Agilent, TapeStation Analysis Configuration Guide

Introduction

The Benchling Connect, Agilent TapeStation Analysis connector is a component used in the context of the Benchling Connect platform to parse data from Agilent TapeStation Analyzers to an Allotrope Simple Model (ASM) and make that data available within the Benchling UI in the context of a Run.

The Benchling Connect, Agilent TapeStation Analysis connector is a ‘file-based’ based connector, meaning that it processes .XML file exports generated by the TapeStation Analysis 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 TapeStation Analysis connector for use with the Benchling platform, there are multiple steps that need to be followed across both the TapeStation Analysis and Benchling user interfaces. 

This guide details the steps to be taken in both applications in order to configure the integration.

Steps within Agilent TapeStation Analysis Software

The Agilent TapeStation Analyzers use two software applications, collectively referred to as Agilent TapeStation Software. The Agilent TapeStation Controller applications is used for the setup and execution of experiments on the instrument, while Agilent TapeStation Analysis is used for reviewing and analyzing data generated using the Analyzer platform. 

The following steps should be performed by the user within the Agilent TapeStation Software.

Prior to performing experiment (within TapeStation Controller): 

- Updating Sample Identifiers (optional)

At conclusion of the experiment (within TapeStation Analysis):

- Generate the .XML export of experiment data.

- Ensure the .XML file is place within the watched directory configured via the Benchling Connection.

Updating Sample Descriptions within Agilent TapeStation Controller

For tracking experimental results, it is always recommended that the user provide sample identifiers at the point of data collection that correspond to entities registered within Benchling.

The TapeStation Controller application allows users to import sample identifiers as sample description during the set up of an experiment. The descriptions may be entered individually, or imported from a (.csv, .txt, or .doc) file. If a .csv format is used, then a well identifier (e.g. A1, B1, C1) may included as the first column and the sample description in the second column - to insure the desired mapping of the sample to its location within the ScreenTape.

Generating XML export of experimental data from Agilent TapeStation Analysis

Following the completion of the experiment and review of the resulting data, the user should use the Export to XML option under the Export Data menu and specify the location to save the data. This location should match the directory specified in the Connection configured within Benchling.

Note, the TapeStation Analysis application will create a folder,
C:\Users\<user>\Documents\Agilent\TapeStation Data during installation and will use this as the default export location. The user should update this location unless they intend to associate this folder with the Connection in Benchling.

Additionally, while exporting data the user if provided the option to include an image of the ScreenTape gel and the individual electropherograms - the user may choose to export these image files, however, these files are not processed by the TapeStation Analysis Connector at this time.

Steps within Benchling

From within Benchling, a user must:

1. Enable the TapeStation Analysis Connector on the tenant [internal admin console]

2. Configure a TapeStation Analysis Connection

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

4. Configure a Run schema for the TapeStation assay: to generate a sample list (if desired) and to record 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.

Data returned by TapeStation Analysis Connector

The Benchling Connect, TapeStation Analysis Connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the TapeStation file export. The data is processed in a two step process; step one from TapeStation Analysis .XML 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 Electrophoresis ASM data model. Details about this ASM schema can be found here:

https://github.com/Benchling-Open-Source/allotropy/…/allotrope/schemas/adm/electrophoresis

The connector then converts the ASM to a sample data .csv, where each row represents an individual sample; a peak data .csv, where each row represents a peak identified within the electropherogram; and a region data .csv where each row  represents a region defined within the electropherogram. All three files also include with metadata about the experiment. The sample data and peak data .csv files will be returned in all cases, while the region data .csv will only be generated for those cases in which regions have been defined. 

For TapeStation Analysis, all three files will typically contain the following columns (if available within the data):

• Brand Name
• Product Manufacturer
• Device Identifier
• Equipment Serial Number
• Data System Instance Identifier
• File Name
• UNC path
• Software Name
• Software Version
• ASM Converter Name
• ASM Converter Version
• Analyst
• Analytical Method Identifier - corresponds to the Assay Type used on the TapeStation
• Method Version
• Experimental Data Identifier - corresponds to the original TapeStation file (e.g. .RNA, .gDNA)
• Measurement Identifier
• Measurement Time
• Compartment Temperature degC
• Device Identifier
• Device Type
• Detection Type
• Location Identifier - corresponds to well number
• Description - corresponds to 'sample description'
• Sample Identifier - corresponds to ScreenTape ID and well number

Additionally, the sample data .csv will include columns calculated for each sample, such as:

• Concentration
• DIN
• RINe

The peak data .csv will include additional columns pertaining to each peak, such as:

• Peak Identifier
• Peak Name
• Peak Height RFU - reported as relative fluorescent units
• Peak Start
• Peak End
• Peak Position
• Peak Area
• Relative Peak Area %
• Relative Corrected Peak Area %
• Comment
• AssignedQuantity
• CalibratedQuantity
• FromPercent
• ToPercent
• Molarity
• RunDistance

The region data .csv will include additional columns pertaining to each region, such as:

• Region Identifier
• Region Start
• Region End
• Region Area
• Relative Region Area %
• Comment
• AverageSize
• Concentration
• Molarity

Sample files can be found here.

Configure Run Schema to employ Agilent TapeStation Connection

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

As part of the Run schema creation, the user should specify 'Agilent TapeStation' 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

Agilent TapeStation Analysis Connector Requirements

* This is the version of the TapeStation Analysis software with which the adapter has been developed and tested. The adapter may work with other versions of the TapeStation Analysis software, but that must be verified by the user.

Revision History

2024/06/12

Initial Version

2024/09/18

Added Github testdata link