Organize your data in Benchling

Benchling offers a structured approach to manage your research data through projects, folders, tags, and studies - each designed to help you organize and retrieve information more easily while ensuring the right level of access for different users and teams. Whether you're setting up a shared space for your team, managing individual workflows, or linking related datasets across experiments, Benchling provides flexible tools to match how your lab works.

Organizing your data well makes it easier to collaborate, apply permissions, surface insights through filters and tags, and maintain consistent documentation practices. This guide provides step-by-step instructions to help you set up and manage your workspace effectively.

Projects

Projects serve as the primary container for your data in Benchling, encompassing notebook entries, entities such as sequences and experiments samples. 

Use projects to keep work organized around specific teams, or functional areas. Well-structured projects make it easier to manage permissions, filter content, and collaborate with others.

Create a project

1. Click on the briefcase icon on the left navigation bar
2. Select the local create icon to create a project
3. Enter a Project Name and optionally enter a Description if you would like to provide more information about the project itself
4. Click Manage Access to set the permissions of the project (see the permissions section of this article for more details)
   • Select the users(s), team or organization and the permission level
   • Click Add to add the selected collaborators.
   • Click Done to go back to the project creation window
5. Click Create project

Folders

Folders provide an additional layer of organization within projects, allowing you to categorize data effectively. They help break down complex projects into manageable sections - such as by experiment or research focus - so that users can navigate and contribute more efficiently.

Create a folder

1. Open the desired Project
2. Click the + icon and select Folder
3. Enter a Folder Name
4. Confirm the Location within the project
5. Click Create

Common project & folder structures

Team-based: One project per team or department, with folders for each experiment or study

Example:

Project: Protein Engineering team

├── Folder: Study 1

├── Folder: Study 2

├── Folder: Study 3

└── Folder: Study 4

Target-based: One project per research initiative or therapeutic area

Example:

Project: Target A

├── Folder: Transfection Studies

├── Folder: Clone Screening

├── Folder: QC Results

└── Folder: Reports and Analysis

Function-based: Projects for functional categories like cell line development, molecular biology core…etc

Project: Cell Line Development

├── Folder: Transfection Studies

├── Folder: Clone Screening

├── Folder: QC Results

└── Folder: Reports and Analysis

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
   
    

Tags

Tags are custom fields that help in categorizing and filtering objects across Benchling. They allow you to label data with custom attributes like sample type, or instrument used, making it easier to search, sort, and report across large datasets.

Add tags

1. Open the desired object (e.g., sequence, notebook entry)
2. Click the Information icon on the right
3. Enter the Tag Name and Value (optional)
4. Click the + icon to create the tag

Note: Tags facilitate advanced searches.

Studies

Studies allow you to group related data, such as entries, datasets, and tasks, providing a comprehensive view of your research. Use them to coordinate timelines, organize milestones, or evaluate cross-functional data within a structured framework. 

Studies can link to any "studyable" object in Benchling - including notebook entries, entities, datasets, and workflow tasks. This means you can flexibly associate a wide range of data with a single study record to keep everything connected.

Linked objects remain accessible both from their original location (e.g. project and folders) and from the study overview, allowing for easy navigation between the experimental record and study summary. Setting up a study requires a study schema to be configured by users who have Admin permissions on the tenant.

Create a Study

You can create a study either from the Study icon in the Navigation bar and using the local create option or from the Global create menu. 

1. Click the Global create icon and select Study
2. Select the appropriate Study Schema from the menu
3. Enter a Name and a description (optional)
4. Choose the Study Design Entry to outline the study plan, from a template or create a new one from a blank entry
5. Fill in any other value fields that are customized based on your study schema
6. Click Create

Associate entities to a Study

There are several ways to connect your experimental data to a Study, using Notebook tables, adding Studies via the metadata page of an object, or with auto-linking. With auto-linking, when you create new notebook entries directly from the Study Overview page, the objects created within those entries will be automatically linked to that study. 

You can link also link entities to a study by adding a study column to your a Notebook table: 

1. Right click on the column header to insert a column and select the Studies option from the menu
2. In the table type the name of the Study you’d like to link to the entity, click on the name of the Study in the search bar to add it
   1. You can associate the entity with more than one Study if you use the entity across multiple studies   

This will assign an entity that you register to the study and make it visible to you under the study’s listing or search page. 

Archive Data

Benchling provides options to archive and delete data, ensuring flexibility in data management. Use archiving to clean up active workspaces without losing historical context, and permanent deletion for removing obsolete content - while staying compliant with your organization’s retention policies. 

Note: European industry users and academics can permanently delete any item after archiving it. All other industry users cannot.

To archive data: 

1. Navigate to the object you would like to archive
2. Go to the metadata tab of your object
3. Click the red icon to archive the object

Restore archived data

1. Look for the archived object
   • From the project, registry or global search tool, make sure to set up a filter on the Archived objects
2. Select the object and go to the metadata tab
3. In the metadata tab click the icon to Unarchive

Permanently deleting data (EU customers only)

1. Ensure the object is archived
2. Open the object and click the info button on the right
3. Click Delete

Caution: Some data may be restricted from permanent deletion due to compliance policies. 

Frequently asked questions

Q: Can I change the color of my project and/or folders?

A: Currently, Benchling does not support custom colors.

Q: How do I filter projects shared with me?

A: Use the Project Filters to view projects:

• All Projects
• My Projects
• Shared with Me
• Team(s)
• Organization

Note: Adjust the Results per Page setting for better navigation.

Q: What are best practices for project structure in academic settings?

A: Consider structuring projects by course sections or research groups, and use folders for individual experiments or student work.