Create and publish new presets
Add new
When building a new preset assign a preset name and define the list and order of measurments in this preset. If there are no errors with the preset the measurements will be displayed in a preview panel to the right where the preset calculations can be tested to ensure they are correct before publishing the preset for use in new studies.
Every preset must have weight recorded in grams due to a requirement for dosing calculations, if your study requires body weight calculations such as an average weight to be recorded contact Benchling Support to provide this. The weight field is locked from editing but can be moved using drag and drop into the desired order.
Although changes cannot be made to the weight calculation, the name of this measurement can be changed if required by using the pencil icon that is revealed when hovering over the grey bar and saving a new name such as "Body weight". The units however cannot be changed, contact support if you have additional requirements regarding animal weights.
A list of measurements without calculations can be created whereby only the name and optional unit are defined. When the name and unit (if required) are entered click on the Tick to the right of the row to save or the x to remove from the list. This can have a calculation added at any time by clicking on the name to open the add calculation page.
Adding a measurement with a calculation
Calculation components
There are two types of calculations:
- External - Incorporating other measurements in this preset in the formula (no inputs defined)
- Internal - Incorporating only the inputs defined above in the formula.
Note: A formula cannot contain a combination of measurements and inputs.
When adding a measurement with a calculation a new page will open with additional fields to define the formula and apply advanced configuration. All previously created measurements will appear under the "calculation" section to be used when building a calculation using these.
If this calculation needs new inputs that are not previously created then these are added to be used in the calculation in the first section of this form along with the field to record the Measurement name and optional unit.
To add a calculation with inputs:
- Click add input
- Enter a name and unit (optional)
- Click add input again
- Enter a name and unit (optional) for a second input
- Repeat as required
- Use the blue chips to build the formula
- Click on the names of these inputs to the left of the calculation section as well as the components about the formula field to build the formula for this calculation.
E.g Tumor volume (mm3)
Input 1 : Width (mm)
Input 2 : Length (mm)
Formula : Width * Width * Length/2
Use the blue chips [+], [-], [8], [π], [ave], [(], [)] to build the formula. 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)
Applying advanced configuration
Some presets will require additional configuration, see below a description of each of the available settings to apply.
- All inputs required
- This can be disabled for any SUM or Average calculations. 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.
- 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.
Migrate presets between tenants
To quickly migrate presets from your test tenant to prod tenant:
- From your test tenant click on export in the ... menu to the right of the table for a single preset.
- A .json file is downloaded to your computer under the name of that preset
- In your test tenant click on the Import option under Create preset
- Review and update this preset as required
- Test calculations using the preview panel on the right
- Click Save to create preset
- When ready select the preset and use the bulk action to publish to make this preset available for future studies.
Update 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 follow the steps below:
- Click on Clone in the ... menu to the right of the table for the preset.
- Make the relevant changes required.
- To add calculations or change inputs and configuration, click on the names of the measurement and click Save measurement to apply
- Use the preview panel to test calculations
- Click save to create this preset
- Use the bulk action option to Delete the old version of this preset
- Use the bulk action option to Publish the new preset
FAQ
Why can I not clone or export my presets?
- 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.
What happens when I delete a preset? is there any impact to previous studies?
- When a preset is deleted it is no longer available to be selected for studies. There are no impacts to previous studies. If you accidentally delete a preset, please contact Benchling Support to request this to be undeleted.
Why am I told that my name is not unique when creating inputs for my calculation?
- 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.
- This is required to ensure accurate mapping for inputing measurements and so that the user know exactly which input is which when creating alerts and exporting raw data.