Purpose 

To provide details about the necessary steps to implement the Applied Biosystems Data Connector Q dPCR data connector for use with the Benchling Connect platform.

Introduction

The ThermoFisher Applied Biosystems (AB) Absolute Q data connector a component used in the context of the Benchling Connect platform to parse data from Absolute Q digital PCR systems to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run.

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

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

Steps within AB Absolute Q dPCR

The user is expected to enter Sample Name values within the Absolute Q UI under the ‘SETUP’ tab that conform to entity identifiers within Benchling, either existing entity IDs or entities they wish to register upon processing of results. The Absolute Q software does not provide a utility for importing Sample Names from a file.

Alternatively, the user should create a plate within Benchling that uses the same barcode as the Absolute Q plate, and fill that plate with the entities being assayed.

Note: The Absolute Q plates are pre-barcoded, however they are a 16 well (4 well x4 column) plate and thus would need to be modeled as a partial 24-well plate or a custom 16-well plate within Benchling

If the user intends for samples to be treated as technical replicates, the sample should be given the same Sample Name and add to the same Group 

The user must also specify the samples as ‘Replicates’ within the ‘Edit Groups’ modal.

Performing file export from AB Absolute Q dPCR

The user is expected to generate a .csv export from the ‘RESULTS’ tab by clicking the download icon and selecting ‘Download CSV’.

Despite formatting the export as a .csv file, the Absolute Q software does not include the ‘.csv’ file extension. Therefore the .csv must be added when saving the exported file.

Default AbsoluteQ naming format:

With .csv manually added:

The user should save the exported file - with the .csv extension added - within the target directory specified during Connection configuration.

Steps within Benchling  

From within Benchling, a user must:

1. Enable the AB Absolute Q data connector on the tenant [internal admin console]

2. Configure a AB Absolute Q Connection

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

4. Configure a Run schema to accept data from AB Absolute Q and records Results

For details on completing these steps, please reference the Benchling Connect Installation Guide.

Data returned by the AB Absolute Q data connector

The Benchling Connect - AB Absolute Q data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Absolute Q file export. The data is processed in two steps; step one from Absolute Q export to the .json based ASM, and step two from the ASM .json to a .csv file for ingest to Benchling. 

The data is processed in a two step process; step one from AB Absolute Q export to the .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 ASM schemas 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
• brand name
• product manufacturer
• file name
• UNC path
• software name
• ASM converter name
• ASM converter version
• experimental data identifier - this corresponds to the RUN field in Absolute Q
• container type
• plate well count
• measurement identifier
• measurement time
• target DNA description
• location identifier
• well plate identifier
• device type
• reporter dye setting
• total partition count
• number concentration - this corresponds to counts/uL
• positive partition count

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
• total partition count
• number concentration - this corresponds to counts/uL
• positive partition count
• device control identifier

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

• device identifier
• brand name
• product manufacturer
• file name
• UNC path
• software name
• ASM converter name
• ASM converter version
• experimental data identifier - this corresponds to the RUN field in Absolute Q
• sample identifier
• target DNA description
• average total
• average concentration
• sd concentration
• cv
• average positives

Sample files can be found here.

Configure Run Schema to employ ThermoFisher Absolute Q dPCR 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 Absolute Q dPCR' 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

Data Connector Requirements

* This is the version of AB Absolute Q with which the data connector has been developed and tested. The data connector may work with other versions of SoftMax Pro, but that must be verified by the user.

Revision History

2023/11/14

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)