Configuring your Benchling In Vivo tenant helps your team standardize study creation, metadata usage, sample tracking, and device setup. This guide outlines how to manage users, glossary entries, devices, presets, and authentication integrations. 

User management

From the Users section, individually or bulk perform the following actions: activate, suspend, resent invitation, revoke invitation, change user role to admin or member. 

Add user accounts

1. Click on the Manage Team icon and then navigate to the Users sub-menu
2. Click Invite users
3. Enter user email, clicking Add user to add additional user emails 

Once you’ve entered the emails of all the users you want to invite, click Save

Manage user roles

1. Click on the Manage Team icon and then navigate to the Users sub-menu
2. Use the checkboxes at the left to select one or more members of the team
3. Click the Actions dropdown and select option to either Change role to administrator or Change role to member as needed for your team 

Suspend user accounts

1. Click on the Manage Team icon and then navigate to the Users sub-menu
2. Use the checkboxes at the left to select one or more members of the team
3. Click the Actions dropdown and select option to suspend 

Note: the user’s role must be member in order to suspend their account. If they are an administrator, change their role to member before proceeding. 

Configure the glossary 

The glossary allows you to define terminology that is specific to your team and the studies conducted in your lab. Metadata, Observation types, Samples, Deceased reasons, Species & Strains, Treatments and Presets can all be customized to your requirements.

Access the glossary 

1. Click on the Manage Team icon and then navigate to the Glossary sub-menu
2. Customize the following terminology to your use cases
   • Metadata
   • Observations
   • Samples
   • Deceased
   • Species & Strains
   • Treatments
   • Presets

Configure metadata in the glossary

Metadata allows you to define additional custom fields to be captured across study execution. The default system fields for each schema are summarized below, and therefore do not need to be created as custom metadata.

Add custom metadata

1. In the glossary, click on the Metadata tab, then select the desired schema to manage:
   • Study
   • Groups
   • Animals
   • Cages
   • Samples
   • Attachments
   • Treatments
2. Click Add Category
3. Choose a field type
   • Select: accepts only one choice from a list of predefined text values
   • Multi-select: accepts multiple choices from a list of predefined text values
   • Date: accepts only a date
   • Text: accepts letters, numbers and symbols without any constraints
   • Number: accepts integers, decimals and exponential numbers
4. Specify the name of the new field
5. If the field was created as Select or Multi-select, add options
6. Click Save

Once saved, your metadata categories can be customized for specific use cases.

• For Study metadata, configure Studies Forms to customize what study metadata fields are shown during study creation and what fields are required by default
• For Groups metadata, configure Studies Groups to define which group metadata fields are shown during study creation and what fields required by default
• For Animal and Cage metadata, fields can be added ad-hoc during study execution through Add metadata
• For Samples, Attachments and Treatment metadata, all fields will be displayed automatically as optional fields

Configure observations

You can define the list of available observations to be used during study execution

1. In the glossary, navigate to the Observations tab
2. Select relevant terms using the check boxes. As you check each option, it will appear in the Selected observations list to the right of the menu
3. Expand each observation to assign scale types, values and grading information as a reminder to any user who will be appointing scores to each observation as they are recorded
4. Click Save 

Configure sample types

You can create and manage the list of sample types that can be collected during study execution. Administrators can manage custom sample types, edit details, or archive sample types in bulk. Sample types must be unique, and any corresponding labels must also be unique relative to other labels. Sample types can have one of two statuses: active or archived. Active sample types can be used by end users while archived sample types are unusable. Archived sample types can be unarchived at any time to become active, so long as uniqueness criteria are met.

Add new sample types

1. In the glossary, navigate to the Samples tab
2. Click Add new
3. Enter a unique name for the sample type
4. Add an optional unique label to have an abbreviation or alternative name for the sample type

Note: This will sync to Benchling’s Registry with collected samples and will appear in study exports.

5. Select optional details that should be recorded with the sample (weight, volume, width, length, depth)
6. Hover over the row number and select the red X to remove any unwanted rows
7. Click Create

Note: You can copy-and-paste multiple sample types from a spreadsheet to add them in bulk. You can also copy-and-paste sample details across different sample types for faster sample type creation.

Edit sample types

Only sample type labels and details can be edited. You cannot update the name of a sample type. To rename a sample type, archive the existing sample type and create a new sample type with the desired name.

