Benchling offers multiple ways to share data, facilitating collaboration and efficient data management. Whether you're moving or copying objects, exporting data, using worklists, or working with datasets, Benchling provides tools to streamline these processes.

Move or copy Benchling objects

Moving or copying data is useful when you want to reorganize content across teams, separate personal drafts from shared project work, or clone templates for reuse. It ensures your data remains structured and accessible in the right place without having to manually recreate content in Benchling just to reorganize data. 

Move or copy a single object

1. Navigate to the object you want to move or copy
2. Right-click on the object to open the context menu
3. Select Move to Folder or Copy To
4. Choose the destination folder or project
5. Confirm the action

Move or copy objects in bulk

1. Click on the Global search icon and click the directional arrow to enter the expanded Search view
2. Use filters to locate the objects you want to move or copy, then use the checkboxes next to each object or click the top-left checkbox to select all the objects you want to move or copy
3. Select Move to Folder or Copy To in the toolbar
4. Choose the destination folder or project

Export projects, folders, and data

Exporting allows you to download data from Benchling for offline access, archival purposes, reporting, or sharing with collaborators outside of Benchling. Whether you're wrapping up a project or sending data to a regulatory team, exports ensure your content can travel beyond Benchling for offline access or sharing.

Choose projects or folders to export all of your data 

1. Click on your avatar, located at the bottom left-hand side. Select Data Export to launch the tool
2. You can export many file types from here
   • To export projects or folders, select All Items, which will export everything in a given project or folder as a ZIP file
   • Click the drop down menu to select the projects or folders you want to export.
   • Choose whether you want to export these files as PDFs or HDML
3. The exported files will be emailed to you. You’ll receive a download link in your inbox once the export is complete

Export an individual project or folder

You can export individual folders directly from the project or folder browser. To export a folder directly:

1. Navigate to the folder in your project tree
2. Right-click on the folder
3. Click Export
4. Choose PDF or HTML
5. Benchling will email you a ZIP file with the folder contents
6. Click on your avatar at the bottom left-hand side
7. Click Data Export to launch the tool
8. Select All Items to export everything in a given project or folder as a ZIP file
9. Choose the projects or folders you want to export
10. Select the export format: PDF or HTML
11. Click Export
12. The exported files will be emailed to you. You’ll receive a download link in your inbox once the export is complete

Export data from the Notebook

Notebook entries are exported as PDFs or HTML files. Plasmid maps within entries are exported as GenBank files. Protocols linked to an entry are also exported as PDF files.

1. Open a lab notebook entry and click the Information icon on the right. At the bottom of the panel, click Export Entry
2. An export of the entry will be emailed to you, and you will be prompted to download a .zip file containing your entry. This .zip file will contain a PDF version of the entry and copies of any files attached to the entry

Export data from the Registry

Exporting Registry data allows you to analyze records externally, share information with collaborators, or back up your current state. You can export by schema or entity type in a structured CSV format.

1. Navigate to the Registry application
2. Using the checkboxes in the expanded view, select the entities you’d like to export 
3. Click Export and choose the desired format (e.g., CSV, GenBank)
4. The exported files will be emailed to you

Export data from the Inventory

1. Navigate to the Inventory application
2. Using the checkboxes in the expanded view, select the containers you wish to export
3. Click Export and choose Export selection to CSV
4. The CSV file will be downloaded to your computer

Note: Exporting data is useful for creating backups, sharing with external collaborators, or conducting offline analyses.

Use Worklists to find and share lists of objects

Worklists help you organize and operate on sets of related samples or entities. They’re especially useful for cross-functional tasks like preparing materials for an assay, reviewing sample groups, or coordinating handoffs between teams. Worklists let you manage, filter, share, and take action on your selections in bulk. You can find your list of recent Worklists by clicking on the Home icon. 

Create and share a new Worklist

There are multiple ways to create a Worklist. You can do it from the expanded view of the Registry and Inventory applications, or in structured tables, which allow you to create and add items to a new Worklist in a single step. You can also create a Worklist in the Home menu. By default a worklist will be accessible only to the user that created it. Worklists can be shared with colleagues by modifying worklist settings. 

1. Click the + icon next to Recent Worklists and choose the type of worklist
2. Use the textbox to specify a name
3. Optionally click Manage access to add users, teams, or organizations to the Worklist, when finished adding them and defining their access policy, click Done
4. Click Create Worklist to save your new Worklist 

Note: Sharing worklists facilitates collaboration by allowing team members to access and manage shared collections of items.

Add Items to a Worklist

After creating a worklist, you can add either entities or containers to it. Anywhere you see the Worklist icon, you can add items to a worklist - this includes Registry search, entity metadata page, inventory search, container pages, and insights dashboards. 

