ThermoFisher Scientific, Qubit 4 Configuration Guide

Purpose 

To provide details about the necessary steps to implement the ThermoFisher Scientific, Qubit 4 data connector for use with the Benchling Connect platform.

Introduction

The ThermoFisher Scientific, Qubit 4 data connector is a component used in the context of the Benchling Connect platform to parse data from ThermoFisher Scientific's Qubit 4 spectrophotometer using the Qubit 4 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 4 data connector is a ‘file-based’ based data connector, meaning that it processes comma-separated values (.csv) exports generated by the Qubit 4 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 4 data connector for use with the Benchling platform, there are multiple steps that need to be followed across both the Qubit 4 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 4

From within ThermoFisher Scientific, Qubit 4 software a user must:

(i) Perform a csv file export compatible with the Benchling Connect, Qubit 4 data connector 

(ii) Ensure that the file is placed with the watched directory configured via a Benchling Connection.

Exporting Data From Qubit 4

On the Concentration, Graph, RNA IQ results, or Home screen, press Data

On the Export data screen, check the selection box to the left of each data set you wish to export

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

Select CSV and press Export to export the 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™ 4 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:

1. Enable the ThermoFisher Scientific, Qubit 4 data connector on the tenant [internal admin console]

2. Configure a Qubit 4 Connection

3. Create a Result schema to structure the data to be recorded

4. Configure a Run schema to accept data from Qubit 4 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 4 data

The Benchling Connect - ThermoFisher Scientific, Qubit 4 data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Qubit 4 file export. The data is handled in a two step process; step one from Qubit 4 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 4 data connector supports fluorescent spectrophotometric measurements of micro-volume samples.

These data are structured using the Allotrope Spectrophotometry ASM data model. Details about the this ASM schema can be found here:

https://github.com/Benchling-Open-Source/allotropy/blob/main/src/allotropy/allotrope/schemas/adm/spectrophotometry/BENCHLING/2023/12/spectrophotometry.schema.json 

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 4, the csv files will typically contain the following columns (if available within the data):

• Device Identifier
• Brand Name
• Model Number
• 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
• Detector Wavelength Setting*
• Detector Wavelength Setting Unit**
• Excitation Wavelength Setting*
• Excitation Wavelength Setting Unit**
• Mass Concentration*
• Mass Concentration Unit**
• Original Sample Concentration
• Qubit Tube Concentration
• Standard 1 Concentration
• Standard 2 Concentration
• Sample Volume Setting
• Excitation Setting
• Emission Setting
• Experiment Type
• Device Type
• 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.

**To account for cases of multiple units of samples/measurements (sample-separate-unit-column & measurement-separate-unit-column files only, these fields will be included in the csv file(s).

Sample files can be found here.

Configure Run Schema to employ Qubit 4 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 4 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 4 Data

Refer to the example files in the repository below if you would like to test this configuration pattern with demonstration data. 

https://github.com/Benchling-Open-Source/allotropy/blob/main/tests/parsers/thermo_fisher_qubit4/testdata/thermo_fisher_qubit4_example_1.csv 

ThermoFisher Scientific, Qubit 4 Data Connector Requirements

*This is the version of Qubit 4 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 4 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 4 Data Connector Requirements with Qubit 4 User Guide label/ external 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