1. From the sample type table, use the checkboxes to select the samples you want to edit
2. Select Bulk actions > Edit
3. Edit the label or details, or the sample type if you have not used the sample type before
4. Click Update

Note: When you update a sample type label, the change will automatically apply to all samples of that type within the tenant. This update will not trigger webhooks, so if you’re using the In Vivo Sync app, the corresponding samples in Benchling won’t update automatically. To sync the new label across to existing samples in Benchling, see how to run a backfill for the relevant samples or studies using the In Vivo Sync app.

Archive sample types

By default, all archived sample types are hidden from view in the Samples tab of the glossary. To show archived samples, click the X button next to the default filter Status is equal to Active at the top of the table. Archived sample types cannot be selected by a user

1. From the sample type table, use the checkboxes to select the sample types you want to remove
2. Select Bulk actions > Archive to archive
3. The sample types will be marked as archived but can still be viewed by clearing the filter

To unarchive a sample type:

1. Click the Filter dropdown
2. Edit the filter to be Status is equal to Archived to display only archived samples
3. From the sample type table, use the checkboxes to select the sample types you want to unarchive
4. Select Bulk actions > Unarchive

The sample types will be marked as Active.

Configure deceased reasons

You can define the reasons an animal can be marked as deceased in your tenant. 

1. In the Glossary, navigate to the Deceased tab
2. Select relevant reasons to mark an animal as deceased:
   • Euthanized
   • Found dead
   • Not found
   • Other
3. Click Save

Configure species and strains 

1. In the glossary, navigate to the Species & Strains tab
2. Click Add species to define the species you want to add. Once added, define the Strains
3. Click Add strain for each additional strain you want to add
4. Click Save

Configure treatments, disease induction and pre-treatments

Define the names of the compounds, test articles or agents that are available for animal dosing. A Treatment could be used as a Treatment, Pre-treatment or Disease Induction. All agent names are configured in this list. 

• Treatments: Experimental therapeutics administered to animals in groups. Treatment articles are assigned to groups during study design. Only animals assigned to the specified group will be able to receive a dose of the treatment
• Pre-treatments: Administer therapeutic compounds to animals before study group assignment
• Disease induction: Administer disease inducing agents to animals. Animals do not have to be in study groups before dosing

To add a treatment, disease, or pre-treatment to the tenant: 

1. In the glossary, navigate to the Treatments tab
2. Click Add treatments to enter the name of the material. Multiple treatments can be added to your glossary at the same time. To do this, click Add new after entering the previous drug details
3. Click Save

Note: When the In Vivo Sync is enabled to link your Core Benchling and In Vivo tenants, treatments do not need to be added to this glossary as users will search through Benchling Registry rather than this glossary. Both the Benchling registry and In Vivo glossary can be used in the same study.

Configure and manage presets

A preset is a predefined set of measurements that can be recorded throughout the study no more than once per day. Presets are comprised of one or more measurements (e.g., weight, tumor volume) that are the key components of the study graphs, study alerts, and study tasks.

Every preset must have weight recorded in grams due to a requirement for dosing calculations. The weight field can be renamed or reordered, but cannot be removed. Contact Benchling Support if you have additional requirements regarding animal weights such as body weight averages. 

To create a new preset without a calculation: 

1. In the glossary, navigate to the Presets tab
2. Click Create preset then select Add new from the dropdown menu and define the name of the preset
3. Using the Add measurement dropdown, select Without calculation and if needed, define the measurement name and unit
4. Click the check icon to confirm the measurement
5. When all measurements are added, reorder by dragging the six dot icon. This will be the order that will appear to the users when executing the study
6. Click Save preset to save the preset

To create a new preset with a calculation:

1. In the glossary, navigate to the Presets tab
2. Click Create preset then select Add new from the dropdown menu and define the name of the preset
3. Using the Add measurement dropdown, select With calculation which will open a new modal where you can define the formula

   • If the calculation needs new inputs that were not previously defined, click Add input and optionally define input name and unit, repeat as required

