MabTech, Apex Configuration Guide

Purpose

To provide details about the necessary steps to implement the MabTech Apex connector for use with the Benchling Connect platform.

Introduction

The Apex connector is a component used in the context of the Benchling Connect platform to parse data from the MabTech, Apex software to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run. The Apex software is used in conjunction with MabTech's line of ELISpot/FluoroSpot/FociSpot plate-based readers.

The Benchling Connect - Apex connector is a ‘file-based’ based connector, meaning that it processes multi-sheet Excel (.xlsx) exports generated by the Apex software. The data within the file export is then accessed by Benchling Connect through the use of a ‘watched’ file folder on the local computer hosting a Benchling Gateway, which has been configured via a Connection from within Benchling.

In order to successfully implement the Apex connector for use with the Benchling platform, there are specific steps that need to be followed across both the Apex software and Benchling user interfaces. 

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

Steps Within the Apex Software

Within the Apex software, users can specify the file location of their spot counting results. The steps below outline how the data connector compatible Excel (.xlsx) file can be exported from Apex.

Exporting Individual Plate Data

1. Following a Read of a plate by the software, click the Save button at the top of the Apex main window.
   
   
   
   
2. A new window of the File Explorer (Windows OS) or Finder (MacOS) will open. Name the plate data directory to a user preferred name. Note: Naming of the plate data directory will also set the 'Plate Name' in all results files that are contained in this folder.
   
   
3. Set the location of the plate data directory to the same folder that will be used when configuring the Connection within Benchling, 'watched' folder. It is recommended to place these folders within the C:\Users\Public\Documents folder since this location does not require Administrative rights to create new files and folders.
   
   
   
   
4. Click the Save As button -- Opening of the plate data directory will show all of the files that were saved including the data connector compatible .xlsx file with the shared name of the plate data directory.
   
   
   
   If any spot counting parameters are changed, plates can be resaved by clicking the Save button. Note: This will override any files saved previously. 
   
   Although the plate data directory will contain additional results files/sub-directories, the Apex connector will only parse results that are in the multi-sheet Excel file (.xlsx).

Exporting Multiple Plates

The Apex software allows for users to obtain spot counting results from multiple plates in a single Excel file. To perform this export, users should:

1. Open multiple plates into the Apex software.
2. Click the Export button at the top of the Apex window.
3. Select the All Open Plates Excel option for export.
   
4. Click the Export button.
5. A new window of the File Explorer (Windows OS) or Finder (MacOS) will open. Name the Excel file to a user preferred name.
   
   
6. Set the location of the Excel file to the same folder that will be used when configuring the Connection within Benchling, 'watched' folder.

Steps within Benchling

From within Benchling, a user must:

1. Enable the MabTech, Apex data connector on the tenant [internal admin console]
   
2. Configure a Apex Connection
   
3. Create a Result schema to structure the data to be recorded
   
4. Configure a Run schema to accept data from Apex 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 Apex data

The Benchling Connect - MabTech, Apex data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Apex file export. The data is handled in a two step process; step one from Apex .xlsx 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 (BENCHLING/2023/09). Note, while the MabTech, Apex is typically referred to as an ELISpot/FluoroSpot Analyzer, the data can be effectively modeled as plate reader with optical imaging capabilities.

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 connection then converts the ASM .json to a well file .csv file, in which each row of the file represents a well of the plate. For Apex, the well file will typically contain the following columns (if available within the data):

• Device Identifier
• Model Number
• Equipment Serial Number
• Software Version
• UNC Path
• ASM converter name - name of data connector library
• ASM converter version - version of data connector library
• File Name
• Measurement Identifier*
• Measurement Time
• Sample Identifier
• Device Type
• Analyst
• Detection Type - This refers to ‘optical-imaging’
• Container Type - this refers to ‘well plate’
• Plate Well Count - number of wells
• Location Identifier - this refers to the well position
• Well Plate Identifier - this refers to the plate barcode
• Exposure Duration Setting
• Illumination Setting
• 'Image Feature'(s) - these column header(s) will vary depending on the label used for feature(s) derived from images.

* 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.

Configure Run Schema to employ MabTech Apex Connection

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

As part of the Run schema creation, the user should specify 'MabTech Apex' 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

MabTech Apex Connector Requirements

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

Revision History

2024/05/17

Initial Version

2024/09/03

Update link to referenced schemas in Github

2024/09/18

Added Github testdata link