Benchling In Vivo’s Workflow feature provides a centralized interface for completing actions on study animals—such as collecting samples, recording measurements, logging observations, and dosing—with a minimal amount of clicks. It provides a guided interface walking the scientist through data collection and study execution. In Workflows, you can:

• Assign animal identifiers
• Record cage food and fluid intake
• Record measurements
• Collect samples
• Record observations
• Administer doses of treatments
• Mark animals as deceased
• Connect with instruments

When kicking off a Workflow from a task, Workflows are automatically populated based on task configurations and allow for seamless task execution across the full cohort.

How to configure Workflows 

Before capturing data, you’ll need to configure your Workflow. Configuration defines what data you plan to collect, the order of execution, and any instruments or devices to use. Each Workflow is configured at the start of execution and can’t be saved for reuse.

During setup, you’ll walk through each component — General, Measurements, Samples, Observations, Dosing, and, if enabled, Cage food and fluid. Within each component, you can customize collection fields and set After saving navigation instructions to control what happens once data is entered. Devices can also be linked at this stage to automatically input values into the correct fields.

Access Workflows

• Open your study and click the Workflow tab in the left navigation bar
• Or, open Workflows through the task schedule: click Schedule, select a task, and then select Execute task in the top right

Configure a workflow

When you click into Workflows you are automatically prompted with a Workflow setup window. Each workflow includes five main components:

• General: Workflow settings that control display and navigation
• Measurements: Data to be collected, display settings, and the option to assign animal IDs
• Samples: Which samples may be collected and related settings
• Observations: Which observations may be collected and related settings
• Dosing: Which treatments will be dosed and related settings

Each component outside of general settings includes an After saving field, which determines what happens once data is saved. This enables Workflows to automatically move to the next section for streamlined, hands-free navigation during execution. The options for the After saving field include:

• Focus search bar: Move the cursor to the search bar for ID scanning or searching by an animal identifier (often set for the start on field and/or the last step in the workflow)
• Toggle measurements: Progress to animal measurements for the selected animal
• Toggle samples: Progress to sample collection for the selected animal
• Toggle observations: Progress to observations for the selected animal
• Toggle dosing: Progress to dosing for the selected animal
• Move to next animal: Progress to the next sequential animal automatically (often set for the last step in the workflow)

Once all desired components of the Workflow have been configured, click Continue to proceed to workflow execution. You can relaunch the setup window by selecting Workflow Setup in the top right of the workflow execution page. 

General: Set general settings

Click into the General section of Workflow setup. 

• Use Show treatment groups to toggle whether the Treatment Group will be visible. If the study is blinded, leave this off
• Adjust the date you would like to record to match the calendar date to record for workflow actions
• Toggle ID method to search by to choose the identifier used in the search bar
• Toggle Display identifier to select which identifier will be shown during workflow execution
• Update Start on to set the first action to perform during workflow execution

Measurements: Specify measurements to capture

1. Open the Measurements section in Workflow setup
2. Select the checkboxes for the measurement fields to collect.
3. If multiple measurements will be recorded, drag and drop them into the desired order
4. Use Change default cursor position to set the cursor to a specific measurement field. This reduces clicks and ensures the correct measurement is taken first when multiple measurements are recorded at once
5. Use Weight percentage change from to adjust the reference value for calculating relative weight change, which displays next to newly recorded weights
6. Update Assign identifiers if additional animal identifiers (such as tag, tail, or ear IDs) still need to be recorded. This displays as an additional field under the Measurements data tab, where new identifiers can be entered or scanned in with a barcode scanner
7. Set the After saving navigation instructions to define what Workflows should do once data is saved

Note: Available measurements are defined by the Preset specified when the study was created

Samples: Specify samples to collect

1. Open the Samples section in Workflow setup
2. Select the checkboxes for the samples to collect
3. If multiple samples will be collected, drag and drop them into the desired order for collection
4. Toggle Autogenerate sample ID to automatically generate identifiers. Deselect this option to manually enter unique sample names
5. Set the After saving navigation instructions to define what Workflows should do once data is saved

Note: Available samples are defined in the samples glossary, as specified by an administrator in the Manage teams page.