     Note: A formula cannot contain a combination of measurements and inputs

4. Configure the formula of the calculation by clicking on the names of the inputs to the left of the calculation section and the components about the formula field to build the formula for this calculation.
   • If a component that you require is not available in this list please contact Benchling Support.
   • When using ave, ensure that the inputs are separated by commas and are placed inside the brackets. i.e ave(input1, input2, input3)
   • When using π, ensure that the brackets after Pi are empty. ie. Pi()/6 *(width * length * depth)
5. Apply advanced settings as needed. See below a description of each of the available settings to apply
   • All inputs required
     • When enabled, the user must enter a value for every input in the formula in order to carry out the calculation. When disabled, the calculation will be carried out regardless of the number of inputs that have been recorded. This can be disabled for any SUM or Average calculations.
   • Measurement is a tumor volume
     • This setting is specific to subcutaneous tumor oncology study types whereby additional data analysis methods such as Time to reach target tumor volume are available.
   • Enable input auto swap
     • This setting is also relevant to subcutaneous tumor study types whereby the largest input value must be saved as the length in order to calculate tumor volume correctly.
     • When a measurement has been saved with width as the largest value in error, upon saving the values are automatically swapped to ensure the tumor volume calculation is correct.
     • To use this feature select which two inputs should be swapped using the dropdown fields provided.
6. Click Save measurement
7. When all measurements are added, reorder by dragging the six dot icon. This will be the order that will appear to the users when executing the study
8. Click Save preset

A preset must be published in order to use in a study. Use the preview panel to test calculations. When ready, select the preset, then click Bulk actions and select Publish. 

Note: Once published, a preset is locked and cannot be modified.

Edit presets

When unpublished, presets can be edited by clicking on the preset name from the table and making changes before clicking save. However, when published, presets are locked and so cannot be edited. 

To make changes to a published preset:

1. In the glossary, navigate to the Presets tab
2. Navigate to the preset that requires updates, click on the … menu and select Clone
3. Update the preset with the desired modifications.
4. Click Save preset
5. Use the Bulk action option to Delete the old version of this preset
6. Use the Bulk action option to Publish the new preset

Migrate presets between tenants

Presets can be migrated between tenants by exporting configurations from a source tenant and importing into a destination tenant. 

1. In the source tenant, navigate to the Manage Team and go into the glossary and enter the Preset tab
2. Navigate to the desired preset to export. Click on the … menu > Export. A .json file is downloaded to your computer under the name of that preset
3. In the destination tenant, navigate to the Manage Team and go into the glossary and enter the Preset tab
4. Click Create preset and select Import from the menu. Review and update this preset as needed
5. Click Save to create the preset
6. Use the Bulk action option to Publish the preset to make this preset available for future studies

Study configuration

The Studies tab allows administrators to customize configurations for specific study types and use cases. In this section, Forms, Reviews, Requests, Cage cards, Groups, and Study Codes are customized to your requirements. If there are 

Access the studies configuration

1. Go to Manage Team and go into Studies
2. Navigate to each section to customize configurations for your use cases:
   • Forms: Customize study creation forms for your team. Define what study metadata fields are shown during study creation and what is required by default
   • Reviews: Configure review process for study approval before a study can be started. Reviews can be triggered based on custom conditional requirements
   • Requests: Enable users to ask for support from colleagues by submitting relevant information and samples
   • Cage cards: Determine how cage cards are printed and which fields of metadata are included
   • Groups: Define what group metadata fields are shown during study creation and what is required by default
   • Study codes: Set up study codes templates for use in your research

Configure study forms

Study forms allow for the customization of study metadata during study design. In each form, customize the sections that will be shown when creating a study and what study metadata is required. Forms can serve as templates for studies with differing study metadata across your use cases. 

The default sections are:

• Information - Study name and description
• Team - Users who have access to the study
• Cages and animals - Used to quickly create cages and animals for the study
• Presets - Defines the data structure of the study
• Alerts - Enables users to create alerts linked to measurements
• Tasks - Setup tasks to be performed in the study
• Attachments - Upload files during study creation 

The Information and Team sections are required by default to create a study. All other sections can be removed and new sections can be added to specify custom study metadata. To create a study form: 

