Meso Scale Diagnostics, Discovery Workbench Configuration Guide

Purpose

To provide details about the necessary steps to implement the Meso Scale Diagnostics, Discovery Workbench data connector for use with the Benchling Connect platform.

Introduction

The Meso Scale Diagnostics, Discovery Workbench data connector is a component used in the context of the Benchling Connect platform to parse data from Discovery Workbench software to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run. The Discovery Workbench software is used in conjunction with MESO QuickPlex SQ 120, the MESO SECTOR S 600, and SECTOR PR instruments.

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

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

Steps within Discovery Workbench Software

The following steps should be performed by the user within Discovery Workbench:

CSV File Export

For exporting the supported CSV file, users should configure the Experiment Data Table.

Once the data table is appropriately formatted, the data can be easily exported. Right-clicking on any column header produces a pop-up window:

Save Table As... . Allows you to save the table as a .csv, .txt, .jpg, or .png file.

The user should select the .CSV option to generate the Discovery Workbench supported instrument file output.

The user should set the export file location to match the directory specified during Connection configuration within Benchling.

Steps within Benchling

From within Benchling, a user must:

1. Enable the Meso Scale Diagnostics, Discovery Workbench data connector on the tenant, reach out to Benchling Support via the in-app chat or by emailing support@benchling.com to request this!

2. Configure a Discovery Workbench Connection

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

4. Configure a Run schema to accept data from Discovery Workbench 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.

Create Result Schema for Discovery Workbench data

The Benchling Connect - Meso Scale Diagnostics, Discovery Workbench data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Discovery Workbench file export. The data is handled in a two step process; step one from Discovery Workbench .csv file 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 Plate Reader 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 

The data connector then converts the ASM to a well file .csv file, in which each row of the file represents a well of the plate; and a measurement file .csv file, in which each row of the file represents a measurement - which in the case of Discovery Workbench corresponds to the data from each spot. 

For Discovery Workbench, the measurement file and well file will typically contain the following columns (if available within the data):

• Product Manufacturer
• Device Identifier
• Model Number
• Equipment Serial Number
• Software Name
• Software Version
• ASM converter name - name of data connector library
• ASM converter version - version of data connector library
• ASM file identifier
• File Name
• UNC Path
• Measurement Identifier*
• Measurement Time
• Well Plate identifier - this refers to the plate barcode
• Well 
• Location identifier - spot position
• Sample Identifier - this defaults to “<Well Plate Identifier> <Location Identifier>” 
• Plate Well Count - number of wells
• Analyst
• Assay identifier
• Container Type
• Device Type 
• Detection Type - this will refer to Luminescence
• Mass Concentration (pg/mL)
• Luminescence*

* Note that in the case of the well data file, these columns will be duplicated and annotated with a number for each measurement.

Sample files can be found here.

Associating Discovery Workbench Results with Entities in Benchling.

The Discovery Workbench text file export does not include sample information - even if a plate layout was defined within the instrument UI. The Sample Identifier returned by the .csv files produced by Connect only refers to the plate and well. Therefore, if a user desires to have the data associated with the entity within the plate, the Result Schema should be configured to have the entity be referenced as a 'Computed' field based off of the plate well.

Configure Run Schema to employ Discovery Workbench Connection

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

As part of the Run schema creation, the user should specify 'MSD Workbench' 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

Meso Scale Diagnostics, Discovery Workbench Data Connector Requirements

* These are the versions Discovery Workbench with which the data connector has been developed and tested. The data connector may work with other versions of Discovery Workbench, but that must be verified by the user.

Revision History

2024/11/26

Initial Version