Creating a study in Benchling In Vivo allows your team to design, execute, and manage in vivo experiments from start to finish. This guide walks you through the study creation process, including setting up treatments, alerts, tasks, and team access—all designed to streamline eventual data collection and analysis.

Create a new Study

The study creation process can be started in 2 ways:

1. From the Studies table, by clicking Create new study
2. Click the + icon in the navigation bar

Once you’ve done this you will be prompted to select a study creation form. If only one study creation form template exists on your tenant, clicking either of the buttons above will immediately start the process. However, if multiple templates have been configured, a study creation form will need to be selected.

1. Search for the name of the study creation form template using the search bar
2. Click the radio button beside the template
3. Click Next

Clone a Study 

Cloning a study design is a quick method to pre-populate the study creation form with information that was used in a similar previously conducted study.

Note: Only studies created after January 29, 2024 can be cloned.

1. Click the Studies icon in the main navigation bar
2. Click ••• at the end of the row for the study that needs to be cloned
3. Click Clone Study
4. Enter a Study Name for the new study
5. Progress through the study creation form and make changes as required

Note: Cloning a study automatically creates a study creation form draft that can be resumed at any time. Studies can’t be cloned if the original form template has been deleted by a tenant administrator.

Study creation form sections

After the study creation template has been selected, a list of form sections will be visible on the left side. If you do not see any of the sections below then they have not been configured as part of the template. Tenant administrators have the ability to add or remove sections within Manage Team. Learn how to add or remove sections from a study form when configuring your In Vivo tenant. 

The sections below walk you through what you need to fill out in each section before you can create your new study. 

Information

1. Enter a Study name, this is a required field that must be greater than 3 characters in length
2. Enter a Description for the study, this is an optional field
3. If a Study Code has been configured in the tenant, a dropdown menu will be available to select the correct code template. Note that this will only be visible if more than one code template exists. If only one exists, it will automatically be applied
4. If Projects have been configured via the API, a dropdown menu will be available to select the Project this study belongs to
5. Select the Study start date using the date picker at the bottom of this section
6. Click Next

After clicking Next, you will be brought to the next section in your study creation template, the order of sections can also be changed by administrators and may not be the same as indicated below.

Team

1. Select each user on your tenant that should have access to the study
2. Select either Write or Read permissions for each selected user
   • Write: The user will have the ability to add, amend and delete data in the study.
   • Read: The user will have the ability to see the study and associated data but can’t make changes
3. If the study is being registered on behalf of another user, select I’m registering it for someone else located beneath your own details
   • Use the dropdown menu to select the new study owner
4. Click Next

Cages and animals

1. Enter the number of cages that will be used for the study
2. Click Generate
3. If needed, change the name of each cage
4. Set the number of animals in each cage under the Subjects heading.
5. Set the Sex of the animals in each cage
6. Click on the date picker under the D.O.B heading to set the date of birth
7. Click Next

Note: Cages and animals do not need to be created at this stage if the details are unknown. It is possible to click Next at any time to skip the section and create them in the future.

Groups & Treatments

Create groups

1. In the Groups tab, click Add treatment groups
2. Enter the Name of each group, clicking Enter on the bottom row will automatically create a new Group row
3. If needed, change the Color of each group by double clicking on the color of each row. Select the new color by using the color picker or by entering a hex code
4. Enter the number of animals for each group
5. Any other columns that are visible have been configured by your tenant administrator as custom metadata. Required fields will be indicated with (req.) in the column header
6. Click Add metadata to add additional columns that have not been configured to display automatically
7. Click Save
8. Select the Control group for the study using the dropdown menu located under the table
9. Select either Arithmetic or Geometric mean to be displayed in graphs generated in the study
10. Select either Standard deviation or Standard error of the mean 

Note: It is possible to copy and paste group information directly from a spreadsheet if it is formatted in the same order.

Add a disease model

Diseases represent disease induction agents with their own set of metadata fields, separate from general treatments. These are recorded distinctly in the tenant. Diseases can be administered to any animal at any time, regardless of group configuration. 

1. Click the Diseases tab
2. Click Add a disease
3. Search for and select the disease model being used for the study under Name
4. Select the Dosing Method to be used
   • The Custom option will enable additional units to be selected, including cells
5. Set the dose information which is dependent on the dosing method selected
   • Dose
   • Stock concentration
   • Volume
   • Dose volume
6. Complete any custom metadata fields that have been added by your administrator
7. Click Add disease
8. Repeat the steps above if multiple disease models are being used in the same study

See how to use dosing and treatment tools for more instructions on using diseases.

