Purpose 

To provide details about the necessary steps to implement the BMG LabTech, MARS adapter for use with the Benchling Connect platform.

Introduction

The BMG LabTech, MARS adapter a component used in the context of the Benchling Connect platform to parse data from the MARS software to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run. The MARS software is used in conjunction with the PHERAstar FSX, CLARIOstar and CLARIOstar Plus plate readers/softwares. The MARS software is a stand-alone analysis suite that ingests the experiment files from the respective plate reader softwares and can perform analyses of experimental data.

The Benchling Connect - BMG LabTech, MARS adapter is a ‘file-based’ based adapter, meaning that it processes CSV file exports generated by the MARS 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 BMG LabTech, MARS adapter for use with the Benchling platform, there are specific steps that need to be followed across both the MARS software and Benchling user interfaces. 

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

Steps within MARS software

Prior to steps within MARS, it is assumed that the following steps have been performed within a BMG LabTech plate reader software:

1. Experimental measurements obtained
2. Upload Test Run of experimental data into MARS Software

Following these steps, within the MARS Software users should perform the following steps outlined below:

(i) Configure a CSV export compatible with the Benchling Connect, BMG MARS connector.

(ii) Ensure that the file is placed with the watched directory configured via Benchling Connection.

Supported Detection Methods / Calculated Data

BMG LabTech plate reader softwares allow users to perform experiments using different Detection Methods, depending on the configuration of the instrument being used.

Detection Methods include: absorbance, luminescence, and fluorescence. At present the Benchling Connect, BMG MARS connector is capable of processing data recorded from absorbance and fluorescence measurements.

Within the MARS Software, users can perform analyses of their experimental data including statistical analysis, standard curve calculations, data corrections and enzyme/binding kinetics. At present the Benchling Connect, BMG MARS connector is only capable of processing raw data from the MARS Software.

Export CSV file from MARS Software

1. In the Formats and Settings tab, select File Export to open the MARS File Export options
2. Under File content options, select "Add header and fit results to file"
3. Under File Name and Location options, specify the File Watch directory configured via Benchling Connection as the output directory. This can be done either by inserted the path into the text box or select the directory through the File Explorer after pressing the
4. The File Name can be left to default or changed to user defined name
5. File Extension and Separator should be set to CSV and ","
6. Remaining content within the options should be left to default

As mentioned above in the "Supported Detection Modes / Calculated Data" section, the Benchling Connect, BMG MARS connector only supports raw data exports at present.

To export only the raw data from MARS, users should select in the Navigation / Data Selection Tree, Raw Data only -- the data will appear visible in the main window and the square box adjacent to the text will be colored.

To export the expected file format compatible with the BMG MARS connector, the user should select the MicroPlate View in the main window.

Exporting of the expected CSV file can be done by pressing the button adjacent to the plate layout.

The file should be present in the file watch directory following these steps.

Steps within Benchling

From within Benchling, a user must:

1. Enable the BMG MARS adapter on the tenant [internal admin console]

2. Configure a BMG MARS Connection

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

4. Configure a Run schema to accept data from BMG MARS 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.

Data returned by MARS adapter

The Benchling Connect - MARS adapter uses the Allotrope Simple Model (ASM) to structure the information parsed from the BMG LabTech MARS file export. The data is processed in a two step process; step one from MARS export to the .json based ASM, and step two from the ASM .json to (2) .csv files available for ingest to Benchling - the well file in which each each row corresponds to a well of a plate, and a measurement file .csv, in which each row of the file represents a measurement.

• The Benchling Connect - BMG MARS connector supports the raw data/analyses that are performed using the MARS software from measurements taken from BMG LabTech's suite of multi-mode plate readers. Multi-mode plate readers are instruments that are capable of performing Absorbance, Fluorescence, and Luminescence measurements.

  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/plate-reader/ 
  

  The connector then converts the ASM to a well file .csv, structured such that each row of the file represents a well of the plate; and a measurement file .csv, in which each row of the file represents a measurement.

  The well file and measurement file can contain the following columns (if available within the data):

  • Device Identifier
  • Model Number
  • Product Manufacturer
  • File Name
  • UNC Path
  • Software Name
  • ASM Converter Name
  • ASM Converter Version
  • Analyst
  • Measurement Identifier - this is a UUID generated as part of data conversion
  • Measurement Time
  • Experiment Type
  • Device Type - this will be 'plate reader' in all cases
  • Analytical Method ID
  • Experimental Data ID
  • Container Type - this will be 'well plate' in all cases
  • Plate Well Count 
  • Well Plate Identifier
  • Location Identifier
  • Sample Identifier
  • Compartment Temperature
  • Detection Type - this will refer to Absorbance, Fluorescence, or Luminescence
  • Detector Wavelength Setting* - where applicable
  • Detector Bandwidth Setting* - where applicable
  • Excitation Wavelength Setting* - where applicable
  • Excitation Bandwidth Setting* - where applicable
  • ‘Measurement’* - this column header will vary depending on the modality: absorbance, fluorescence, or luminescence - e.g absorbance_mAU

   

Configure Run Schema to employ BMG LabTech, MARS Connection

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

As part of the Run schema creation, the user should specify 'BMG LabTech, MARS' 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

BMG LabTech, MARS Adapter Requirements

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

Revision History

2024/08/09

Initial Version

2024/08/14

Update guide to specify only absorbance and fluorescence detection modes are supported