Thermo Fisher Scientific, Genesys On-Board Software Configuration Guide

Purpose 

To provide details about the necessary steps to implement the ThermoFisher Scientific, Genesys On-Board Software connector for use with the Benchling Connect platform.

Introduction

The ThermoFisher Scientific, Genesys On-Board Software connector is a component used in the context of the Benchling Connect platform to parse data from ThermoFisher Scientific's GENESYS 40/50/140/150/180 and BioMate 160 spectrophotometers to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run.

The Benchling Connect, ThermoFisher Scientific, Genesys On-Board Software connector is a ‘file-based’ based connector, meaning that it processes .CSV exports generated by the ThermoFisher Scientific, Genesys On-Board 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 ThermoFisher Scientific, Genesys On-Board Software connector for use with the Benchling platform, there are several steps that need to be followed across both the ThermoFisher Scientific, Genesys On-Board Software and Benchling user interfaces. 

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

Steps within ThermoFisher Scientific, Genesys On-Board Software

The Genesys On-Board software offers 6 different spectrophotometry application modules:

C-Mode - instrument determines a calibration factor based on the concentration and absorbance measurement of a standard. The instrument then performs continuous absorbance measurements to automatically determine the concentration of samples based on this factor.

Fixed - Recording spectrometer readings at different dedicated wavelengths and performing simple calculations

Kinetics - Recording time dependent readings at a fixed wavelength and is dedicated for measuring rate curves.

Scan - Spectrum recording

Live Display - instrument performs continuous absorbance measurements automatically

Quant - Quantifying sample concentrations via calibration

Exporting from Experiment

After completing the series of measurements from your experiment:

Exporting from Data Viewer

Export the results with the Export button, ensuring the file format is exported as a CSV. The file must be exported via USB port and saved locally to the 'File Watched' directory configured via Connection within Benchling.

Note -- At present, only the Fixed application module exports are supported by the Genesys On-Board Software connector.

Steps within Benchling

From within Benchling, a user must:

1. Enable the ThermoFisher Scientific, Genesys On-Board Software connector on the tenant [internal admin console]

2. Configure a ThermoFisher Scientific, Genesys On-Board Software Connection

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

4. Configure a Run schema to accept data from ThermoFisher Scientific, Genesys On-Board Software 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.

Creation of Result schema for ThermoFisher Scientific, Genesys On-Board Software data

In order to record results returned via the integration a Result schema must be created. This can be done prior to configuration of the Run schema, or within the context of the Run schema Output File configuration. 

The Benchling Connect - ThermoFisher Scientific, Genesys On-Board Software connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the ThermoFisher Scientific, Genesys On-Board Software file export. The data is handled in a two step process; step one from ThermoFisher Scientific, Genesys On-Board Software 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 Spectrophotometry ASM data model. Details about the this ASM schema can be found here:

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

The connector then converts the ASM to one of:

sample file .csv - structured such that each row of the file represents a sample

measurement file .csv - in which each row of the file represents a measurement

The sample and measurement csv files can contain the following columns (if available within the data):

• Device Identifier
• Model Number
• Product Manufacturer
• File Name
• Software Name
• ASM Converter Name
• ASM Converter Version
• Measurement Time*
• Experiment Type
• Measurement Identifier*
• Sample Identifier
• Device Type
• Detection Type
• Detector Wavelength Setting*
• Absorbance*
• Result

* To account for experiments with multiple measurements these columns will be duplicated (as needed) and will be annotated with a number for each measurement (sample file only). 

ThermoFisher Scientific, Genesys On-Board Software Connector Requirements

*This is the version of Genesys On-Board Software that the Benchling Connector was developed and tested against. Processing exports from other version of the software may be possible, but this would need to be confirmed by the user.

Revision History

2024-12-12

Initial Version