ThermoFisher Scientific, NanoDrop Eight Configuration Guide

Purpose 

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

Introduction

The ThermoFisher Scientific, NanoDrop Eight data connector is a component used in the context of the Benchling Connect platform to parse data from ThermoFisher Scientific's NanoDrop Eight spectrophotometer using the NanoDrop Eight software to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run.

The Benchling Connect, NanoDrop Eight data connector is a ‘file-based’ based data connector, meaning that it processes tab-separated values (.tsv) or .txt exports generated by the NanoDrop Eight application. 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 NanoDrop Eight data connector for use with the Benchling platform, there are multiple steps that need to be followed across both the NanoDrop Eight 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, NanoDrop Eight

From within ThermoFisher Scientific, NanoDrop Eight a user must:

(i) Perform a tsv file export compatible with the Benchling Connect, NanoDrop Eight data connector 

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

Exporting Data From NanoDrop Eight

Measurement data can be exported in three formats:

• comma-separated values (.csv) containing
  • whole spectrum data in columns
  • report data in columns
  • both report and spectrum data combined in columns

• tab-separated values (.tsv) containing
  • whole spectrum data in columns
  • report data in columns
  • both report and spectrum data combined in columns
  • whole spectrum data in single column for TQ Analyst

• NanoDrop Eight software (.n8db) files containing spectra and measurement
  results for each exported experiment

*User is expected to export tab-separated values (.tsv) and select to export 'both report and spectrum data combined in columns'. This is the expected file format compatible with the NanoDrop Eight data connector.

Configuring Auto-Export

• From the Home screen, select Settings, System Settings

• In the Auto Export options, first enable auto-export
• Select the File Path for auto-export -- File Path should be set by the User to the 'watched' file directory that has been configured via a Connection to Benchling
• Select in the file format options, tab-separated values (.tsv) and select to export 'both report and spectrum data combined in columns'. This format is the expected file format that is compatible with the NanoDrop Eight data connector.

When finished measuring samples in an Experiment, clicking the End Experiment icon will automatically export the selected file type and format to the 'watched' file directory configured to the Benchling Connection.

*Users is encouraged to configure the Auto Export feature to eliminate intermediate manual steps when exporting files.

Steps within Benchling

From within Benchling, a user must:

1. Enable the ThermoFisher Scientific, NanoDrop Eight data connector on the tenant [internal admin console]

2. Configure a NanoDrop Eight Connection

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

4. Configure a Run schema to accept data from NanoDrop Eight 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 NanoDrop Eight data

The Benchling Connect - ThermoFisher Scientific, NanoDrop Eight data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the NanoDrop Eight file export. The data is handled in a two step process; step one from NanoDrop Eight export (.tsv) to the .json based ASM, and step two from the ASM .json to a .csv file available for ingest to Benchling. 

The Benchling Connect - ThermoFisher Scientific, NanoDrop Eight data connector supports UV-VIS spectrophotometric measurements of micro-volume samples for a wide variety of analytes (Nucleic Acid, Protein, Cell Optical-Density).

These data are structured using the Allotrope Spectrophotometer 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).

For NanoDrop Eight, the csv files will typically contain the following columns (if available within the data):

• Model Number
• Device Identifier
• Equipment Serial Number
• ASM converter name - name of data connector library
• ASM converter version - version of data connector library
• File Name
• Analyst
• Measurement Identifier*
• Measurement Time
• Location identifier - this refers to the sample position
• Sample Identifier 
• Experiment Type
• Device Type
• Detector Wavelength Setting*
• Detector Wavelength Setting Unit**
• Absorbance*
• Mass Concentration
• Absorbance Spectrum Data Cube -- measurement files only
  • Wavelength
  • Absorbance
• Calculated Results
  • A260/280
  • A260/A230

* To account for cases of multiple measurements per sample, these fields will include an index
(e.g. _1, _2, _3,...) corresponding to the number of measurement.

**To account for cases of multiple units of samples/measurements (sample-separate-unit-column & measurement-separate-unit-column files only, these fields will be included in the csv file(s).

Sample files can be found here.

Configure Run Schema to employ NanoDrop Eight Connection

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

As part of the Run schema creation, the user should specify 'ThermoFisher Scientific NanoDrop Eight' 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

Example NanoDrop Eight Data

Refer to the example files in the repository below if you would like to test this configuration pattern with demonstration data. 

https://github.com/Benchling-Open-Source/allotropy/tree/main/tests/parsers/thermo_fisher_nanodrop_eight/testdata

ThermoFisher Scientific, NanoDrop Eight Data Connector Requirements

*This is the version of NanoDrop Eight 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

2024/04/22

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