ThermoFisher Scientific, NanoDrop One Configuration Guide

Purpose 

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

Introduction

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

From within ThermoFisher Scientific, NanoDrop One, a user must:

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

Export Formats from NanoDrop One Software

Measurement data can be exported in four formats:
• as comma-separated values (.csv) files containing the measurement results and
details for each exported experiment
• as tab-separated values (.tsv) files containing x,y coordinates for every spectral
data point for each exported experiment
• as NanoDrop (.sql) files containing spectra and measurement results for each
exported experiment

Note: At present, the Benchling NanoDrop One Connector is only compatible with CSV exports. As a result, spectrum and kinetic data exported from the instrument software are not currently supported by the Connector.

Exporting from NanoDrop One Software

Export data at end of experiment
– when finished measuring samples, tap
– from End Experiment box, set Export Data to an available export location
Note: User is expected to connect PC to NanoDrop One instrument via USB port and set export location to file watch directory configured via Benchling connection
– tap
– from Export box, select one or more formats to export to CSV and tap Export

– after “Export Success” message, tap OK
– tap End Experiment

Steps within Benchling

From within Benchling, a user must:

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

2. Configure a ThermoFisher Scientific, NanoDrop One Connection

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

4. Configure a Run schema to accept data from ThermoFisher Scientific, NanoDrop One 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, NanoDrop One 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, NanoDrop One connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the ThermoFisher Scientific, NanoDrop One file export. The data is handled in a two step process; step one from ThermoFisher Scientific, NanoDrop One 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 Benchling Connect - ThermoFisher Scientific, NanoDrop One data connector supports UV-VIS spectrophotometric measurements of micro-volume samples.

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

• Device Identifier
• Brand Name
• Model Number
• Product Manufacturer
• ASM converter name - name of data connector library
• ASM converter version - version of data connector library
• File Name
• Measurement Identifier*
• Measurement Time
• Container Type
• Sample Identifier
• Batch Identifier 
• Experiment Type
• Device Type
• Baseline Absorbance
• Detector Wavelength Setting
• Detector Wavelength Setting Unit**
• Electronic Absorbance Reference Bandwidth Setting
• Nucleic Acid Factor
• Mass Concentration*
• Mass Concentration Unit**
• Absorbance*
• Calculated Results
  • A260/A280
  • 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.

ThermoFisher Scientific, NanoDrop One Connector Requirements

*This is the version of NanoDrop One 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.

**The NanoDrop One Software runs on the stand-alone instrument itself as an external device to computer connected to Benchling.

Revision History

2024/08/19

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