ThermoFisher Scientific, VISIONlite Configuration Guide

Purpose 

To provide details about the necessary steps to implement the ThermoFisher Scientific, VISIONlite connector for use with the Benchling Connect platform.

Introduction

The ThermoFisher Scientific, VISIONlite connector is a component used in the context of the Benchling Connect platform to parse data from ThermoFisher Scientific's GENESYS 30, 40, 50, 140, 150, 180, BioMate 160, Evolution 201, 220, 260 Bio, 350 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, VISIONlite connector is a ‘file-based’ based connector, meaning that it processes .CSV exports generated by the ThermoFisher Scientific, VISIONlite. 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, VISIONlite connector for use with the Benchling platform, there are several steps that need to be followed across both the ThermoFisher Scientific, VISIONlite 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, VISIONlite

The VISIONlite software offers 4 different spectrophotometry application modules:

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

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

Scan - Spectrum recording

Quant - Quantifying sample concentrations via calibration

Fixed Application

After completing the series of measurements:

Export the results with the Export results command, ensuring the file format is exported as a CSV

Quant Application

After completing the series of measurements:

Export the results with the Export results command, ensuring the file format is exported as a CSV

Scan Application

After completing the spectral scan measurements:

Use the Save Spectrum command to store the spectrum (.csv or JCAMP-DX) -- CSV format for compatibility with VISIONlite connector.

Rate Application

After completing the time series measurements:

Export the results with either the Export results command or Save data set, ensuring the file format is exported as a CSV

Note -- At present, only Fixed, Quant, and Scan application module exports are supported by the VISIONlite connector.

Steps within Benchling

From within Benchling, a user must:

1. Enable the ThermoFisher Scientific, VISIONlite connector on the tenant [internal admin console]

2. Configure a ThermoFisher Scientific, VISIONlite Connection

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

4. Configure a Run schema to accept data from ThermoFisher Scientific, VISIONlite 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, VISIONlite 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, VISIONlite connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the ThermoFisher Scientific, VISIONlite file export. The data is handled in a two step process; step one from ThermoFisher Scientific, VISIONlite 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
• Analyst
• Measurement Time*
• Experiment Type
• Measurement Identifier*
• Sample Identifier
• Device Type
• Detection Type
• Detector Wavelength Setting*
• Processed Data Identifier
• Mass Concentration*
• Absorbance*
• Absorption Spectrum Data Cube
  • Wavelength**
  • Absorbance**

* 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). 

**Columns present in measurement data file for spectral scan measurements, capture spectrum data per wavelength.

ThermoFisher Scientific, VISIONlite Connector Requirements

*This is the version of VISIONlite 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

2024-10-16

Initial Version

2024-12-13

Update memory requirements for VISIONlite