Use the In Vivo Sync app

In Vivo Sync enables your team to synchronize data between your Benchling In Vivo and Benchling Core tenants. Allowing you to reference Registry entities, like treatments, directly within In Vivo studies and sync In Vivo records into Registry. 

This guide covers how to access the app, check the progress of syncing activity, run a backfill, and use synced data within studies.

Access and navigate the Sync app in your Benchling core tenant 

1. In your Benchling core tenant, click the Connections icon in the navigation bar
2. Click into the Apps tab
3. To open the app, click In Vivo Sync
4. To view schemas, add or update field mappings, Use the Configuration sub-tab

Access and navigate Sync pages in your In Vivo tenant 

1. To track progress of the Sync activity in your In Vivo tenant, click on the Manage team icon in the navigation bar
2. Expand the Integrations section
3. Click Benchling Sync
4. Monitor the Activity in the first tab

Note: To monitor the sync for a particular study, filter this table by the study name or visit the Benchling Sync page within the study.

If errors occur:

1. To show the errors, click View errors
2. To see information about the error and how to resolve it, click on the Error message
3. Once the issue causing the error has been resolved select all applicable errors
4. To retry the failed sync items, click Retry Sync events under Bulk actions 

Run a backfill

The backfill process creates and updates Registry entities for corresponding In Vivo data that hasn’t been synced across your tenants. With this feature enabled, administrators can select specific date ranges, review the number of items to be synced, monitor backfill progress in real time, and cancel backfill operations if needed, all directly from the In Vivo tenant.

This helps ensure that historical data remains consistent across systems, especially after integration updates or sync issues.

1. To initiate a backfill, click on the Manage team icon in the sidebar
2. Expand the Integrations section
3. Click Benchling Sync
4. Visit the Backfills tab
5. Click Run backfill, and setup the backfill according to date and item type and optionally restrict the backfill to selected studies
   • Note: All items that were created or updated within the date range selected will be backfilled
6. To monitor the backfill, refresh the page regularly to see the number of completed items
7. To view any sync errors, click on the date in the Created at column
8. To Cancel the backfill, click … and then Cancel backfill

Important Notes

• Permission: Before running a backfill, ensure that the In Vivo Sync app has write access to all projects and folders that the studies are being synced into.
• Rate Limits: Backfills are designed to respect Benchling’s API rate limits and will progress steadily without affecting real-time sync operations.
• Partial Backfills: If only a subset of measurements needs syncing, carefully choose appropriate date ranges to avoid unnecessary data transfer.

Using Registry entities as treatments in In Vivo

You can use custom entities in In Vivo as treatments by syncing them via the app. To use a Registered entity as a treatment:

1. Ensure the entity exists in the correct schema in your Benchling core tenant
2. In the Sync App, confirm that an admin has added the correct schema to the elements list
3. Open or create a study in your In Vivo tenant
4. Treatment tab of the Treatment groups page, click Add New
5. To search for an entity to use as a treatment, type into the treatment name field, a dropdown of options with matching registry IDs or names will be available for selection
6. Click the Benchling logo icon to open this entity in your Benchling core tenant 

Note: Only Registry entities that meet schema and filter criteria will appear in the dropdown. If the entity is invalid, it won’t be available in the dropdown.

Configure the Benchling integration folder

Each study must be linked to a folder in your Benchling Core tenant to sync:

1. Create or identify a folder in Benchling, and ensure that the In Vivo Sync App has sufficient permissions to write to this folder
2. When creating Study forms, ensure a study metadata field called “Benchling folder ID” has been created and added to the form in any metadata section
3. During study creation, search for the folder the Benchling integration section
   • Type to search for the folder by name and select the correct folder from the dropdown This ensures all synced records route to the correct Registry folder

Update the Benchling integration folder

If you need to update the folder after the study has been created: 

1. Navigate to the Settings tab of the study you need to update in your In Vivo tenant
2. In the Benchling Integration tab, search for the new folder location
3. Click Save
4. Contact your tenant administrator to run a backfill of this study to move all study data to this new location

Frequently asked questions

Q: Why don’t I see the correct treatment options in my In Vivo treatment name dropdown?

A: Make sure the registered treatment entity:

• Exists using the correct entity schema
• Meets any filter conditions set in the Sync App configuration
• Is a custom entity, Formulations are not supported 

Q: Can I edit synced data in Benchling?

A: No. Synced data should only be edited in its system of origin. Editing Registry entries created by the sync can impact data accuracy and will be overwritten with future updates in the In Vivo tenant.