Observations: Specify observations to record

1. Open the Observations section in Workflow setup
2. Select the checkboxes for the observations to record
3. If multiple observations will be recorded, drag and drop them into the desired order
4. Set the After saving navigation instructions to define what Workflows should do once data is saved

Note: Available observations are defined in the observations glossary, as specified by an administrator in the Manage teams page. A Record Normal and save button is automatically available during workflow execution for recording a normal observation on an animal.   

Dosing: Configure dosing

1. Open the Dosing section in Workflow setup
2. Select the checkboxes for the treatments to be dosed
3. If multiple treatments will be administered, drag and drop them into the desired order of administration
4. Toggle Skip dosing for animals that do not require any treatments to automatically bypass dosing for animals that should not receive the treatment and move directly to the next action
5. Toggle Use new body weight to record a new weight for dosing calculations without logging it as a daily measurement. This is useful if you perform daily measurement capture in the morning, then dose in the afternoon but need an updated weight for dose calculations
6. Set the After saving navigation instructions to define what Workflows should do once data is saved

Note: If dosing is weight-based, the system will auto-calculate dose volume based on the most recent recorded weight. Available treatments are defined in the Treatment groups page of the study.

Cage Food and Fluid: Track consumption

If food and fluid tracking is toggled on for the study preset, there will be a sixth component called Cage Food and Fluid available in the configuration of a workflow. 

To configure Cage Food and Fluid in Workflows:

1. Open the Cage Food and Fluid section in Workflow setup
2. Toggle Enable food intake tracking to capture food weight per cage
3. Toggle Enable fluid intake tracking to capture fluid weight per cage
4. Toggle Set recording time to associate a custom time with food and fluid measurements
5. Set the After saving navigation instructions to define what Workflows should do once data is saved

Collect data with devices in Workflows

Configure devices to write data into specific fields present in a Workflow. This can simplify searching for animals by using a RFID or barcode scanner and it can simplify data entry through connections to measurement values from the preset. In Workflows, devices can write to the following fields:

• Assign IDs
• Preset Measurements
• Weight at dosing
• Search Bar

In order to use a device in Workflows, it must be configured for the study. To configure the device for the study:

1. Enter the study you are working on and click the Devices icon in the blue navigation bar
2. Click Connect device
3. Select the correct device and click Connect. If the device has been previously registered correctly, the software should instantly recognize the device and display the name.
4. Beside the device, click on the dropdown menu and select the field that the device should target. This can be a measurement in your preset or search bars. Alternatively you can select follow focus to input data directly to the cursor position.
5. Click X to close the device connection screen. The software is now ready to receive data.

You can configure devices to write data directly into specific fields in a Workflow. This makes it easier to search for animals using an RFID or barcode scanner and streamlines data entry by pulling in preset measurement values from instruments like a scale or caliper.

In Workflows, devices can write to these fields:

• Assign IDs: inputs data into the assign IDs field
• Preset measurements: inputs data into the select measurement field from the preset
• Weight at dosing: inputs data into the weight field when dosing
• Search bar: inputs data into the search bare
• Follow focus: inputs data directly where the cursor is positioned

To use a device in Workflows, it must first be configured for the study. Any new devices must be set up by an administrator in Manage Teams before they can be used in a study.

To configure a device in a study:

1. Enter the study and click the Devices icon in the blue navigation bar
2. Click Connect device
3. Select the correct device and click Connect. If the device has been registered, the software will recognize it and display the name
4. Beside the device, open the dropdown menu and select the field the device should target
5. Click X to close the device connection screen. The configuration is automatically saved

How to use Workflows

Once a Workflow has been configured, you can begin data capture. Execution follows the sequence you defined during setup, starting with cage-level food and fluid tracking if enabled, or with the first action specified in your General settings.

