Bio-Rad CFX Maestro Software Configuration Guide

Preston
Preston
  • Updated

Purpose 

To provide details about the necessary steps to implement the CFX Maestro software connector for use with the Benchling Connect platform.

Introduction

The CFX Maestro software connector is a component used in the context of the Benchling Connect platform to parse data from Bio-Rad qPCR instruments to an Allotrope Simple Model (ASM) and make that data available within the Benchling UI in the context of a Run.

The Benchling Connect, CFX Maestro software connector is a ‘file-based’ based connector, meaning that it processes .csv exports generated by the CFX Maestro 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 CFX Maestro software connector for use with the Benchling platform, there are several steps that need to be followed across both the CFX Maestro software and Benchling user interfaces. 

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

Steps within CFX Maestro Software Connect Adapter

From within CFX Maestro software, a user must:

First, configure a .csv export by either exporting all data sheets to excel, or making a custom export.

    • Exporting all data sheets to excel
      1. Select Export
      2. Select Export All Data Sheets to Excel
      3. Be sure the export is saved as a .csv file
    • Making a custom export
      1. Select Export
      2. Select Custom Export, the custom dialog box will appear

    1. Select CSV from the Export Format dropdown list
    2. Be sure to select Well, Fluorophore, Target Name, and Sample Name. Additional sample descriptors can be selected
    3. DO NOT customize the column names
    4. Select Export
    5. Save the export as a .csv file

Finally, ensure that the file is placed within the watched directory.

 

Note: Output .csv files must contain the following columns:

Well, Flour, Content, Sample, Biological Set Name, Cq

 

Note: The expected file extension for the CFX Maestro connector is .csv, other file extensions are not currently compatible. Reach out to your Benchling representative for additional file extension support.

 

Limitations:

Currently Melt Curve, End Point, and Replicate Group calculations (Cq Mean and Cq Std. Dev.) data is not supported, however future updates can include this. The export from CFX Maestro can contain these fields, however it will not be imported to Benchling.

 

Steps within Benchling

From within Benchling, a user must:

  1. Enable the CFX Maestro software connector on the tenant
  2. Configure a CFX Maestro software connection
  3. Create a Result schema to structure the data to be recorded
  4. Configure a Run schema to accept data from CFX Maestro software 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.

 

Creation of Result schema for CFX Maestro Software 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 - CFX Maestro software connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the CFX Maestro software Connect Adapter file export. The data is handled in a two step process; step one from CFX Maestro software Connect Adapter 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 qPCR 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/pcr/BENCHLING/2023/09/qpcr.schema.json

 

The connector then converts the ASM to “well file” .csv - structured such that each row of the file represents a well of the plate.

 

CFX Maestro Software Connector Requirements

Item Specification
CFX Maestro Software Instrument Software Version 7*
Operating System Minimum: Microsoft Windows 7 SP1 Pro

Hard Disk Space

Minimum: 128 GB

RAM Minimum: 4GB RAM
Processor Minimum: 2.4 GHz, Dual Core
Gateway Benchling Gateway installed on PC, able to communicate on port 443

*This is the version of CFX Maestro 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. Reach out to your Benchling representative if there a specific version you are using that is incompatible with the connector.

 

Revision History

Date/Time: Oct 22, 2024

Initial Version: Version 1

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