Add treatments and pre-treatments

Treatments and pre-treatments let you track the delivery of compounds to animals in your study. Use pre-treatments to model compounds given before animals are assigned to study groups. Treatments model compounds delivered to specific groups of animals and can only be administered once animals are assigned to a group configured with that treatment.

1. Click the Treatments tab
2. Click Add a treatment
3. Select either Treatment or Pre-treatment
   • Treatment: Can only be administered to animals in groups
   • Pre-treatment: Can be administered to any animal regardless of group status
4. Search for and select the treatment being used in the study under Name
5. Select the Dosing Method to be used
6. Set the dose information which is dependent on the dosing method selected
7. Complete any custom metadata fields that have been added by your administrator
8. Click Add treatment
9. Repeat the steps above for each treatment that is being used in the study. A separate entry is needed for different doses of the same treatment

See how to use dosing and treatment tools for more instructions on using treatments and pre-treatments.

Configure groups with treatments

1. Click the Configuration tab
2. Click on the first Group
3. Select each Treatment that will be administered to animals in that group. Multiple treatments can be assigned to each group if needed
4. Repeat the steps above for each group
5. Click Next

Select a Preset

1. Click on the measurement Preset that will be used in the study
   • Once selected, a list of the measurements and associated calculations will be displayed to the right
2. Click Next

If you are tracking food and/or fluid, and you’ve enabled the Food/Fluid tracking feature, then you will want to toggle on the enable food/fluid tracking option at the bottom of the preset page. This feature is currently in LA and enables real-time, cage-level intake tracking in preclinical studies.

Note: If you need to collect measurements that are not in an existing preset, you will need to contact your tenant administrator who can manage presets in the Manage Team. Learn how to manage presets by navigating to configuring your In Vivo tenant.

Alerts

1. Click Add Alert
2. Select an option for When
   • As soon as: The alert will trigger once when the condition is met for the first time
   • Everytime: The alert will trigger everytime the condition is met
3. Select an option for Metric. This list will be determined based on the measurements that exist in the preset
4. Select an option for Condition
   • Is greater than: The alert will trigger when a recorded measurement value is greater than the assigned amount
   • Is less than: The alert will trigger when a recorded measurement value is less than the assigned amount
   • Has increased by: The alert will trigger when the recorded measurement has increased by a specified %
   • Has decreased by: The alert will trigger when the recorded measurement has decreased by a specified %
5. Set the Amount. This is the measurement value that will be used to determine if the conditions above have been met
6. If increased by or decreased by has been selected, set the Compared to the option
   • First measurement recorded: Each recorded measurement will be compared against the first measurement recorded for that animal to determine if the condition has been met
   • Most recent measurement: Each recorded measurement will be compared against the most recent measurement recorded for that animal to determine if the condition has been met
7. Set the Alert action. This is custom text that will display when the alert is triggered in the study. This text should include clear guidance on the appropriate action on an animal a user should take when the alert is triggered, such as to "Contact the veterinarian" or "Remove from study"
8. Select the Alert type
   • Warning: Triggered alerts will display as a temporary banner that will be visible in the bottom left corner. This will automatically disappear after 5 seconds
   • Critical: Triggered alerts will display as an overlay that requires the user to acknowledge and manually dismiss
9. Click Create
10. Repeat the steps above if additional alerts are required in the study
11. Click Next

Tasks

There are multiple different types of tasks that you can create in a study. Once you choose your task type, the details that you will need to enter to configure that task type will change. In this section, we show how to create a task, then break down all the information that you will need to enter in each section for each specific type of task.

1. Click Add Task, then give you task a name and optional description
2. Use the task type dropdown to define the type of task
   • Measurement: A task to collect measurements that exist within the study preset
   • Sample: A task to collect samples from animals
   • Observation: A task to record clinical observations on animals
   • Dosing: A task to dose animals with a treatment
   • Other: Any other task that can simply be described using plain text rather than using defined data capture functionality
3. Click Next

The section below walks you through the steps for configuring the execution portion of each type of task you can select. 

Execution

Measurement task

Sample task

Observation task

Dosing task

Other task

There is no execution step for this type of task.

Schedule

When you get to the schedule tab, you choose one of three options that defines how often the task is performed and based on the frequency you will add different information. 

