Beckman-Coulter, PharmSpec Configuration Guide

Purpose

To provide details about the necessary steps to implement the Beckman-Coulter, PharmSpec Connector for use with the Benchling Connect platform.

Introduction

The Beckman-Coulter, PharmSpec Connector is a component used in the context of the Benchling Connect platform to parse data from PharmSpec software to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run. The PharmSpec software is used in conjunction with the Beckman-Coulter, PharmSpec Particle Counter instrument.

The Benchling Connect - PharmSpec Connector is a ‘file-based’ based connector, meaning that it processes Excel files (.xlsx) exports generated by the PharmSpec software. The data within the file export (.xlsx) 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 PharmSpec Connector for use with the Benchling platform, there are specific steps that need to be followed across the PharmSpec software.

This guide details the steps to be taken in the PharmSpec software for manual export of the results file in order to configure the integration. 

Steps within PharmSpec software

The following steps should be performed by the user within PharmSpec software.

1. Select Reports, Historical Reports--the Historical Reports window will open.
   
2. Select the search criteria for the test report(s) to be viewed/exported.
3. Click Apply--the test report(s) that meets the search criteria is shown.
4. To save one test report to the computer, select the report. Click Export

The user should set the file destination to be the target directory (watched directory) specified during Connection configuration.

Steps within Benchling

From within Benchling, a user must:

1. Enable the PharmSpec Connector on the tenant [internal admin console]
2. Configure a PharmSpec Connection
3. Create a Result schema to structure the data to be recorded
4. Configure a Run schema to accept data from PharmSpec and records Results

For steps 1 - 4, please reference the Benchling Connect Installation Guide for details related to creating and installing a Gateway and configuring a Connection.

Create Result Schema for PharmSpec data

The Benchling Connect - PharmSpec Connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the PharmSpec file export (.xlsx). The data is processed in a two step process; step one from PharmSpec export to the .json based ASM, and step two from the ASM .json to .csv files available for ingest to Benchling - the region file - where each line corresponds to a group of replicate runs of a single well.

Details about the Light Obscuration ASM schema can be found here:

https://github.com/Benchling-Open-Source/allotropy/blob/main/src/allotropy/allotrope/schemas/adm/light-obscuration/BENCHLING/2023/12/light-obscuration.schema.json  

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

• device identifier
• model number
• equipment serial number
• data system instance identifier
• asset management identifier
• file name
• UNC path - this corresponds to the complete file path of data file 
• software name
• software version
• product manufacturer
• ASM converter
• ASM converter version
• measurement identifier
• sample identifier
• sample role type 
• measurement time
• detector view volume
• flush volume setting
• data processing omission setting
• sample volume setting
• particle size setting
• repetition setting
• dilution factor setting
• distribution Identifier
• cumulative count
• cumulative particle density
• average cumulative count
• average cumulative particle density

   

Configure Run Schema to employ PharmSpec Connection

The Run schema can be created from the menu under Feature Settings.

As part of the Run schema creation, the user should specify 'Beckman-Coulter PharmSpec' 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

Example PharmSpec Data

Refer to the example files in the repository below if you would like to test this configuration pattern with demonstration data. 

https://github.com/Benchling-Open-Source/allotropy/blob/main/tests/parsers/beckman_pharmspec/testdata/hiac_example_1.json 

Beckman-Coulter, PharmSpec Connector Requirements

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

Revision History

2024/07/18

Initial Version