From there, Workflows guide you step by step through data collection. You can search for or scan cages and animals, record measurements, collect samples, log observations, administer doses, and mark animals as deceased, all within the same streamlined workflow. As data is entered, Benchling applies calculations and ensures results are immediately visible in animal profiles, graphs, and exports.

Execute a workflow

1. Once the Workflow setup is complete, click Continue
2. If tracking food and fluid, search for, scan in, or select the first Cage under Cages then proceed to Recording Food and Fluid Intake
3. To begin performing any other actions, search for, scan in, or select the desired animal under Animals to get started with data collection

Note: At this point, whichever option you’ve selected under General for Start on will appear first.

Filter animals in a workflow

You can apply filters after workflow execution begins to narrow which animals are displayed.

1. Click the Filter button to the left of the search bar
2. Choose whether All or Any conditions must be met for animals to appear
3. Select from the available filter criteria:
   • Cage name: the cage in which the animal is housed
   • Study group: the study group the animal belongs to
   • Living status: living or deceased
   • Alert: animals with resolved or unresolved alerts
   • Sex: the sex of the animal
   • Metrics: the metric values as defined in the preset (e.g., weight, tumor volume in presets
4. To add more conditions, click Add condition
5. To remove a condition, click the X next to the row
6. When ready, click Filter to apply

Record food and fluid intake

Benchling automatically calculates the average intake per animal (g/day), which is visible throughout the platform. Benchling uses the following formula to ensures standardized intake metrics for downstream analysis in group-housed settings. 

• (Food In − (Food Out + Spillage)) ÷ Days Lapsed ÷ Living Animals in Cage = grams consumed per day per animal
  • Food In: The amount added at the beginning of the tracking period.
  • Food Out: The remaining amount at the end of the tracking period.
  • Spillage: Optional field for uneaten food found in the cage (Only applied to food and not fluid).
  • Days Lapsed: The number of days between when Food In and Food Out values were recorded.
  • Living Animals in Cage: The number of living animals in the cage at the time of recording Food Out.

Note: This same logic applies to fluid intake calculations using Fluid In and Fluid Out. 

1. Navigate to the target cage in your workflow
2. Enter values for:
   • Food In (g)
   • Fluid In (g)
3. Later the same day, enter values for:
   • Food Out (g)
   • Fluid Out (g)
   • (Optional) Spillage (g)
4. (Optional) Add comments for context
5. Click Save

Note: You must record In values before Out values to trigger calculations. Out values are unavailable until In values are entered. Mark animals as deceased to keep intake calculations accurate. This updates future calculations only and does not retroactively change past cage data.

Record measurements

Create a measurement

1. Click the Measurements subtab
2. Enter the value manually or input from a connected device
3. Click Save

Edit or delete a measurement

1. Click the Measurements subtab
2. Click the caret icon next to the measurement you want to edit or delete
3. Click Edit or Delete
4. If you edit, re-enter the value manually or scan from a connected device, then click Save
5. If you delete, type DELETE in the confirmation field, then click Delete metric

Assign animal identifiers

1. Click the Measurements subtab
2. If Assign identifiers has been configured in Workflows, the identifier field will appear at the top of the page
3. Enter the new identifier manually or scan barcodes
4. Click Save

Note: Measurements and identifier associations must be completed together before saving.

Manage an alert

When recording measurements, alerts help flag data that exceeds conditions defined when the study was created:

• Critical alerts: A popup appears when a saved measurement exceeds a critical threshold. This stops the workflow until you acknowledge the popup and close the window.
• Warning alerts: A temporary banner appears when a saved measurement exceeds a warning threshold. This disappears automatically after a few seconds and does not interrupt your workflow.

Cages or animals with unresolved alerts are marked with a small red circle beside their name. You can also filter the workflow view to display only animals with active alerts.