• One off: A task that will only need to be performed once
• Recurring: A task that will be performed in a recurring pattern (eg. Monday and Wednesday each week)
• Conditional: A task that needs performed once a condition is met (eg. age is 35 days)

One off

1. Set the date that the task needs to be performed
2. One off tasks will be considered all day tasks by default. If they need to be performed at a particular time then disable this option and manually set the duration
3. Click Next

Recurring

1. Set how frequently the task will repeat, use the text box to enter a number and use the dropdown to set if it repeats over the course of days or weeks
2. Set the date that the task frequency will begin and end
3. Recurring tasks will be considered all day tasks by default. If they need to be performed at a particular time then disable this option and manually set the duration
4. Click Next

Conditional

1. Select the condition
   • Age (days): The age of each animal
   • Study day: The number of days post the study start date
   • Tracking day: The number of days post the tracking date for each animal
2. Enter each day that the task should be performed separated by commas, Tab key or Enter key
3. Conditional tasks will be considered all day tasks by default. If they need to be performed at a particular time then disable this option and manually set the duration
4. Click Next

Target

1. Select if the task applies to All animals in the study or only animals in particular Groups
   • If the Groups option is chosen, select each Group that the task applies to
2. Click Next

Assignees

1. Select each Study User who should be automatically assigned to each instance of this task
2. Click Submit

Repeat the steps above for each task that needs to be performed in the study. Then click Next to proceed to the next section of the form. 

Note: The Study execution timezone will default to the timezone set by the user who is creating the study. Change this is the study is to be executed by a team in a different timezone.

Attachments

Files

1. Click the Files tab
2. Click Upload File
3. Find the file on your computer and click Open
   • Alternatively, drag and drop the file into the area indicated
4. Change the File Name if the default is not preferred
5. Complete any additional metadata fields that have been configured by your tenant administrator
6. Click Save
7. Repeat the steps above for any additional files

Links

1. Click the Links tab
2. Click Add a link
3. Enter the Link name
4. Enter the URL
5. Complete any additional metadata fields that have been configured by your tenant administrator
6. Click Save
7. Repeat the steps above for any additional links

Click Next to proceed to the next section of the form. 

Custom sections

Any additional sections in the study creation form have been specifically configured by your tenant administrator to capture other important information. Required fields will be marked with a (required) tag, otherwise fields can be treated as optional. 

Click Next to proceed to the next section of the form.

Summary

This is a read-only summary of content entered into the previous sections. 

To make amendments, hover over any section and click Edit. Once reviewed, click Create to create the study.

Drafts

Save a study creation form as a draft

Click Save as draft at any time during the study creation process. Clicking Next between each section will also automatically save progress as a draft. Progress will be saved and can be resumed at a later date.

Note: this will fail if any required fields in the current section have been left incomplete. Ensure all required fields are populated.

Resume a study creation draft

1. Click the Studies icon in the main navigation bar.
2. Click the Drafts tab
3. Click the draft Name you would like to resume
4. Continue the study creation process as normal

Delete a study creation draft

1. Click the Studies icon in the main navigation bar
2. Click the Drafts tab
3. Select the draft Names you want to delete
4. Click Bulk Actions
5. Click Delete
6. Type DELETE in block capitals
7. Click Delete

Update a study

Most of the information captured in the study creation form can be amended or added post-creation within study settings.

Inside the study, click Settings

In the settings tab of the study, navigate to the following sections to change the information listed below: 

• Information
  • Study name
  • Description
  • Project
  • Study start date
• Team
  • Add or remove users
  • Change user permissions between read and write
• Preset
  • Select a new preset
• Alerts
  • Add new alert
  • Edit existing alerts
  • Delete alerts
• Tasks
  • Add new task
  • Edit existing tasks
  • Delete tasks
• Metadata
  • Amend previously recorded metadata
  • Add new fields 

Ensure that you click Save to save any changes you make. 

Note: It is not possible to change the preset if alerts have been configured or data collected in the study.

Danger zone

1. To complete a study, click Complete study
   • Click Complete study again to confirm
2. To cancel a study, click Cancel study
   • Click Cancel study again to confirm
3. To delete a study, click Delete study
   • Type DELETE in block capitals
   • Click Delete study

Frequently asked questions

Q: How do I edit team members after study creation?

A: Open the study > Settings > Team to add, remove, or change permissions.

Q: Can I delete or update a treatment?

A: Yes. In the Treatments tab, select a treatment, click Bulk actions, and choose Delete or Edit.

Q: Why can’t I change the preset?

A: Once data is collected or alerts are created, the preset is locked. You’ll need to clone the study to change it.

Q: Can I edit tasks?

A: Tasks can be edited from the Tasks tab. Task type and target animals cannot be edited after creation.

Q: What parts of a study get cloned?

A: Most parts of the study creation form get cloned; however a study name and study code are required. Note that only the design aspects of the study are cloned. No animals, measurements, samples, observations or doses are cloned.