Purpose 

To provide details about the necessary steps to implement the Roche, Cedex HiRes data connector for use with the Benchling Connect platform.

Introduction

The Roche, Cedex HiRes data connector a component used in the context of the Benchling Connect platform to parse data from the Cedex HiRes software to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run. The Cedex HiRes software is used in conjunction with the Cedex HiRes Analyzer.

The Benchling Connect - Roche, Cedex HiRes data connector is a ‘file-based’ based data connector, meaning that it processes comma-separated values (.csv) file exports generated by the Cedex HiRes 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 Roche, Cedex HiRes data connector for use with the Benchling platform, there are specific steps that need to be followed across both the Cedex HiRes software and Benchling user interfaces. 

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

Steps within Cedex HiRes software

(i) Configure a CSV export compatible with the Benchling Connect, Agilent Gen5 connector.

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

Exporting CSV file from Cedex HiRes Software

1. Select the Export to file option in the Functions menu of the Cedex Control Center. The Measurement List dialog box appears with the EXPORT TO FILE button located at the bottom of the dialog box.
2. Select a single measurement from the list by clicking on the field to the left of the desired line. To choose a set of measurements, hold down the <Ctrl> button while selecting the appropriate lines.
   
3. In the Export dialog box, individual Parameter and String delimiters can be defined
4. In the Location area, the target path to be used for storage of the export file is entered. The button on the right of the entry field opens a dialog box in which the path can be directly selected. The name of the file is automatically generated.
   Note: User should set the target path to the file watch directory configured via Benchling Connection
5. To choose a set of parameters, keep the <Ctrl> button pressed while making selections. The preset options are:
   
   - All Parameters: All parameters about the measurement.
   - Cell Data: Data for each and every cell and object detected in the measurement.
   - Overall Results: Results such as average cell diameter, %viability, total cell concentration, viable cell concentration, etc.
   
   Note: User should select All Parameters to export
6. In the File format area, select the CSV file format
7. Click on the EXPORT SELECTED DATA button.

Steps within Benchling

From within Benchling, a user must:

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

2. Configure a Cedex HiRes Connection

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

4. Configure a Run schema to accept data from Cedex HiRes 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 Cedex HiRes data connector

The Benchling Connect - Cedex HiRes data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Roche, Cedex HiRes file export. The data is processed in a two step process; step one from Cedex HiRes export to the .json based ASM, and step two from the ASM .json to (2) .csv files available for ingest to Benchling - the sample data file in which each each row corresponds to a sample run by the instrument.

The Benchling Connect - Roche, Cedex HiRes connector supports the cell-counting detection functionality of the Cedex HiRes Analyzer. Cell counting analyzers determine the cell concentration and viability of cell suspensions.

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

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

The connector then converts the ASM to a sample data file .csv, structured such that each row of the file represents a sample run by the instrument.

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

• Device Identifier
• Model Number
• Software Name
• File Name
• ASM Converter Name
• ASM Converter Version 
• Analyst
• Measurement Identifier - this is a UUID generated as part of data conversion
• Measurement Time
• Sample Identifier
• Batch Identifier
• Cell Type
• Cell Density Dilution Factor
• Sample Volume (μL)
• Viability (%)
• Total Cell Density (10^6 cells/mL)
• Viable Cell Density (10^6 cells/mL)
• Dead Cell Density (10^6 cells/mL)
• Average Live Cell Diameter (μm)
• Total Cell Count
• Viable Cell Count
• Dead Cell Count

Configure Run Schema to employ Roche, Cedex HiRes Connection

The Run schema can be created from the menu under Feature Settings.

As part of the Run schema creation, the user should specify 'Roche, Cedex HiRes' 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

Roche, Cedex HiRes Data Connector Requirements

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

Revision History

2024/08/09

Initial Version

2024/09/03

Add link to referenced schemas in Github