Roche, Cedex Bio HT (Cell Culture Analyzer) Configuration Guide

Matt
Matt
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Purpose 

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

 

Introduction

The Cedex Bio HT adapter 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 adapter is a ‘file-based’ based adapter, 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 adapter 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:

Screenshot 2023-05-05 at 11.59.37 AM.png

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  adapter 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 adapter

The Benchling Connect - Cedex BioHT cell culture analyzer adapter 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 adapter does translate the Test Codes into the corresponding analyte name.

Details about the cell culture analyzer ASM schema can be found here:

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

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

  • model number
  • device serial number
  • 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
  • osmolality mOsm/kg

 

Roche Cedex Bio HT  Adapter Requirements

 

Item Specification
Roche Cedex Bio HT  Cedex Bio HT Analyzer version 6.0
Operating System 64-bit Windows 10 or greater (per Cedex BioHT requirement)
Memory 512MB RAM or greater (per Cedex BioHT requirement)
Processor Intel Pentium 800MHz CPU or higher (per Cedex BioHT requirement)
Gateway Benchling Gateway installed on PC, able to communicate on port 443

 

Revision History

2023/11 Initial Version

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