Search and sort a Worklist

1. Use the type filter to narrow down items
2. Use the Filters dropdown for additional filtering options
3. To sort you can:
   • Click on the column header to sort by that column
   • Use the Sorting option to sort by multiple fields, and click Apply

Re-order and save a Worklist

1. Click the gear icon of the Worklist and select Worklist order from the menu
2. Drag and drop items in the worklist to manually re-order items
3. Click Save to preserve the new order

Delete items from a Worklist

1. Use the checkboxes to select the items to you’d like to remove
2. Click the trashcan icon to delete them from the worklist

Delete a Worklist

1. Navigate to your worklists, select the worklist(s) you wish to delete
2. Click the trash can icon on the right to delete the worklist(s)

Note: Deleting a worklist does not delete or archive the items in the worklist.

Using Datasets to share data 

Datasets provide a way to consolidate experimental results and structured data into one central record. They support downstream analysis, help standardize how data is reviewed, and make it easy to share findings with collaborators or query them later as part of a broader study, semi-structured data objects that are searchable and live in folders. They support capturing structured data ready for analysis and are flexible in usage.

Creating Datasets

Datasets can be created through:

• Analysis: Generate datasets as outputs from analyses.
• API: Programmatically create datasets using Benchling's API.
• Connect Runs: Import data from instruments or external systems.

Organizing and Sharing Datasets

• Datasets can be organized within folders for better management.
• They can be tagged and linked to studies, making them accessible within the context of specific research projects.
• Datasets are searchable, allowing for easy retrieval and analysis.

Note: Utilizing datasets enhances data traceability and supports collaborative research efforts.

Permissions and access

Projects are the foundation of access control for most items in Benchling. Permissions on a project determine who can view, create, and modify its contents. Each project must have an owner, and for many tenants, the owner must be an organization. If the owner is an organization, all admins of that organization will have admin access to the project. Project admins can assign additional collaborators permissions to the project. Each user or team can be granted one of the following levels:

• Read: Can view all project contents but cannot make changes
• Append: Can create items within the project
• Write: Can create, edit, and archive items within the project
• Admin: Can manage collaborators, modify project settings, and archive content

Permissions are cumulative; for example, if a user is added with Read access and also belongs to a team with Write access, they will have Write access. 

Folders inherit permissions from the parent project but can also have more specific permissions added at the folder level. If a user has access to a folder but not the parent project, only the folder displays in the Projects panel of the workspace. 

Folders can never be less permissive than their parent project. If a user has Write access to a project, they will have at least Write access to all subfolders in that project. We recommend applying the least permissive access policies to projects and granting additional access to their contained folders, as needed.

Note: Folder permissions are currently not supported in the warehouse or Insights dashboards.  No user will ever see data they don't have access to, but if they don't have at least Read access at the project level they will not be able to find the objects from folders they have access to in the warehouse or Insights dashboards.  All other features like search, Insights Analyses, and the Projects panel will work as expected.

Enable or disable folder permissions

To enable or disable folder permissions, you must be a Tenant Admin.

1. Open the Tenant Admin Console
2. Click Settings, then click Permission Controls
3. Turn on or turn off folder permissions as appropriate

Note: Folders must have permissions removed before disabling folder permissions tenant-wide. If you have admin access to the relevant folders, Benchling will remove any existing folder permissions as part of turning off folder permissions. If you don’t have admin access to those folders, you’ll get a message indicating which folders need to be updated and no changes will be made.

Permission levels

The table below displays the actions users can perform at the project or folder level with default general access policies.

Set project and folder permissions

1. Click the briefcase icon to open the Projects panel
2. Right-click on the project or folder name and click Manage access. Alternatively, open the desired project or folder, click the gear icon next to the project or folder name, then click Manage access
   
   

3. Add new collaborators in the top search bar by searching for user, email, team, organization, or app. Specify the general access policy that should be granted to the user in the right dropdown, and click Add
4. To update project permissions for existing users, use the dropdowns under Access Policies. To update Folder permissions for existing users, use the top search bar to search for the collaborator, select the general access policy that should be granted in the right dropdown, then click Add
5. To remove user permissions from a project or folder, click the … icon next to the collaborator and click Remove. At the folder level, you can only remove user permissions that were granted at the folder level
6. Click Done if you are setting permissions for a new project or folder or Save if you are updating permissions for an existing project or folder
   
    

Frequently Asked Questions

Q: How do I export DNA sequences in specific formats?

Benchling allows exporting DNA sequences in various formats, including GenBank (.gb), FASTA (.fasta), CSV (.csv), SVG (.svg), RDF (.rdf), and ZIP archives.

Q: Are there permissions associated with sharing worklists?

Yes, when sharing a worklist, you can set permissions for collaborators: READ, WRITE, or ADMIN, controlling their level of access and editing capabilities.

Q: What happens when I delete a worklist?

Deleting a worklist removes the worklist itself but does not delete or archive the items contained within it.