1. In the studies tab, navigate to Forms
2. Click Create new, enter the name of your new form and click Save and continue and the configuration for your new form will load in.
3. Choose if this form will be used for creating Internal studies (conducted in your own facility) or External studies (conducted outside your own facility)
4. Define the sections shown to the users during study creation
   • Deselect sections that are not relevant
   • Reorder sections by selecting the six-dots
     Note: It is recommended to deselect Cages and animals in this form. It is also recommended to maintain preset before Alerts and Tasks
5. Configure a section with custom study metadata defined in the glossary. To do this, click Add section
   • Enter a Section Name and select the relevant study metadata fields to include. The selected items will appear on the right side
   • To re-order them, simply drag and drop. You can also make the field required by clicking the checkbox
   • When the section is configured, click the Save button
   • Repeat this process to create additional custom sections as you want within the same form
6. Configure a section for the integration with the Benchling Tenant. (If you are not using the in Vivo Sync, skip this section)
   • Select the Add section
   • Define the name as Benchling Integration
   • Add the Study metadata field “Benchling Integration Folder ID” and make it Required
   • Click Save
7. Click Save when complete. The form will now be accessible by all users

Edit a study form

When a Study Form is edited, changes will only be shown for future studies created with this form. Previous studies will not be affected. 

1. In the Studies tab, navigate to Forms
2. Click the Form name in the table
3. This will load in the configuration, enabling you to make changes
4. When edits are complete, click Save 

Delete a Study Form

When a Study Form is deleted, users will not be able to use the form during study creation. Previous studies that have been created with this form will not be affected. 

1. In the Studies tab, navigate to Forms
2. Using the checkboxes, select the forms you want to delete
3. Click Bulk actions and click Delete
4. Type DELETE into the text box and confirm by clicking Delete section

Configure study reviews

The review feature can be configured by admins from the Studies submenu on the Manage teams page. The feature is used by teams who want to review study information prior to approving the study to commence. Reviews can be triggered for all studies, internal studies or external. In addition, reviews can be triggered based on study metadata conditions. 

Multiple review templates can be configured sequentially, in which case a review cannot be submitted until the first review template has been completed. 

When you create a new review process you must navigate through four parts:

• General: Name the review and set the criteria that trigger it
• Reviewers: Choose who can approve or reject the study
• Review form: Define the fields study authors must complete before submission
• Summary: Preview and confirm the setup before publishing

Create a new review template

1. In the Studies tab, navigate to Reviews
2. Click Create new review
3. In the General section, enter your Review name and specify which studies it will apply to:
   • All studies
   • Internal studies
   • External studies
4. If multiple review processes are configured, a Review dependency can be configured. Specify if there is a dependency to another review template, or if there is no dependency
5. If the reviews should be triggered based on study metadata, click Add condition to define the study metadata field and the value that needs to be entered by the user for the review process to trigger. You can add multiple conditions and specify if all or any need to match for the review to activate after the study is created
   • Note: This can only apply fields that are text or select values
6. Click Continue to proceed to Reviewers
7. In the Reviewers section, select the users who have the authority to approve this review process. If multiple reviewers are selected, customize the order of the review with the options below:
   • All reviews are required, but can be in any order 
     All of the selected users will have to approve the review before the study can be started. This can be done in any order
   • All reviews are required and in a specific order
     All of the selected users will have to approve the review before the study can be started This must be done in the order you define. To change the order, drag and drop the name of each user to the desired location
   • A minimum number of reviews are required
     A specific number of users must approve the review before the study can be started. Enter the number into the number field
8. Click Continue to proceed to Review form
9. Customize the  form that must be filled in by reviewers if the review process triggers in their study. You can use the following field types:
   • Group title - Use this to define a new section of fields
   • Text - A basic text field
   • Long text - A longer text field suitable for capturing lengthy responses
   • Select - A field that enables users to select from a list of provided options
   • Multi-select - A field that enables users to select multiple options
   • Date - A basic date field
10. Click Continue to proceed to Summary
11. In the Summary, test and confirm the details of the study review template. When complete, click Save and create

Note: New review processes only apply to future studies. They do not retroactively affect existing ones.

Edit a review template

1. In the Studies tab navigate to Reviews
2. Click the name of the review template to update, this will bring you to the configuration page
3. Make the necessary updates and click Continue
4. When the updates are complete, click Save and update

Note: Edits apply only to new studies created after the update.

