Purpose 

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

Introduction

The Cedex Bio HT data connector is a component used in the context of the Benchling Connect platform to parse data from Roche Cedex Bio HT cell culture analyzers to an Allotrope Simple Model (ASM) and make that data available within the Benchling UI in the context of a Run.

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

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

Steps within Roche Cedex Bio HT 

The user is expect to generate an archive file (.txt) as describe in the Cedex Bio HT operators manual shown below:

The user is then expected to place this Cedex archive file in a target directory which is specified during Connection configuration, when creating a Cedex Bio HT Connection within the Benchling UI.

Steps within Benchling 

From within Benchling, a user must: 

1. Enable the Roche Cedex Bio HT data connector on the tenant [internal admin console]

2. Configure a Roche Cedex Bio HT  Connection

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

4. Configure a Run schema to accept data from Roche Cedex Bio HT and records Results

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

Data returned by Cedex BioHT data connector

The Benchling Connect - Cedex BioHT cell culture analyzer data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Cedex BioHT file export. The data is processed in a two step process; step one from Cedex BioHT export to the .json based ASM, and step two from the ASM .json to a single sample file .csv file available for ingest to Benchling. The Cedex BioHT data connector does translate the Test Codes into the corresponding analyte name.

Details about the solution analyzer ASM schema can be found here:

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

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

• model number
• equipment number
• product manufacturer
• file name
• software name
• software version
• ASM converter name
• ASM converter version
• device identifier
• analyst
• measurement identifier
• measurement time
• data processing time
• sample identifier
• sample role type
• batch identifier
• acetate <unit>
• alanine-glutamine <unit>
• alanine-glutamine corrected <unit>
• ammonia <unit>
• arabinose <unit>
• asparagine <unit>
• aspartate <unit>
• calcium <unit>
• cholesterol <unit>
• ethanol <unit>
• formate <unit>
• galactose <unit>
• glucose <unit>
• glutamate <unit>
• glutamine <unit>
• glycerol <unit>
• Ig Fab human <unit>
• IgG human <unit>
• IgG mouse <unit>
• iron <unit>
• lactate <unit>
• ldh <unit>
• magnesium <unit>
• nitrate <unit>
• phosphate <unit>
• potassium <unit>
• pyruvate <unit>
• sodium <unit>
• sucrose <unit>
• sucrose corrected <unit>
• total protein <unit>
• optical density OD
• absorbance (mAU)
• osmolality mOsm/kg
  

Sample files can be found here.

Configure Run Schema to employ Roche Cedex BioHT 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 BioHT' 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 Bio HT Data Connector Requirements

Revision History

2023/11/14

Initial Version

2024/09/4

Update ASM that Roche Cedex BioHT uses to Solution Analyzer ASM schema

Update additional fields that are expected from sample file CSV

2024/09/18

Added Github testdata link