[Beta] 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. 

Note: At present, the Waters Empower data connector is designated as a Beta, meaning that the connector has been tested on minimal example data, with acknowledgment of limitations of the functionality of the connector. Current functionality as well as limitations are included in this guide below.

Steps within Empower

From within computer hosting Empower and the software itself, a user must:

1. Install and establish a Benchling Gateway on the host computer
   1. Refer to ‘Benchling Connect Installation Guide’ for setup instructions
2. Ensure the Benchling Gateway stays in an active state and is accessible to the internet
3. If sending run data to Empower from Benchling…
   1. A ‘Method Set Template’ needs to be created in Empower. 
   2. Fields that change run-to-run can be marked as non-fixed fields. In Benchling, these fields can be filled out by the user each time a run is used
   3. The setup of specific ‘Method Set Templates’ in Empower, only needs to occur once. They can be used indefinitely.
4. Execute a run and save a file either locally or in a remote directory.
   1. There is no need to place this file in a ‘Benchling Watched Directory’ as with some other connectors.

Steps within Benchling

From within Benchling, a user must:

1. Establish a Benchling connection with Empower - See section below for details
2. Ensure the connection is active
3. Configure a Run Schemas, this only needs to be created initially - See section below for details
4. Configure an Entity Schema, this only needs to be created initially - See section below for details
5. In an Entry,
   1. Insert a Registration Table (Insert -> Registration Table)
      1. Enter the ‘Entity Name’ and other fields that were configured.
      2. Samples that were registered in the Benchling ‘Registries’ can be linked under a field, such as ‘Sample’, by searching for it.
      3. NOTE: this step can be templatized within the entry
   2. Load the Run Schema (Insert -> Run)
      1. Enter information into the fields and add in the linkage to the entities that were created in the registration table
      2. Click ‘Create’
      3. Select ‘ Generate and send to connection’ to send the data to Empower. A run can then be activated in Empower using this information
      4. Select ‘Retrieve data’ to pull the results back to Benchling

Establishing a Benchling Connection with Empower

3. The following fields are required in the Connection:
   1. Gateway
   2. Username
   3. Password
4. The following fields are required in either the Connection or the Run Schema. It is recommended to enter fixed fields in the Connection and variable fields in the Run Schema.
   1. Project
   2. Database - can be omitted, if so, Empower will use the same default database that is used when the software is used on the PC

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

Making a Run Schema - Sending Data to Empower and Pulling Data from Empower to Benchling 

A run schema is made up of four distinct sections: ‘metadata’, ‘run fields’, ‘input file configurations’, and ‘output file configurations’. If a user wishes to send data to Empower from Benchling and also retrieve data, follow all of these steps when making a Run Schema. If a user only wants to retrieve data from Empower to Benchling, they can skip the ‘Input File Configuration’

Meta Data

• Add the name and other preferences at the top of the schema

Run Fields

• There are required fields that are necessary to send and retrieve data
  • To send data, the required fields are:
    • template_name - the name of the sample set method template to use - get this value from “Method Name” of the template in the Empower software
    • sample_set_method_name -  the name to use for the newly created sample set
    • vial_start_position (optional but recommended) - the vial start position argument to provide to the template when creating the sample set method
  • To retrieve data, the required fields are:
    • sample_set_name OR sample_set_id - the name of ID of the sample set to retrieve data for - get this value from the “Sample Set Name” or “Sample Set Id” of the sample set in the Empower software
• Under ‘Definition’, search for the desired entity’ or  field type

Input File Configurations

1. Configure the display name
   1. Enter a header for the input file
2. Configure sources and destinations
   1. Click the “+” next to ‘Sources’
   2. Under the ‘Start from’ box, select the ‘Run Field’ related to the Entity Schema entered above. In this case “Injections”
   3. Ignore ‘Destinations’