Delete a review template

1. To delete a review template, navigate the Studies tab and open Reviews
2. Use the checkboxes to select the review template to delete
3. Click Actions, select Delete
4. Type DELETE into the field to confirm. Then click Delete review template

Note: You cannot delete a review process if it’s listed as a dependency for another review. Remove the dependency first, then delete.

Configure a study request template

This feature is used by teams who want to request colleagues to perform certain actions related to their studies. For example, you could have a pathology request template used to ask your pathology department to perform IHC on a defined list of samples. To create a request template: 

1. In the Studies tab, navigate to Requests
2. Click Create request
3. In the General section, enter the Request Name. Click Continue
4. Select the Assignees, or the users who are able to respond to or action the request. Click Continue to move to Request form
5. Use the form builder to create a custom form to be completed by the Assignees when adding the request to the study. Click Add field to add a new field to the form. Specify the field type, field properties and define if the field is required. The following field types are available:
   • Group title: Use this to define a new section of fields.
   • Text: A basic text field
   • Long text: A longer text field suitable for capturing lengthy responses
   • Select: A field that enables users to select from a list of provided options
   • Multi-select: A field that enables users to select multiple options
   • Date: A basic date field
6. Click Continue to proceed to Summary
7. In the Summary, test and confirm the details of the request template. When complete, click Save and create

Edit a study request template

1. In the Studies tab open Requests
2. Select the Request Template to update. This will bring you to the configuration page.
3. Make the necessary updates and click Continue
4. When the updates are complete, click Save and update

Configure cage cards

Cage cards are generated for every cage created in Benchling In Vivo. By default, cage cards include the following information:

• Cage Name
• Cage Barcode
• Study Name
• Animal Name
• Animal DOB
• Animal Sex
• Animal Strain

Additional Study or Cage metadata can be added to the cage card. You also have the ability to place up to eight custom fields on the cage cards that will be printed across your team. 

1. To add custom metadata to the cage cards, open the Studies tab and click on Cage Cards
2. Select up to 8 metadata fields to appear on printed cage labels
3. Click Save 

Configure study groups

After adding custom Group metadata fields to your team Glossary, define which fields display by default during study creation and which fields are required.

1. Open the Studies tab and click on Groups
2. Select the fields to display during study creation. Drag and drop the fields to reorder to your preferred order, click the checkbox to require the group metadata
3. When complete, click Save 

Configure study codes

Study codes are unique IDs that are generated by the system to manage differing study types within an organization. For example; an organization with separate teams conducting behavioral studies and metabolic studies may want separate counts whereby the former receives an ID in the format BHV-001, and the later CMD-001. 

1. Open the Studies tab and click on Study Codes
2. Click Create a study code
3. Enter a study code Title, the title should be descriptive to the study type as it is the identifier displayed to the user during study creation
4. Use the Add component buttons to build the template in the correct order
   • Text (optional): Used to enter static text to be included in the study code
   • Year (optional) : Used to insert the current year into the study code in either YY or YYYY format
   • Sequence (required): This is used to determine the next sequential number for new studies of the same template
     • Confirm the first number under "Begin count from: " This will be the number given to the next study created using this template and will count sequentially for each subsequent study
     • Select if this should continue to count sequentially despite a year change or if the count should return to 1 at the start of each year
     • Click Save
5. Click Save

Integrations

As an administrator, you can manage integrations including Single sign-on, API keys, Devices and the In Vivo Sync to the Benchling tenant. To access integrations, click into the Integrations tab of the Manage team menu. 

Configure single sign-on

Benchling In Vivo supports single sign-on (SSO) through both SAML and OAuth protocols. Benchling supports OAuth-based SSO for Okta and Azure AD. SAML-based SSO allows you to integrate a supported identity provider (IDP) with Benchling In Vivo so users must sign in through your organization’s chosen provider. Once SSO is configured, users can be forced to sign in to Benchling In Vivo through the chosen IDP. This allows you to tie all accounts to a centralized directory, enforce password requirements, implement multi-factor authentication, and more.

The general process is as follows:

1. Configure SSO with your IDP and enable SSO in 'soft mode', where users can use username and password, as well as SSO, to log in
2. Test SSO with a subset of users to ensure functionality is correct
3. Enable and enforce SSO for all users to remove the option for username and password sign-in

You can perform steps 1 and 2 yourself, however Benchling Support must complete step 3. 

