Beckman Coulter, Echo Plate Reformat Software Configuration Guide

Purpose 

To provide details about the necessary steps to implement the Echo Plate Reformat Software connector for use with the Benchling Connect platform.

Introduction

The Echo Plate Reformat Software connector is a component used in the context of the Benchling Connect platform to parse data from Beckman Coulter's Echo liquid handlers to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run.

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

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

Steps within Echo Plate Reformat Software

From within Echo Plate Reformat Software, a user must:

1. Configure a CSV export compatible with the Benchling Connect, Echo Plate Reformat Software connector.
2. Execute the export of that file from their Echo Plate Reformat Software session.
3. Ensure that the file is placed with the watched directory.

Configuring CSV export from Echo Plate Reformat Software

To configure the compatible CSV export from the Echo Plate Reformat Software, 

User should open the Preferences/Options window from the Tools menu

Required fields to configure within this window:

• Output Options
  
  User should select the Run-Specific Output Files
  
  
• Transfer Reports
  User should configure CSV as the Transfer Report file type -- CSV is currently the only compatible file type with the Echo Plate Reformat Software connector
  
  User should set the Directory path to the path of the watched directory configured via Benchling Connection

Optional fields to configure within this window:

• Transfer Reports
  
  User can configure the Format in the Output Format Builder
  
  
  
  Expected format of the CSV file (with the available data)
  
  Header
  
  Run ID
  Run Date/Time
  Application Name
  Application Version
  Protocol Name
  User Name
  
  Body
  
  Date Time Point
  Source Plate Name
  Source Plate Barcode
  Source Plate Type
  Source Well
  Destination Plate Name
  Destination Plate Barcode
  Destination Plate Type
  Sample ID
  Sample Name
  Transfer Volume
  Actual Volume
  Fluid Composition
  Transfer Status
  Fluid Units
  Survey Fluid Volume
  Current Fluid Volume
  Fluid Type
  
  Footer
  
  Instrument Name
  Instrument Model
  Instrument Serial Number
  Instrument Software Version
  
  NOTE: Include Exception Report is supported by the connector to capture transfers that were not initiated because of a failed survey.

Steps within Benchling

From within Benchling, a user must:

1. Enable the Echo Plate Reformat Software connector on the tenant [internal admin console]
   
   
2. Configure a Echo Plate Reformat Software Connection
   
   
3. Create a Result schema to structure the data to be recorded
   
   
4. Configure a Run schema to accept data from Echo Plate Reformat Software 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 Echo Plate Reformat Software 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 - Echo Plate Reformat Software connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Echo Plate Reformat Software file export. The data is handled in a two step process; step one from Echo Plate Reformat Software 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/tree/main/src/allotropy/allotrope/schemas/adm/liquid-handler/BENCHLING/2024/11

The connector then converts the ASM to:

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

For the Echo Plate Reformat Software, the measurement file will typically contain the following columns (if available within the data):

• Model Number
• Equipment Serial Number
• Software Name
• Software Version
  
• Instrument Software Version
• ASM converter name - name of data connector library
• ASM converter version - version of data connector library
• ASM file identifier - ASM JSON file generated by the connector
• Data System Instance Identifier
  
• UNC Path
• File Name
• Measurement identifier*
• Device Type
• Measurement Time - time of transfer
• Analytical Method Identifier - Protocol ID
• Experimental Data Identifier - Run ID
• Run Date/Time - time of Run start
• Source Well Plate identifier - this refers to the source plate barcode
• Destination Well Plate identifier - this refers to the destination plate barcode
• Source Well Location identifier - this refers to the source well position
• Destination Well Location identifier - this refers to the destination well position
• Source Location identifier - this refers to the source plate name
• Destination Location identifier - this refers to the destination plate name
• Aspiration Volume (μL)
• Transfer Volume (μL)
• Sample Identifier 
• Current Fluid Volume
• Survey Fluid Volume
• Intended Transfer Volume
• Source Labware Name
• Destination Labware Name
• Fluid Composition
• Fluid Type
• Transfer Status

Echo Plate Reformat Software Connector Requirements

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

Revision History

2025/04/04

Initial Version