Meso Scale Diagnostics, Methodical Mind Configuration Guide

Purpose

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

Introduction

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

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

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

Steps within Methodical Mind Reader Module

The following steps should be performed by the user within Methodical Mind's Reader Module.

Following Read of Plate(s):

- Updating the Plate Barcode (required)-- if instrument is unable to read plate barcode

File Export Options

By default, the Methodical Mind Reader Module is configured to export a single standard format data file per run to the C:\ECLResults\ directory. Data from plate runs are automatically exported to a text file. 

The export file will be named by default using the plate barcode and the date and time that the plate was read as follows: Plate Barcode_Read Date and Time.txt. Note: Users can also rename the file with their own customized file name.

Options to modify the export settings are available in Reader Module / Export Configuration.

The following options should be modified:

• Export Data Location - The user should set the Export Data Location to match the directory specified during Connection configuration within Benchling.
  
  
• Standard Export - YES [Default]. The user is expected to set this field to "Yes" as only the  Standard format is compatible for the data connector.
• Custom Export - OFF, this export format is not compatible with the data connector.
  
  Note: Format is used to export data to older versions of the MSD Discovery Workbench application. 
  
  
• One Export for Multi-Plate Reads - YES. This will ensure that the data from all plates are included in a single file. The user may choose to export data from each plate to separate files (default), but each file will need to me imported via Benchling Connect separately.

Measuring multiple plates

Methodical Mind allows users to measure multiple plates per run. 

The Benchling Connect, Methodical Mind data connector supports the processing of multiple plates per file. In all cases it is highly recommended that the user provide barcodes within Methodical Mind which correspond to plate barcodes used in Benchling, but especially so when performing experiments with multiple plates.

The Methodical Mind software supports the capture of barcodes affixed to the plate (using the integrated barcode scanner on the instrument), or the manual entry of barcodes if the instrument is unable to read the plate barcode.

The plate barcodes provided in Methodical Mind may correspond to existing plate barcodes in Benchling, or may represent barcodes they intend to register as part of processing the file. The plate barcodes used in Methodical Mind will appear within the "well plate identifier" column in the data returned to Benchling (discussed below). Failure to do so will present challenges for associating the experimental data with the plate and associated entities within Benchling after the fact.

Steps within Benchling

From within Benchling, a user must:

1. Enable the Meso Scale Diagnostics, Methodical Mind 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 Methodical Mind Connection

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

4. Configure a Run schema to accept data from Methodical Mind 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 Methodical Mind data

The Benchling Connect - Meso Scale Diagnostics, Methodical Mind data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Methodical Mind file export. The data is handled in a two step process; step one from Methodical Mind .txt 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 Methodical Mind corresponds to the data from each spot. 

For Methodical Mind, 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
• File Name
• UNC Path
• Measurement Identifier*
• Measurement Time
• Well Plate identifier - this refers to the plate barcode
• Location identifier - this refers to the well and spot position
• Sample Identifier - this defaults to “<Well Plate Identifier> <Location Identifier>” 
• Plate Well Count - number of wells
• Analyst
• Container Type
• Device Type 
• Detection Type - this will refer to Luminescence
• 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 Methodical Mind Results with Entities in Benchling.

The Methodical Mind 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 Methodical Mind 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 Methodical Mind' 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, Methodical Mind Data Connector Requirements

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

Revision History

2024/03/27

Initial Version

2024/09/04

Add link to referenced schemas in Github

2024/09/18

Added Github testdata link