The URL of your Benchling In Vivo tenant is a critical component in the set up of SSO. The format of a Benchling In Vivo URL is most commonly [yourcompanyname][test/dev].invivo.benchling.com (e.g. ExampleCompany.invivo.benchling.com). If your URL ends with overwatchresearch.com as opposed to invivo.benchling.com, replace invivo.benchling with overwatchresearch in the URLs described in this section. 

Configure OAuth SSO with Okta 

1. In Okta, in the blue navigation bar click Applications > Applications
2. Click the green Add Application button
3. Click the green Create New App button
4. Set the Platform to Web and select OpenID Connect
5. Enter the Application name Benchling In Vivo
6. Upload the Benchling logo (optional)
7. Set the login URL to the following:
   • For PROD tenants
     • https://yourcompanydomain.invivo.benchling.com/api/login/sso/okta/callback
   • For TEST tenants
     • https://yourcompanydomaintest.invivo.benchling.com/api/login/sso/okta/callback
   • For DEV tenants
     • https://yourcompanydomaindev.invivo.benchling.com/api/login/sso/okta/callback

8. Set the logout URL to the following
   • For PROD tenants
     • https://yourcompanydomain.invivo.benchling.com/api/logout
   • For TEST tenants
     • https://yourcompanydomaintest.invivo.benchling.com/api/logout
   • For DEV tenants
     • https://yourcompanydomaindev.invivo.benchling.com/api/logout
9. Click Save
10. Retrieve your Client ID and Client Secret at the bottom of the next screen
11. Click the Assignments tab and add the users who are to access Benchling In Vivo
12. Complete the configuration in Benchling In Vivo
    • Navigate to Manage Team > Integrations > Single Sign-on and click the Okta subtab
    • Enter the Domain, Client ID and Client secret
    • Toggle Enable Okta SSO to turn SSO on
13. Click Save when complete to enable SSO in 'soft mode'

Configure OAuth SSO with Azure 

1. Sign in to your company Azure account (with admin access)
2. Click on Azure Active Directory
3. Select Enterprise Applications
4. Click New Application
5. Click Create your own application
6. Set the name to Benchling In Vivo
7. Select Register an application to integrate with Azure AD (App you're developing) option
8. Select web and set redirect URL to the following:
   • For PROD tenants
     • https://yourcompanydomain.invivo.benchling.com/api/login/sso/azure/callback
   • For TEST tenants
     • https://yourcompanydomaintest.invivo.benchling.com/api/login/sso/azure/callback
   • For DEV tenants
     • https://yourcompanydomaindev.invivo.benchling.com/api/login/sso/azure/callback
9. Select Register
10. From Azure Active Directory select App registrations
11. Select application Benchling In Vivo from the app registrations list
12. Click Certificates and Secrets
13. Click New Client Secret
14. Enter a description and select an expiry to suit your needs
15. Click Add
16. Save the resulting Client secret value as you will not be able to view this again
17. Click Authentication
18. Set the logout URL to the following:
    • For PROD tenants
      • https://yourcompanydomain.invivo.benchling.com/api/logout
    • For TEST tenants
      • https://yourcompanydomaintest.invivo.benchling.com/api/logout
    • For DEV tenants
      • https://yourcompanydomaindev.invivo.benchling.com/api/logout
19. Click Save
20. Optionally, click on branding and add the Benchling logo to help enhance the UI for end users
21. In the same section, set the homepage to the following:
    • For PROD tenants
      • https://yourcompanydomain.invivo.benchling.com/api/login/sso/azure
    • For TEST tenants
      • https://yourcompanydomaintest.invivo.benchling.com/api/login/sso/azure
    • For DEV tenants
      • https://yourcompanydomaindev.invivo.benchling.com/api/login/sso/azure
22. Navigate back to the Azure Active Directory
23. Click on Enterprise Applications
24. Select Benchling In Vivo
25. Click Assign users and groups
26. Click Add user
27. Select users > assign
28. Click Properties
29. Set assignment required to YES

30. Select save

    Note: Please ensure the app has been granted the correct admin approval to allow users to sign in in the "permissions" section of the enterprise application under "security."

