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What is a preset?
What is a preset?

What measurements can be captured and how what can you do with these in Benchling In Vivo?

Updated over a week ago

A preset is a predefined set of measurements that can be recorded throughout the study no more than once per day. The user is be presented with a library of options that have been added to that tenant and selects the appropriate preset for the study either during study creation or from the study settings.

  • A single preset can be selected per study, if multiple measurements need to be collected, the selected preset must include ALL measurement options that will be recorded throughout the study.

    • Measurements in a preset are optional, if they exist on a study the option to record these is presented but not required.

    • Note, once a study is underway and measurements are captured, the selected preset can not be changed.

The preset will define the specific variable(s) that will be recorded for each measurement. This may utilize a formula, leveraging the variables to automatically calculate the measurement. For example, using a formula, width, length and breadth of a tumor can be used to calculate the volume of a tumor

What are the calculation options in a preset?

  1. Internal calculations

A calculation where the variables in the formula are recorded ONLY for the purpose of calculating the measurement. E.g Tumor volume, the length and width are the variables which are not relevant to track, randomize by and/or graph by themselves, only the final output “tumor volume” is significant in this regard.

For this type of calculation you can apply additional configuration:

  • Auto Swap: Whereby the values recorded for length and width of tumor volume are swapped to ensure the larger is always recorded as length.

  • Not all variables are required: Whereby the calculation will be carried out without all fields having a value recorded, I.e A preset is set up to calculate the average of 5 readings, only 3 values are entered and the average is still calculated.

2. External calculations

A calculation where the variables used in the formula are recorded as separate measurements on the same day that can be either entered directly by the user or calculated as an internal calculation. Each of these measurements will be tracked and graphed independently as well as available for use in randomization and summarized in grouped reports.

Key points to note:

  • Only one value for each metric can be recorded per day (e.g body weight can be recorded no more than once per day for each animal)

  • Often customers model observation scoring readouts that are summed to record a total score so that alerts, graphs and exports can be utilized.

  • Calculations in a preset can only include variables that are captured on the same day

  • You can import your study data from a spreadsheet as long as the imported measurements are included in the preset

  • You can only randomize by measurements that are available in the selected study preset.

  • Any measurement on a preset can be used as a condition on a study alert.

  • Cages can be moved from one study to another providing both studies use the same preset.

  • Contact Support to request a preset to be updated, renamed, added or deleted.

    • In this request please provide a list of measurements, units and formulas as well as the name that should be given to this preset.

Available calculation components

  • Add

  • Subtract

  • Divide

  • Multiply

  • Sum

  • Average

  • If

    • if one value is larger than/smaller than another user inputted value or a hard coded value, apply a calculation

    • if not apply a different caluclation

For more complex study types contact your benching representative to discuss what can and cannot be supported in a preset.

Example Preset

Take the preset below as an example: Subcutaneous Tumor - Bi flank:

  • Two tumors are implanted and each need to be recorded as individual tumors with calculated volumes using the internal calculation width*width*Length/2.

  • The total of both tumors is summed together for the Total tumor volume for animal welfare purposes and calculated as an external calculation right_flank + left_flank

  • In this example the final calculated measurement “total tumour vol” will not be calculated until a value for both left and right tumor volumes have been recorded on this day (all variables are required)

As part of the onboarding processes, the Benchling implementation team will determine with the best information at that time, what presets need to be created to assemble the necessary preset library for the customer.

How are presets used in a study?

Measurements included in the study preset can be recorded no more than once per day using the following data entry options:

  • Workflow - for real time data capture with connected lab devices

  • Import - for bulk entry of data across multiple measurements for one day.

    • Note: Smart swap cannot be applied at import.

  • Animal profile - for one off ad hoc entries for individual animals

  • Data tables - for real time and bulk data capture in a tabular interface and to ultilize formulas across multiple days.

    • Note: Smart swap cannot be applied in data tables.

Data captured in presets inform:

  • Animal measurement history

  • Real time graphs

  • Alerts: all measurements including internal variables (e.g. length, width) can be used as conditions triggering alerts.

  • Data Exports (Excel and GraphPad prism)

  • Randomization.

  • Dosing calculations based on Body weight.

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