Beckman Coulter, Biomek Configuration Guide

Purpose 

To provide details about the necessary steps to implement the Beckman Coulter Biomek connector for use with the Benchling Connect platform.

Introduction

The Beckman Coulter Biomek connector is a component used in the context of the Benchling Connect platform to parse data from Beckman Coulter Biomek Liquid Handler software to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run.

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

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

Steps within Biomek Software

From within Beckman Coulter Biomek, a user must:

1. Configure a .csv export compatible with the Benchling Connect, Beckman Coulter Biomek connector.
2. Execute the export of that file from their Biomek session.
3. Ensure that the file is placed with the watched directory.

Types of Logs

NOTE: The Beckman Coulter Biomek connector currently only supports the UnifiedPipetting log from Biomek

Generating compatible .csv

Log files are used to generate reports and capture the history of a method run. Log files can be
printed using a standard text editor or by inserting them into a spreadsheet program, such as
Microsoft Excel.

NOTE: For generating the compatible CSV file with the Beckman Coulter Biomek connector, the user is expected to insert the log information into a Microsoft Excel spreadsheet and generate a .CSV file

Steps within Benchling

From within Benchling, a user must:

1. Enable the Beckman Coulter Biomek connector on the tenant [internal admin console]

2. Configure a Beckman Coulter Biomek Connection

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

4. Configure a Run schema to accept data from Beckman Coulter Biomek 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 Beckman Coulter Biomek 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 - Beckman Coulter Biomek connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Beckman Coulter Biomek logs. The data is handled in a two step process; step one from Beckman Coulter Biomek 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 Liquid Handler 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/liquid-handler/BENCHLING/2024/11/liquid-handler.schema.json

The connector then converts the ASM to one of:

measurement file .csv - in which each row of the file represents a measurement

The measurement csv files can contain the following columns (if available within the data):

• Device Identifier*
• Equipment Serial Number*
• Model Number*
• Product Manufacturer*
• Device Type*
• Data System Instance Identifier
• File Name
• UNC Path
• Software Name
• ASM Converter Name
• ASM Converter Version
• ASM File Identifier
• Measurement Time
• Analytical Method Identifier
• Experiment Type
• Measurement Identifier
• Sample Identifier
• Source Location Identifier
• Destination Location Identifier
• Source Well Plate Identifier
• Destination Well Plate Identifier
• Source Well Location Identifier
• Destination Well Location Identifier
• Aspiration Volume
• Transfer Volume
• Transfer Type
• Injection Volume Setting

*Additional device modules that are utilized by the Biomek liquid handler such as the Pod metadata will include an index following the column name (e.g. Device Type.1)

Beckman Coulter Biomek Connector Requirements

*This is the version of Biomek 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.

Revision History

2024-12-16

Initial Version