31. Complete the configuration in Benchling In Vivo
    • Navigate to Manage Teams > Integrations > Single Sign-on and click into the Active Directory (Azure) subtab
    • Enter the Tenant ID, Application (client) ID and Secret Value
      • The Client and Tenant IDs are located in the essentials section of the overview of the application in MS Azure
    • Toggle Enable Azure AD SSO to turn SSO on
32. Press Save when complete to enable SSO in 'soft mode'

Configure SAML SSO

1. In your IDP, set the login URL to the following:
   •  For PROD tenants
     • https://yourcompanydomain.invivo.benchling.com/api/login/sso/saml2/callback
   • For TEST tenants
     • https://yourcompanydomaintest.invivo.benchling.com/api/login/sso/saml2/callback
   • For DEV tenants
     • https://yourcompanydomaindev.invivo.benchling.com/api/login/sso/saml2/callback
2. In your IDP, set the logout URL to the following:
   •  For PROD tenants
     • https://yourcompanydomain.invivo.benchling.com/api/logout
   • For TEST tenants
     • https://yourcompanydomaintest.invivo.benchling.com/api/logout
   • For DEV tenants
     • https://yourcompanydomaindev.invivo.benchling.com/api/logout
3. In your IDP, set the Name ID format to 'Persistent' and include the following attribute statements:
   • firstName: user's first name
   • lastName: user's last name
   • email: user's email
4. Complete the configuration in Benchling In Vivo
   • Navigate to Manage Teams > Integrations > Single Sign-on and click into the SAML subtab
   • Click Upload file to upload the XML metadata file from your IDP

Note: If your IdP does not offer an XML metadata file, contact Benchling Support with the metadata URL for help completing configuration.

• Enter the Audience and Issuer (entity ID) in the respective boxes
• Toggle Enable SAML SSO to turn SAML SSO on for users in ‘soft mode’
• Press Save when complete

Note: The SAML SSO configuration can be saved without enabling SAML SSO if you would like to preemptively enter configuration details before turning on SAML SSO for users. If the SSO certificate expires, follow the steps above to update the configuration using the new metadata.

Test SSO in soft mode with a subset of users

1. Verify SSO integration using one of the options below. If SSO has been set up correctly, the user should be able to log in to Benchling In Vivo successfully with the following routes
   • Option 1: Users assigned to the Benchling In Vivo application in the IDP should now see Benchling In Vivo in their IDP interface. Users should click on the application to log in
   • Option 2: Navigate to the relevant address below 
     • https://yourcompanydomain.invivo.benchling.com/api/login/sso/okta
     • https://yourcompanydomain.invivo.benchling.com/api/login/sso/azure 
     • https://yourcompanydomain.invivo.benchling.com/api/login/sso/saml2
   • Option 3: Navigate to https://yourcompanydomain.invivo.benchling.com/login. Click Login with SSO
2. Once you have verified that the configuration is working, add all users to the access list in your IDP
   • Note: Any user who does not have access will be locked out of Benchling once SAML is fully enabled in the next step.

Enforce SSO

1. Email Benchling Support at support@benchling.com to enforce SAML for all users. 

All future sign-ons will be forced to go through your IDP instead of the normal username and password flow. Username and password logins will no longer be available for your tenant.

Configure connected devices

As a Benchling admin, you’re responsible for registering, managing, and maintaining connected lab devices. This ensures users can link instruments directly to fields in their studies for automated, accurate data capture. Benchling supports field linking for USB and RS‑232 devices only. Bluetooth and LAN devices can be used in In Vivo if they simulate a keyboard output, but they cannot be utilized in the connected devices feature and thus cannot be linked to specific fields. 

To make a USB or RS‑232 device available for field linking in studies:

1. Plug in and power on the device
2. In the In Vivo tenant, open Integrations from the manage team menu and select Devices
3. Click Add device
4. Click Auto detect to populate hardware details (Vendor ID, Product ID, vendor name, etc.)
5. If detection fails, enter these fields manually:
   • Device name and Device type
   • USB Vendor ID, Product ID
   • Vendor name, Product name
   • Baud rate, Data bits, Stop bits, Parity, Flow control
   • Termination character (e.g. Enter)
   • Response type (e.g. “Number” or “Text”)
6. Click Save

Note: If you use multiple serial devices, use USB adapters with differing chipsets to avoid duplicate IDs when connecting a device to In Vivo. Keep serial device drivers up to date to ensure seamless connectivity. 

