ThermoFisher Scientific, NanoDrop 8000 Configuration Guide

Purpose 

To provide details about the necessary steps to implement the ThermoFisher Scientific, NanoDrop 8000 connector for use with the Benchling Connect platform.

Introduction

The ThermoFisher Scientific, NanoDrop 8000 connector is a component used in the context of the Benchling Connect platform to parse data from ThermoFisher Scientific's NanoDrop 8000 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 8000 connector is a ‘file-based’ based connector, meaning that it processes .txt exports generated by the NanoDrop 8000 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 8000 connector for use with the Benchling platform, there are several steps that need to be followed across both the ThermoFisher Scientific, NanoDrop 8000 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 8000

From within ThermoFisher Scientific, NanoDrop 8000, a user must:

1. Configure a .TXT export compatible with the Benchling Connect, ThermoFisher Scientific, NanoDrop 8000 connector.
2. Execute the export of that file from their ThermoFisher Scientific, NanoDrop 8000 session.
3. Ensure that the file is placed with the watched directory.

Export Formats from NanoDrop 8000 Software

NanoDrop 8000 has three different file formats that can be exported from the software:

• Full Report -- .nd8 file generated after a measurement that can be loaded into the Data Viewer module of the NanoDrop 8000 software
• Report Table Only -- .txt file generated from the Data Viewer module that contains per sample measurement results shown in the Report Table view
• Report & Standards Tables -- .txt file generated from the Data Viewer module contains per sample measurement results and standard curve results shown in the Report & Standards Tables view

Exporting from NanoDrop 8000 Software

Steps outlined below for exporting from the NanoDrop 8000 software are based on assumption that measurements have been performed and a NanoDrop 8000 full report .nd8 file has been created.

For exporting the compatible file for the Benchling Connect NanoDrop 8000 connector, users should:

1. Open the Data Viewer module
2. Select the Reports tab, click Load Report... -- this will open a file explorer window to select the appropriate .nd8 file to import
3. Once imported, select the Reports tab, click Save Report...
4. The Save Report As... window will open, user should select Export Report Table Only
5. A file explorer window should open, user should name and save the .txt file in the file watched directory configured via Benchling Connection

Steps within Benchling

From within Benchling, a user must:

1. Enable the ThermoFisher Scientific, NanoDrop 8000 connector on the tenant [internal admin console]

2. Configure a ThermoFisher Scientific, NanoDrop 8000 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 8000 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 8000 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 8000 connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the ThermoFisher Scientific, NanoDrop 8000 file export. The data is handled in a two step process; step one from ThermoFisher Scientific, NanoDrop 8000 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 8000 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 8000, the csv files will typically contain the following columns (if available within the data):

• Device Identifier
• Model Number
• ASM converter name - name of data connector library
• ASM converter version - version of data connector library
• Analyst
• File Name
• Measurement Identifier*
• Measurement Time
• Container Type
• Sample Identifier
• Batch Identifier 
• Experiment Type
• Device Type
• Detector Wavelength Setting*
• Detector Wavelength Setting Unit**
• Mass Concentration*
• Mass Concentration Unit**
• Absorbance*
• Calculated Results 
  • A260/A280
  • A260/A230

* To account for cases of multiple measurements per sample (sample & sample-separate-unit-column files only), 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).

ThermoFisher Scientific, NanoDrop 8000 Connector Requirements

*This is the version of NanoDrop 8000 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

2024/08/23

Initial Version

2024/10/14

Add description for measurement CSV output and corresponding columns

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