Note: Alerts can be resolved directly in the workflow or later from the measurements section of their animal profiles. Resolving an alert removes the alert from view for all team members, but the action can be undone in the workflow or in the alert history on the animal profile.

Collect samples

Create a sample

1. Click the Samples subtab
2. Select the sample types to collect unless previously specified under Workflow Setup
3. Enter optional fields like volume, comments, or other custom metadata
4. Click Save and close to complete sample collection

Note: Multiple sample types can be selected at once. If recording multiple sample types, toggle between them using the blue hyperlinks on the left side of the popup window.

Edit or delete a sample

1. Click the Samples subtab
2. Click the caret icon next to Actions for the sample you want to update
3. Click Edit or Delete
4. If you edit, re-enter the value, then, click Save
5. If you delete, type DELETE in the confirmation field, then click Delete sample

Record observations

Create an observation

1. Click the Observations subtab
2. Select the observations to be recorded unless previously specified under Workflow Setup
3. Select Record Observations
4. Enter notes and provide a grading, if applicable
5. Click Save

Note: Multiple observations can be selected at once. If recording multiple observations, toggle between them using the blue hyperlinks on the left side of the popup window. Available observations and respective gradings are defined in the observations glossary, as specified by an administrator in the Manage teams page.

Record a normal observation

Record a normal observation to indicate that the animal was assessed and no abnormalities were observed.

1. Click the Observations subtab
2. Select Record Normal and save

Note: You can record a normal observation, record a specific observation, or record neither, but not both at one time. If an observation is selected in the workflow (during setup or execution) and you select Record Normal before saving, only the normal observation will be saved for the animal. If Record observation is selected, the chosen observation will be saved instead.

Edit or delete an observation

1. Click the Observations subtab
2. Click the caret icon next to Actions for the observation you want to update
3. Click Edit or Delete
4. If you edit, re-enter the value, then, click Save
5. If you delete, type DELETE in the confirmation field, then click Delete observations

Dose animals

Log a dosage

1. Click the Dosing subtab
2. Update the dose information if applicable
3. Add any notes in the Notes field
4. Click Save to log the dosage

Note: Dosing appears only if a body weight measurement has been recorded for use in dose calculations, The dosage timestamp cannot be edited from this modal. To manually update timestamps, use bulk dosing in the Doses section of the study, or delete the dosage and re-record it in Workflows.

Delete a dosage

1. Click the Dosing subtab
2. Click the caret icon next to Actions for the dose you want to update
3. Click Delete
4. Type DELETE in the confirmation field, then click Delete dosage

Mark animals as deceased

Mark an animal as deceased

1. Select the animal to update
2. Click Mark as deceased in the top right
3. In the popup window, edit the following fields:
   • Deceased date
   • Reason (required)
   • Additional comment
4. Click Save

Note: Once marked as deceased, animals cannot have new measurements or observations recorded. However, samples can still be collected.

Edit or undo marking an animal as deceased

1. Click the Dosing subtab
2. Click the caret icon next to the Actions dropdown in the Marked as Deceased dialogue box
3. If editing, select Edit and click Save
4. If undoing, select Undo and confirm a new cage for the animal

Frequently asked questions

Q: Do I need to complete all of the configured options in workflow setup, or can I skip certain samples or measurements?

A: You can move between different actions in Workflows regardless of what was specified during workflow setup.

Q: How do I record the type of food or fluid a cage is given?

A: Record this information as animal or group metadata.

Q: Can I record food and fluid intake data for earlier dates?

A: You can backdate entries only if no later entries exist for that cage. Entries must follow strict chronological order. To record at a time other than the current time, enable Set recording time in workflow setup.

Q: Can I track food and fluid intake per individual animal?

A: Intake is calculated as an average per animal based on total cage intake and population. Direct per-animal intake recording is not supported in group-housed settings. For single-housed animals, intake is recorded per animal but still logged at the cage level.