Manage existing connected devices

1. From the Devices list, click the device name
2. Update the configuration (e.g., baud rate, name)
3. Click Save

Delete a connected device

1. Use the check boxes to select device(s) from the list
2. Click Bulk actions and select Delete device
3. Confirm deletion

Note: Device deletion is a permanent action and cannot be undone.

Troubleshooting connected devices

If users are unable to detect or connect to devices, and configuration appears correct:

• Google Chrome is the recommended browser - ensure you are using an up-to-date browser version
• Verify that the USB devices are correctly registered in the device registry by the administrator
• Ensure that the devices you are using are powered on and plugged into the computer

Frequently asked questions

Q: Who can add or manage devices?

A: Only team admins with Manage team access can add, edit, or remove devices. Regular users can link pre-configured devices to fields in studies.

Q: What devices and connection types are supported?

A: Benchling supports USB and RS‑232 (serial) devices. LAN or Bluetooth devices are not supported unless they simulate keyboard input (which cannot be linked to specific fields).

Q: Why isn’t my device showing up when I click “Connect device”?

A: Ensure the device is powered on, plugged in, and that your browser (Chrome) has the correct USB permissions. Also verify Vendor/Product IDs were correctly configured by an admin.

Q: Can I use more than one device at a time?

A: Yes, but for serial devices using USB adapters, each device must use a different chipset to avoid conflicts (e.g. use FTDI and PL2303 adapters for multiple devices).

Q: Why is the device connected but not populating the field?

A: Confirm the following:

• You’re in the correct browser tab (must say “Connected to a serial port”)
• The field you’re using is supported
• The device configuration includes the correct termination character
• Only one tab is connected to the device at a time

Q: What if the field I want to use isn’t available to link?

A: Only certain fields (e.g. workflow inputs, measurement tables) can be linked. If needed, contact Benchling Support to request enablement for additional field types.

Q: Why am I getting an error message when attempting to add in metadata to the glossary?

A: Though there are a few possible causes for an error message when trying to create a new metadata field, a common issue is that the slug ID is already taken. This could be a result of having an archived field that has, or had at it’s inception, the same name of the field that is currently being created. To work around this issue, create the new field with the name ending in ‘v1’ or a similar suffix, and then once the field is create remove the ‘v1’ suffix from the name.  Fields must also have unique names. If you have a conflicting name in an archived field, unarchive the field, change the name (i.e. with suffix ‘archived’), and re-archive the field. 

Q: How do I remove a device from the registry?

A: Go to Manage Team > Devices, select the device, and click Delete Device.

Q: Can I edit metadata fields after creation?

Yes. Go to Glossary > [category], select the field, and click Edit.

Q: How do I deactivate a user?

Go to Manage Team > Users, select the user, and click Deactivate.

Q: What happens if SSO setup fails?

Confirm your Azure IDs and URIs. Contact Benchling Support with the full error message if problems persist.

Q: What’s the difference between study metadata and animal metadata?

Study metadata applies to the full study and is used for sorting/filtering. Animal metadata is unique per subject and shows up in animal tables and exports.

Q: Why can I not clone or export my presets?

A: Any presets that were not created using the preset builder tool are not in the optimal format to be reused and so are locked. Any presets created going forward will have the menu options to clone and export. 

Any presets that cannot be created using the preset builder tool with complex calculations or updates to the weight measurement (such as average body weight or weight in Kg calculations) are managed by Benchling and so will also be locked on your tenant. Please contact support@benchling.com to request updates to locked presets.

Q: What happens when I delete a preset? Are there any impact on previous studies? 

A: When a preset is deleted, it is no longer available for future studies. There are no impacts to previous studies. 

If you accidentally delete a preset, please contact Benchling Support to request this to be undeleted. 

Q: Why am I told that my name is not unique when creating inputs for my calculation?

A: All inputs must be unique across all measurements in this preset (e.g., if there are multiple tumor volume calculations in a preset they cannot all use "length" and "width" as input names, instead they should be named "left length" or "Length 1" etc.)

Q: Why is my device showing as “unselected” in study execution?

A: It is possible that the Vendor/Product IDs were entered incorrectly during configuration. Double-check the accuracy of the Vendor/Product IDs for the applicable device.