachments

1. Click Insert in the toolbar at the top of the entry
2. Choose Attachment
3. Drag and drop a file or click to browse and upload

Entry metadata

Notebook entries can be further modified and classified using the Metadata tab of your entry. In this tab you can: 

1. Add an author by clicking click on the edit icon to the right of the Authors section, searching for a name, and selecting it from the dropdown
   • Remove an author by clicking the X next to their name
2. Moved to a different Project or Folder
3. Apply an entry schema for structured tagging or classification of entries
4. Create custom fields for this entry

Insert Sub-templates

Sub-templates are configured by your local admin and allow you to insert consistent blocks of content across multiple Notebook entries. They save time and promote consistency. To insert a Sub-template: 

1. Click Insert in the toolbar at the top of the entry
2. Choose Sub-template by using the search bar or clicking to expand the Template Collection
3. Select the Sub-template you would like to insert and then click Insert 

Note: Updates to sub-templates do not retroactively change content in entries where they have been inserted.

Working with tables

Notebook tables support spreadsheet-style features. You can use flexible column types, data validations, and formulas to structure experimental records. This improves consistency and helps automate data tracking. To insert a table:

1. Click Insert in the toolbar at the top of the entry
2. Select Table from the menu
3. Select the table size you’d like to insert
4. Click into any cell to enter data

Note: You can rename the table by right clicking on the header, then selecting Rename Table

The Notebook also supports inserting structured tables to help you take various actions with entities directly in the Notebook. For more information on structured tables, see the linked article.

Table formulas

Tables support spreadsheet functions such as SUM, AVERAGE, IF, and XLOOKUP. Use lookup columns to link other Benchling entities and formulas to calculate values across rows. Formulas are powerful tools that support data consistency, reduce manual errors, and automate calculations across experimental records. 

1. Click into the cell you want to modify
   • If you want to apply a formula to the whole column, click on the column header to highlight the whole column
2. Click into the text box next to the fx symbol to enter in the desired formula
   • Click on the fx symbol to see a list of the available formulas
   • Use the suggestions in the text bar to format the formula correctly

For a list of common table formulas that you can use in Benchling, see this article on common table formulas.

Manage table visibility

If you have long tables that you don’t want to scroll through in order to get to the next part of your Notebook entry, you can collapse tables for a more streamlined experience. 

1. Navigate to the top of the table
2. Click the arrow icon in the top-left corner of the table to collapse or expand

Notebook entry limits

When working with notebook entries, you may encounter performance slowdowns as your entries grow.

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.

Managing and Sharing Entries

In collaborative environments, tracking the history of changes to Notebook entries is critical. Benchling automatically timestamps all entry updates, ensuring every action—whether editing, commenting, or syncing—is recorded. These timestamps help maintain data integrity, meet compliance requirements, and trace contributions over time.

Version history

Version history allows you to audit changes made to a notebook entry over time and recover earlier versions if content is accidentally modified or deleted.

1. Open the entry you want to view
2. Click on the history icon in the top right of the entry
3. Click on any version to preview it

Restoring or cloning versions

Once in the version history panel

1. Select the version of the document of interest
2. Click on the button with the 3 dots in the upper right hand corner
3. Click either:
   • Restore to Version you’d like to restore the entry to
   • Duplicate from Version to create a new entry from a version

Exporting and Sharing

You can share your entries with collaborators in read-only format or export data to share outside Benchling. The read-only link allows others to view an entry without editing permissions, preserving the original content for audit or review. Steps to share or export an entry:

1. Click the Share button in the upper-right corner
2. Toggle link sharing on/off or generate a read-only link
3. To export, click the Information icon and select Export entry. You can export entries in formats like PDF or as raw data depending on your configuration. 

If you're exporting Registry or Inventory-linked tables from the entry, Benchling ensures the associated data structure is preserved. For more information about sharing data, see the linked article. 

Use Benchling Sync

Use Benchling Sync to edit attached files on your desktop. This allows you to work offline or use desktop tools like FlowJo or Excel. Changes are saved back to the Notebook automatically.

You can install the Benchling Sync desktop application two ways: from your custom download page or from an attachment in a workable entry.

Install Benchling Sync from the download page

To access your tenant's download page, visit http://tenant_name.benchling.com/desktop, replacing tenant_name with with the name of your tenant.

Install Benchling Sync from an entry

To install the application from an entry: 

1. Click the floppy disc icon in the top-right corner of an attachment to check it out for editing
2. Click Download page at the bottom of the Edit file window that displays
3. Select the download option that matches your operating system, then follow the installation prompts
4. After downloading, you can access the application from your operating system's tray taskbar. You may be required to sign in the first time you edit a file 

Note: Linux is currently not supported.

To use Benchling Sync:

1. Open a notebook entry with an attachment
2. Click the button with the ellipses next to the file
3. Select Check out for Edit
4. Edit the file on your device
5. Save changes to the file to sync the changes back to Benchling

Compatible applications include Microsoft Word, Excel, FlowJo, and more.

IT Administrator Setup for Benchling Sync

Benchling Sync can be deployed and managed at scale by your IT team to ensure consistent access, authentication, and security across your organization. It enables scientists to open, edit, and save files from their desktop directly into Benchling Notebook entries, making it easier to use local analysis tools while maintaining a complete audit trail.

To deploy Benchling Sync for teams at scale, IT administrators can:

• Install Benchling Sync using a managed deployment method (e.g., SCCM, Jamf, Intune)
• Use the Benchling Sync MSI/PKG installers available through Benchling Support
• Configure organization-level authentication and single sign-on (SSO) options
• Set up file handling preferences, such as default editors and file associations
• Manage firewall and proxy settings to ensure the Sync client can connect securely to Benchling's servers

Benchling Sync supports Windows and macOS, and complies with enterprise-grade security standards. For full deployment guidance, IT teams can refer to Benchling’s enterprise IT documentation or contact Support.IT admins can configure installation permissions, manage authentication, and define file types compatible with Sync workflows.

Frequently Asked Questions (FAQs)

Q: Are timestamps visible for frozen chip samples or system-tracked activity?
A: Yes, Benchling records and displays notebook timestamps, including for frozen chips, to ensure experimental traceability and meet audit requirements.

Q: Can I undo changes in my entry?
A: Yes, use standard keyboard shortcuts (Cmd+Z / Ctrl+Z) or click the undo arrow at the top.

Q: How do I turn off link sharing?
A: Go to the Share menu in the entry and toggle off Link Sharing

Q: Why do date inserts sometimes auto-update?
A: When date blocks are placed out of order, they may update automatically to reflect actual entry flow.

Q: Can I delete the default date insert at the top?
A: No, this is system-generated metadata for audit purposes.

Q: What desktop apps work with Benchling Sync?
A: Word, Excel, FlowJo, and many other standard file editors are compatible.

Q: How do I format content more cleanly in the entry?
A: Use headings, horizontal rules, collapsible sections, and tables to create a clean layout.