3. Configure columns for the input file
   1. The ‘Source’ column should have the source from the step above linked, if not select it.
   2. The columns ‘Destination’ and ‘Plate Layout’ can be ignored
   3. Right click on the header of the right most column and select ‘insert column right’
   4. Select ‘Set lookup’, this will open the ‘Configure lookup’ window
   5. In the ‘Start from’ box, select “Source” <Entity Schema>. In this case it would be “Source (Injections (Waters Empower Injections))”
   6. Select the linked item. If there is embedded information, it should be visible and can be selected
   7. Select ‘Continue’
   8. Under ‘Lookup attribute’ select the desired field
   9. Select ‘Insert’
   10. Do this for each desired column, a list of available column headers is available below
   11. NOTE: be sure to include ‘SampleName’ and ‘MethodSetOrReportMethod’ or the process will fail

Column headers that can added to the input table:

AnalysisMethod, CalculationType, CirculationNo, ColumnName, ColumnPosition, ColumnSerialNumber, ColumnUsed, Comments, DataStart, Dilution, DilutionUnits, ELN_DocumentID, ELN_SampleID, ELN_SectionGUID, Factor1, Factor1Operator, Factor1Units, Factor2, Factor2Operator, Factor2Units, Factor3, Factor3Operator, Factor3Units, FinalResultUnits, Function, ICH_AdjAreaPctCutoff, InjectionType, InjVol, InstBatch, ItemCode, Label, LabelClaim, LabelClaimUnits, LabelReference, Level, Lot, LotReleaseTestStage, MethodSetOrReportMethod, MSCalibrationMethod, MSTuneMethod, NextInjDelay, NotebookNumber, NotebookPageNumber, NumOfInjs, OriginalVialId, PeakRatioReference, PostFactor1Units, PostFactor2Units, PrepID, PrepType, Processing, Reference, RunTime, SampleComments, SampleConcentration, SampleMatrix, SampleName, SamplePrep, SampleWeight, SampleWeightUnits, SolventA, SolventB, SolventC, SolventD, SSM_Pattern, TestRequestID, TimePoint, TimePointUnits, UseForPrecision, Vial.

4. Apply transforms to the input file
   1. Not required, can be applied if desired
5. Configure file format
   1. Default ‘File extension’ should be “.csv”

Output File Configurations

1. Configure the Display Name
   1. Enter a name for the header of the output file in the run.
2. Configure the output table
   1. Under ‘Benchling action’, select ‘Record dataset’
      1. Other options can be selected, but most instances will warrant the selection above
   2. Under ‘Output table display’’, select ‘One row per sample’
   3. Under ‘Output table sorting’, select how you want the output sorted
   4. Under ‘Instrument data type’, different file options will be available. Each file contains individual information, but also has some information overlap. A new ‘Output file configurations’ needs to be created for each if a user wants to capture them all.
      1. Peak Table File - Contains information (height, area, etc.) about peaks
      2. Injection File - Contains information about the injections
      3. Data Cube File - Contains the chromatogram data
      4. Fractions File - Contains information about fraction events - Not currently supported for Empower
3. Apply transformations to the output file (optional)
   1. Datasets can be transformed, filtered, etc if desired
4. Configure column mapping
   1. Under ‘Configure Dataset’ enter the columns that you want to capture in the export file
   2. Under ‘Column type’ select the data type
5. Configure delimiter
   1. This should be left as the default (comma)
6. Configure data locale
   1. Select your region
7. Configure dataset
   1. Select a dataset name that describes it clearly

NOTE: Always be sure to press ‘Update’ when making changes to the run schema

If you have any questions or trouble setting up the connection, schemas, etc.,  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

April 25, 2025

Fix typos in Steps within Benchling section

May 09, 2025

• Add further descriptions of steps required to Steps within Empower
• Updates to Steps within Benchling section
  • Added sections:
    • Establishing a Benchling Connection with Empower
    • Making a Run Schema - Sending Data to Empower and Pulling Data from Empower to Benchling
  • Add description of required/optional field configuration