Purpose
To provide details about the necessary steps to implement the ThermoFisher Scientific SkanIt data connector for use with the Benchling Connect platform.
Introduction
The ThermoFisher Scientific SkanIt connector is a component used in the context of the Benchling Connect platform to parse data from a ThermoFisher Plate Reader to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run.
The Benchling Connect,ThermoFisher Scientific SkanIt connector is a ‘file-based’ based connector, meaning that it processes excel (.xlsx) exports generated by the SkanIt. The data within the file export is then accessed by Benchling Connect through the use of a ‘watched’ file directory on the local computer hosting a Benchling Gateway, which has been configured via a Connection from within Benchling.
In order to successfully implement the SkanIt connector for use with the Benchling platform, there are several steps that need to be followed across both the SkanIt and Benchling user interfaces.
This guide details the steps to be taken in both applications in order to configure the integration.
Steps within SkanIt
From within SkanIt, a user must:
- Configure an excel (.xlsx) export compatible with the Benchling Connect, SkanIt connector.
- Execute the export of that file from their SkanIt session.
- Ensure that the file is placed with the file watched directory configured via Benchling Connection.
Current Limitations:
- Absorbance is currently supported, but other modes are not, including: Fluorescence and Luminescence. Other information that a user may request, but is not supported include: time-resolved data, AlphaScreen, kinetic, dispensing, incubator/shaker, and integrated gas module.
- The SkanIt software can also provide calculated values, which may not be supported at present.
Exporting Data from SkanIt
A user creates a Report from the SkanIt Software.
- Select Data Processing > Report / Export
- Right click any step and select Report / Export to add report options on the Results tree
- Click Add> to move selected items on the list and <Remove to remove from the list
- Make sure Absorbance, General information, Session information, Instrument Information, Protocol parameters, Run log, and Layout definition are selected
- Select Format for any of the selected items and choose List or Matrix view
- Currently, the adapter accepts the Matrix view
- Click OK to close the dialog
- Select Save to file and save the file to .xlsx
Steps within Benchling
From within Benchling, a user must:
-
Enable the Thermo Fisher SkanIt connector on the tenant [internal admin console]
-
Configure a Thermo Fisher SkanIt Connection
-
Create a Result schema to structure the data to be recorded
-
Configure a Run schema to accept data from Thermo Fisher SkanIt and records Results
aFor steps 1 and 2, please reference the Benchling Connect Installation Guide for details related to creating and installing a Gateway and configuring a Connection.
Creation of Result schema for SkanIt data
In order to record results returned via the integration a Result schema must be created. This can be done prior to configuration of the Run schema, or within the context of the Run schema Output File configuration.
The Benchling Connect - SkanIt connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the SkanIt file export. The data is handled in a two step process; step one from SkanIt export to the .json based ASM, and step two from the ASM .json to a .csv file available for ingest to Benchling.
These data are structured using the Allotrope Plate Reader ASM data model. Details about the this ASM schema can be found here:
The connector then converts the ASM to a well file .csv, structured such that each row of the file represents a well of the plate; and a measurement file .csv, in which each row of the file represents a measurement.
The well file and measurement file can contain the following columns (if available within the data):
- Product Manufacturer
- Device Identifier
- Model Number
- Equipment Serial Number
- Firmware Version
- File Name
- UNC Path
- Software Name
- Software Version
- ASM Converter Name
- ASM Converter Version
- Measurement Identifier - this is a UUID generated as part of data conversion
- Measurement Time
- Device Type - this will be 'plate reader' in all cases
- Experimental Data ID
- Container Type - this will be 'well plate' in all cases
- Plate Well Count
- Well Plate Identifier
- Location Identifier
- Sample Identifier
- Sample Role Type
- Compartment Temperature
- Device Type
- Detection Type - this will refer to Absorbance, Fluorescence, or Luminescence
- Detector Wavelength Setting* - where applicable
- ‘Measurement’* - this column header will vary depending on the modality: absorbance, fluorescence, or luminescence - e.g absorbance_mAU
* To account for experiments with multiple measurements these columns will be duplicated (as needed) and will be annotated with a number for each measurement.
SkanIt Connector Requirements
Item | Specification |
SkanIt | version 7.0.0.50* |
Operating System | 64-bit edition of Microsoft Windows 10 or 11 (Pro or Enterprise edition) |
Memory | 8 GM RAM |
Processor | Quad-core (or dual-core with four logical processors), 2 GHz or faster |
Gateway | Benchling Gateway installed on PC, able to communicate on port 443 |
*This is the version of SkanIt that the Benchling Connector was developed and tested against. Processing exports from other version of the software may be possible, but this would need to be confirmed by the user.
Revision History
2024-09-03
Initial Version
2024-10-14
Update name of connector to 'Thermo Fisher SkanIt'