Purpose 

To provide details about the necessary steps to implement the Thermo QuantStudio data connector for use with the Benchling Connect platform.

Introduction

The ThermoFisher Applied Biosystems (AB) QuantStudio data connector a component used in the context of the Benchling Connect platform to parse data from AB QuantStudio Real-Time PCR Software to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run. The AB QuantStudio Real-Time PCR Software is used in conjunction with ViiA 7, QuantStudio 6 and 7 Flex Real-Time PCR systems.

The Benchling Connect - AB QuantStudio data connector is a ‘file-based’ based data connector, meaning that it processes text file exports generated by the AB QuantStudio Real-Time PCR software. 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 AB QuantStudio data connector for use with the Benchling platform, there are specific steps that need to be followed across both the AB QuantStudio Real-Time PCR software and Benchling user interfaces. 

This guide details the steps to be taken in both applications in order to configure the integration. 

Steps within QuantStudio Real-Time PCR software

The user is expected to enter Sample Name values within the QuantStudio UI that conform to entity identifiers within Benchling, either existing entity IDs or entities they wish to register upon processing of results. The user may do this by manually entering Sample Names or Importing a Sample Definition File (see p.59 QuantStudio Real-Time PCR System Software - Getting Started Guide, Pub. 4489822).

The user is expected to generate a .txt export from the Export view within the QuantStudio UI. 

The user can select the data to include within the export by selecting the individual tabs.

The data connector is able to process the data within the: Sample Setup, Amplification, Multicomponent, and Results tabs

The user is expected keep the default option to Export Data To One File

The user should select .txt as the file type. Processing of the .xls and .xlsx formats is not currently supported by the data connector.

The user should set the Export File Location to be the target directory specified during Connection configuration.

In order to ensure that the exported files are consistently placed in the target directory for the Connection, the default export location can be set within the QuantStudio preferences menu.

Steps within Benchling

From within Benchling, a user must:

1. Enable the QuantStudio data connector on the tenant [internal admin console]

2. Configure a QuantStudio Connection

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

4. Configure a Run schema to accept data from QuantStudio and records Results

For steps 1 - 4, please reference the Benchling Connect Installation Guide for details related to creating and installing a Gateway and configuring a Connection.

Data returned by AB QuantStudio data connector

The Benchling Connect - AB QuantStudio data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Thermo QuantStudio file export. The data is processed in a two step process; step one from AB QuantStudio export to the .json based ASM, and step two from the ASM .json to (3) .csv files available for ingest to Benchling - the well file in which each each row corresponds to a well in the PCR plate, the measurement file in which each row corresponds to each measurement taken, and the group file in which each row corresponds to a ‘group’ with results aggregated across sample identifier and target DNA. 

Details about the qPCR ASM schema can be found here:

https://github.com/Benchling-Open-Source/allotropy/tree/main/src/allotropy/allotrope/schemas

The well file can contain the following columns (if available within the data):

• device identifier
• model number
• device serial number
• data system instance identifier
  - this represents the computer from which the data was retrieved
• file name
• UNC path - this corresponds to the complete file path of data file 
• software name
• software version
• ASM converter
• ASM converter version
• experimental data identifier - this corresponds to the “Experiment Name” in QuantStudio
• experiment type
• container type
• plate well count
• measurement identifier <reporter dye>
• measurement time
• target DNA description <reporter dye>
• sample identifier
• sample role type <reporter dye>
• well location identifier
• well plate identifier
• device type
• measurement method identifier
• total cycle number setting
• pcr detection chemistry
• reporter dye setting <reporter dye>
• quencher dye setting <reporter dye>
• passive reference dye setting
• automatic cycle threshold enabled setting
• cycle threshold value setting <reporter dye>
• automatic baseline determination enabled setting
• baseline determination start cycle setting <reporter dye>
• baseline determination end cycle setting <reporter dye>
• genotyping determination method
• genotyping determination method setting <reporter dye>
• cycle threshold result <reporter dye>
• normalized reporter result <reporter dye>
• baseline corrected reporter result <reporter dye>
• genotyping determination result <reporter dye>

Those parameters whose values may differ between channels in a multiplexed assay are appended with the <reporter dye> (e.g. VIC, FAM).

The measurement file can contain the following columns (if available within the data):

• device identifier
• model number
• device serial number
• brand name
• product manufacturer
• data system instance identifier
• file name
• UNC path 
• software name
• software version
• ASM converter
• ASM converter version
• experimental data identifier
• measurement identifier
• experiment type
• container type
• plate well count
• measurement time
• sample identifier
• reporter dye setting
• target DNA description
• well plate identifier
• device type
• sample role type
• omit
• measurement method identifier
• pcr detection chemistry
• sample color
• target color
• quencher dye setting
• passive reference dye setting
• automatic cycle threshold enabled setting
• cycle threshold value setting
• automatic baseline determination enabled setting
• baseline determination start cycle setting
• baseline determination end cycle setting
• genotyping determination method
• genotyping determination method setting
• cycle threshold result
• normalized reporter result
• baseline corrected reporter result
• genotyping determination result

The group file can contain the following columns (if available within the data):

• device identifier
• model number
• device serial number
• data system instance identifier
• file name
• UNC path 
• software name
• software version
• ASM converter
• ASM converter version
• target DNA description <reporter dye>
• sample identifier
• sample role type <reporter dye>
• Quantity
• Quantity Mean
• Quantity SD
• Ct Mean
• Ct SD
• Delta Ct Mean
• Delta Ct SE
• Delta Delta Ct
• RQ
• RQ min
• RQ max
• Rn Mean
• Rn SD
• Y-Intercept
• Rsquared
• Slope
• Efficiency
  

Sample files can be found here.

Configure Run Schema to employ ThermoFisher Applied Biosystems, QuantStudio qPCR 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 Applied Biosystems, QuantStudio qPCR' 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

AB QuantStudio Data Connector Requirements

* This is the version of AB QuantStudio RT-PCR Software with which the data connector has been developed and tested. The data connector may work with other versions of AB QuantStudio RT-PCR Software, but that must be verified by the user.

Revision History

2023/11/17

Initial Version

2024/09/18

Added Github testdata link

2024/09/27

Added description of measurement data file .CSV including expected column headers (if available within the data)