Purpose
To provide details about the necessary steps to implement the ThermoFisher Scientific, Qubit Flex data connector for use with the Benchling Connect platform.
Introduction
The ThermoFisher Scientific, Qubit Flex data connector is a component used in the context of the Benchling Connect platform to parse data from ThermoFisher Scientific's Qubit Flex spectrophotometer using the Qubit Flex software to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run.
The Benchling Connect, Qubit Flex data connector is a ‘file-based’ based data connector, meaning that it processes comma-separated values (.csv) exports generated by the Qubit Flex application. 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 Qubit Flex data connector for use with the Benchling platform, there are multiple steps that need to be followed across both the Qubit Flex and Benchling user interfaces.
This guide details the steps to be taken in both applications in order to configure the integration.
Steps within ThermoFisher Scientific, Qubit Flex
From within ThermoFisher Scientific, Qubit Flex software a user must:
(i) Perform a csv file export compatible with the Benchling Connect, Qubit Flex data connector
(ii) Ensure that the file is placed with the watched directory configured via a Benchling Connection.
Exporting Data From Qubit Flex
On the Home screen, press Data to open the Data screen.
To save only individual data entries from a data set, press the data set of interest, and then check the selection box to the left of the samples you wish to export
Press the check box to the left of the samples that you wish to export. You can select multiple samples to export. To select all samples in the data set to export, press the blue check icon on the header row.
After you have selected the data sets or the samples, press Actions, then select Export.
In the Export data screen, select the Export method.
Available options are Cloud (i.e., your Connect™ account), USB, and Network Drive. • To export data to a USB drive, insert the USB drive into the Qubit™ Flex Fluorometer.
Note: User is expected to use the USB connection to export data
To export data directly to a computer:
1. Connect the Qubit™ instrument to the computer using the USB cable.
2. From the computer, access the Qubit™ Flex Fluorometer as an external device.
3. Access the files saved on the Qubit™ instrument using the operating system’s normal file browsing menus.
4. Copy the desired files to the computer.
Note: Files copied from the Qubit™ instrument should be placed in the watched directory configured via a Benchling Connection.
Steps within Benchling
From within Benchling, a user must:
-
Enable the ThermoFisher Scientific, Qubit Flex data connector on the tenant [internal admin console]
-
Configure a Qubit Flex Connection
-
Create a Result schema to structure the data to be recorded
-
Configure a Run schema to accept data from Qubit Flex and records Results
For steps 1 and 2, please reference the Benchling Connect Installation Guide for details related to creating and installing a Gateway and configuring a Connection.
Create Result Schema for Qubit Flex data
The Benchling Connect - ThermoFisher Scientific, Qubit Flex data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Qubit Flex file export. The data is handled in a two step process; step one from Qubit Flex export (.csv) to the .json based ASM, and step two from the ASM .json to a .csv file available for ingest to Benchling.
The Benchling Connect - ThermoFisher Scientific, Qubit Flex data connector supports fluorescent spectrophotometric measurements of micro-volume samples.
These data are structured using the Allotrope Spectrophotometer ASM data model. Details about the this ASM schema can be found here:
The data connector then converts the ASM to a sample data file .csv file (which is structured such that each row of the file represents a sample measured), sample-separate-unit-column data file .csv file (structure such that each row of the file represents a sample measured with columns that contain units having a stand-alone column to represent the unit value), measurement data file .csv file (structured such that each row of the file represents a measurement), measurement-separate-unit-column data file .csv file (structure such that each row of the file represents a measurement with columns that contain units having a stand-alone column to represent the unit value).
For Qubit Flex, the csv files will typically contain the following columns (if available within the data):
- Device Identifier
- Brand Name
- Model Number
- Product Manufacturer
- ASM converter name - name of data connector library
- ASM converter version - version of data connector library
- File Name
- Measurement Identifier*
- Measurement Time
- Container Type
- Sample Identifier
- Batch Identifier
- Experiment Type
- Device Type
- Last Read Standards
- Selected Samples
- Qubit Tube Concentration
- Standard 1 Concentration
- Standard 2 Concentration
- Original Sample Concentration
- Calibrated Tubes
- Operating Minimum
- Operating Maximum
- Operating Range
- Sample Volume Setting
- Excitation Setting
- Dilution Factor
- Fluorescence*
* To account for cases of multiple measurements per sample, these fields will include an index
(e.g. _1, _2, _3,...) corresponding to the number of measurement.
Sample files can be found here.
Configure Run Schema to employ Qubit Flex Connection
The Run schema can be created from the menu under Feature Settings.
As part of the Run schema creation, the user should specify 'ThermoFisher Scientific Qubit Flex as the Connection Schema.
Configure the Output File Processor
For details on configuring the Output File Processor within the Run schema, please refer to these articles.
- Configure the Output File Config of a Benchling Connect Run
- Configure the Output File Processor to Create New Entities
- Configure the Output File Processor to Capture Results
Example Qubit Flex Data
Refer to the example files in the repository below if you would like to test this configuration pattern with demonstration data.
ThermoFisher Scientific, Qubit Flex Data Connector Requirements
| Item | Specification |
| Qubit Flex | Qubit Flex v1.9.0* |
| Operating System | External Device (see Qubit Flex User Guide)** |
| Memory | External Device (see Qubit Flex User Guide)** |
| Processor | External Device (see Qubit Flex User Guide)** |
| Gateway |
Benchling Gateway installed on PC, able to communicate on port 443 |
*This is the version of Qubit Flex Software 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.
**The Qubit Flex Software runs on the stand-alone instrument itself as an external device to computer connected to Benchling.
Revision History
2024/08/09
Initial Version
2024/08/19
- Update Qubit Flex Data Connector Requirements with User Guide label/link
- Add link to Spectrophotometry ASM schema
2024/09/18
Added Github testdata link
2024/10/14
Add description for measurement CSV output and corresponding columns
Add description for separate-unit-column CSV outputs and corresponding columns