Waters, Empower Configuration Guide

Purpose 

To provide details about the necessary steps to implement the Empower Connect connector for use with the Benchling Connect platform.

Introduction

The Empower Connect connector is a component used in the context of the Benchling Connect platform to parse data from HPLC units compatible with Empower software to an Allotrope Simple Model (ASM) and make that data available within the Benchling UI in the context of a Run.

The Benchling Connect Empower Connector is a ‘direct request’ based adapter, meaning that sends a request to the Empower software for specific data files. The data is then imported to Benchling via the connection and Run schema.

In order to successfully implement the Empower Connect connector for use with the Benchling platform, there are several steps that need to be followed across both the Empower and Benchling user interfaces. 

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

Steps within Empower Connect

From within Empower, a user must:

1. Insure that the computer hosting the Empower software is accessible to the internet 
2. Install and establish a Benchling Gateway on the host computer
3. Execute a run and save a file either locally or in a remote directory.
   • There is no need to place this file in a ‘Benchling Watched Directory’. 

Steps within Benchling

From within Benchling, a user must:

1. Establish a Benchling Connection with Empower
   • The following fields are required in either the Connector or the Run schema. It is recommended to enter fixed fields in the Connector and variable fields in the Run schema. 
     • • Gateway
       • Project
       • Database
       • Username
       • Password 
2. Ensure the Empower Connect connection is active
3. Make a Run schema, configuring it appropriately for the specific application
   • A user can request three types of files in accordance with the Liquid Chromatography schema set by ASM. Select them appropriately in the Run schema
     • • Peak Table File
       • Injection File
       • Data Cube File
4. In a project, load the Run schema
5. Enter the Sample Set Name or Sample Set ID of the sample files that are to be requested from Empower
6. Retrieve the data
   
   

Image 1: Benchling Connection set up to communicate with the empower software (some information removed)

Image 2: Run scheme for the Empower Data Cube file shows some configurations and the associated Connection Schema

For step 1, please reference the Benchling Connect Installation Guide for details related to creating and installing a Gateway and configuring a Connection. 

If you have any questions or trouble setting up the connection, reach out to your Benchling Representative for assistance.

Creation of Result schema for Empower Connect 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 - Empower Connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Empower Connect file export. The data is handled in a two step process; step one from Empower Connect 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 Liquid Chromatography ASM data model. Details about the this ASM schema can be found here: Link to Liquid Chromatography ASM Data Model

The connector then converts the ASM to:

• Injection File .csv - where each line corresponds to a LC injection
• Data Cube File .csv - structured such that each row of the file represents a 2-dimensional data measurement (e.g. retention time x absorbance)
• Peak Table File .csv - Information about the peaks that were captured

Output CSV files can contain the following, but may vary depending on the input file.

Current Limitations:

Below are known limitations of the connector currently. These limitations can be eliminated with your help! If you would like to see any additional functionality to this connector, or other connectors, please reach out to your Benchling rep. and let them know you would like to see a specific feature(s) added to the connector! 

Limitations:

• This connector works with Empower software connected to Waters Corporation Alliance HPLC Units. Other units might generate difference in data output
• Currently only data cubes with retention time, not retention volume, are accepted

Empower Connector Requirements

*This adapter was developed with Waters Empower 3.8.1, other versions might work. If they do not, please reach out to your Benchling Representative to update the compatibility.

Revision History

February 6, 2025

Initial Version