Purpose 

To provide details about the necessary steps to implement the Nova Biomedical, BioProfile Flex2 data connector for use with the Benchling Connect platform.

Introduction

The Flex2 data connector is a component used in the context of the Benchling Connect platform to parse data from Nova Biomedical, BioProfile Flex2 cell culture analyzers to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run.

The Benchling Connect - BioProfile Flex2 data connector is a ‘file-based’ based data connector, meaning that it processes text file exports generated by the BioProfile Flex2 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 BioProfile Flex2 data connector for use with the Benchling platform, there are several steps that need to be followed across both the BioProfile Flex2 and Benchling user interfaces. 

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

Steps within BioProfile Flex2

The user should perform measurements following the Instructions for Use provided by Nova Biomedical.

The user is expected to enter Sample ID values within the BioProfile Flex2 that conform to entity identifiers within Benchling, either existing entity IDs or entities they wish to register upon processing of results.

As units are not reported within the Flex2 file export, the default units as specified in the Reference Guide - section 3.5.3.1 (57960F 2023-03) should be used - with the exception that Cell Density should be configured in units of 10^6 cells/mL rather than the default value of 10^5 cells/mL. 

Following the completion of the measurements, the user should generate a SampleResults export file (.csv) following the instructions detailed in section 2-32 of the NovaBio BioProfile Flex2 Quick Reference Guide (57960F 2023-03).

For the purposes of the integration, the user is expected to select either MM DD YYYY or YYYY MM DD as the date format (but not DD MM YYYY), detailed in section 3-24 of the NovaBio BioProfile Flex2 Quick Reference Guide.

The user is then expected to place the SampleResults export file in a target directory which is specified during Connection configuration, when creating a NovaBio Flex Connection within the Benchling UI.

The user can have the export file sent directly to that target directory by following the instructions for networking and shared file access in section 2-35 of the Reference Guide.

If the user wishes to capture a device identifier to indicate the instrument used to collect the data, then the user should configure an Analyzer ID within the settings menu of the Flex instrument, so that this value is included within the export file name.

Steps within Benchling 

From within Benchling, a user must:

1. Enable the NovaBio Flex2 data connector on the tenant [internal admin console]

2. Configure a NovaBio Flex2 Connection

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

4. Configure a Run schema to accept data from NovaBio and records Results

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

Data returned by BioProfile Flex2 Data Connector

The Benchling Connect - Flex2 cell culture analyzer data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Flex2 file export. The data is processed in a two step process; step one from Flex2 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. 

Details about the Solution 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
• software name
• file name
• ASM converter name
• ASM converter version
• device identifier
• analyst
• device type
• temperature degC
• measurement identifier
• measurement time
• data processing time
• sample identifier
• description
• sample role type
• batch identifier
• ammonium mmol/L
• bicarbonate mmol/L
• calcium mmol/L
• glucose g/L
• glutamate mmol/L
• glutamine mmol/L
• lactate g/L
• potassium mmol/L
• sodium mmol/L
• pCO2 mmHg
• carbon dioxide saturation %
• pO2 mmHg
• oxygen saturation %
• optical density OD
• pH
• osmolality mOsm/kg
• viability %
• total cell density 10^6 cells/mL
• cell type
• cell density dilution factor
• viable cell density 10^6 cells/mL
• average live cell diameter μm
• average total cell diameter μm
• viable cell count
• total cell count
  

Sample files can be found here.

BioProfile Flex2 Data Connector Requirements

Revision History

2023/11 Initial Version

2024/06

- Updated details regarding Gateway installation.

2024/09/04

Update ASM used by Nova Biomedical, BioProfile Flex2 connector to Solution Analyzer ASM

Updated expected ASM fields recorded in sample data file CSV

2024/09/18

Added Github testdata link