ThermoFisher Scientific, Genesys30 Configuration Guide

Purpose 

To provide details about the necessary steps to implement the ThermoFisher Scientific, Genesys30 connector for use with the Benchling Connect platform.

Introduction

The ThermoFisher Scientific, Genesys30 connector is a component used in the context of the Benchling Connect platform to parse data from ThermoFisher Scientific, Genesys30 Spectrophotometer 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, Genesys30 connector is a ‘file-based’ based connector, meaning that it processes .tsv/.csv exports generated by the ThermoFisher Scientific, Genesys30. 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, Genesys30 connector for use with the Benchling platform, there are several steps that need to be followed across both the ThermoFisher Scientific, Genesys30 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, Genesys30

From within ThermoFisher Scientific, Genesys30, a user must:

1. Configure a .tsv export compatible with the Benchling Connect, ThermoFisher Scientific, Genesys30 connector.
2. Execute the export of that file from their ThermoFisher Scientific, Genesys30 session.
3. Ensure that the file is placed with the watched directory.

Exporting data from Genesys30

Steps should completed following measurement of sample:

1.  Select to save your file to a USB connected device
2.  When you select  , you will be prompted to save either your data or your method.
3.  Saving your data to a USB connected drive—The file is saved with an automatically generated filename
   consisting of the measurement type and a time and date stamp, e.g.
   Scan_20160325_152122.csv
4.  User should store the saved file in the file watch directory configured via Benchling Connection
   
   In language regions where a period or dot is used as a decimal separator, the files are saved
   as CSV format.
   
   In language regions where a comma is used as a decimal separator, the files are saved as
   TSV format (tab separated values)

Note: Currently the Genesys30 supports only UV-absorbance endpoint and UV-absorbance spectral scan data. Transmittance results are not supported currently.

Steps within Benchling

From within Benchling, a user must:

1. Enable the ThermoFisher Scientific, Genesys30 connector on the tenant [internal admin console]

2. Configure a ThermoFisher Scientific, Genesys30 Connection

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

4. Configure a Run schema to accept data from ThermoFisher Scientific, Genesys30 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, Genesys30 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, Genesys30 connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the ThermoFisher Scientific, Genesys30 file export. The data is handled in a two step process; step one from ThermoFisher Scientific, Genesys30 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:

The data connector then converts the ASM to:

• sample data file .csv file (which is structured such that each row of the file represents a sample measured)
• sample-separate-unit-column data file .csv  file (structure such that each row of the file represents a sample measured with columns that contain units having a stand-alone column to represent the unit value)
• measurement data file .csv file (structured such that each row of the file represents a measurement)
• measurement-separate-unit-column data file .csv file (structure such that each row of the file represents a measurement with columns that contain units having a stand-alone column to represent the unit value).

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

• Device Identifier
• Brand Name
• Product Manufacturer
• Model Number
• File Name
• Software Name
• ASM Converter Name - this refers to the connector that converted to original file to ASM
• ASM Converter Version
• Analyst
• Measurement Identifier
• Measurement Time
• Sample Identifier
• Device Type
• Detection Type
• Container Type
• Experiment Type
• Operating Minimum
• Operating Maximum
• Absorbance
• Absorption Spectrum Data Cube
  • Wavelength
  • Absorbance

Sample files can be found here.

ThermoFisher Scientific, Genesys30 Connector Requirements

Revision History

2024/08/29

Initial Version

2024/09/18

Added Github testdata link

2024/10/14

Add description for measurement CSV output and corresponding columns

Add description for separate-unit-column CSV outputs and corresponding columns