Agilent, OpenLabs CDS Configuration Guide

Purpose 

To provide details about the necessary steps to implement the Agilent, OpenLabs CDS connector for use with the Benchling Connect platform.

Introduction

The Agilent, OpenLabs CDS connector is a component used in the context of the Benchling Connect platform to parse data from Agilent's chromatography systems to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run.

The Benchling Connect, Agilent, OpenLabs CDS connector is a ‘file-based’ based connector, meaning that it processes .rslt (result set) exports generated by the OpenLabs CDS. 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 OpenLabs CDS connector for use with the Benchling platform, there are several steps that need to be followed across both the OpenLabs CDS and Benchling user interfaces. 

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

Steps within OpenLabs CDS

From within OpenLabs CDS, a user must:

1. Configure a .rslt (result set) export compatible with the Benchling Connect, OpenLabs CDS connector.
2. Execute the export of that file from their OpenLabs CDS session.
3. Ensure that the file is placed with the watched directory.

Creating Result Set folder in OpenLabs CDS

A new result set is created from data files that you have added to the navigation table.

1. Select the Data Analysis view
2. From the left navigation table, double click the sequence or single run of interest.
   
3. Right-click another sequence or single run that includes data files that you would like to add into the new result set. From the contextual menu, click Add Data Files...
4. From the Add Data Files [Sequence Folder] dialog box, select the data files to add to the new result set and click OK
   
5. The navigation table now includes all data files of interest. Next, select the files you want to include in a new result set. From the Sequence menu, click Create New Result Set.
6. From the Create New Result Set dialog box, select a method to be associated with the new result set, and specify a path and folder name for the new result set.
   
   NOTE: Set the Destination data path as the File Watched directory configured via your Benchling Connection.
7. (Optional) Users can additionally compress their RSLT file to a zipped file within their File Watched directory if they choose. The Agilent OpenLabs CDS connector is able to process this format along with the standard RSLT file export.

Steps within Benchling

From within Benchling, a user must:

1. Enable the OpenLabs CDS connector on the tenant [internal admin console]

2. Configure a OpenLabs CDS Connection

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

4. Configure a Run schema to accept data from OpenLabs CDS 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 OpenLabs CDS 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 - OpenLabs CDS connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the OpenLabs CDS export. The data is handled in a two step process; step one from OpenLabs CDS 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:

https://github.com/Benchling-Open-Source/allotropy/blob/main/src/allotropy/allotrope/schemas/adm/liquid-chromatography/BENCHLING/2023/09/liquid-chromatography.schema.json

The connector then converts the ASM to one of:

injections file .csv - structured such that each row of the file represents an injection

peak file .csv - structured such that each row of the file represents a peak

datacube file .csv - structured such that each row of the file represents a chromatogram data point

Within the injections file CSV, the following columns should be expected (with the available data present):

• analyst
• device identifier
• product manufacturer
• device id (chromatography module)
• data system instance identifier
• file name
• UNC path
• software name
• software version
• ASM converter name
• ASM converter version
• column part number
• column serial number
• firmware version
• device type
• detection type
• sample identifier
• location identifier
• replicate
• sample amount
• injection ID
• injection time
• injection volume (mL)
• injection source
• acquisition method identifier
• injector position

Within the peaks file CSV, the following columns should be expected (with the available data present):

• analyst
• device identifier
• product manufacturer
• device id (chromatography module)
• data system instance identifier
• file name
• UNC path
• software name
• software version
• ASM converter name
• ASM converter version
• column part number
• column serial number
• firmware version
• device type
• detection type
• sample identifier
• location identifier
• replicate
• sample amount
• injection ID
• injection time
• injection volume (mL)
• injection source
• acquisition method identifier
• injector position
• peak identifier
• retention time (s)
• peak start (s)
• peak end (s)
• peak height (mAU)
• peak area (mAU.s)
• peak width baseline (s)

Within the datacube file CSV, the following columns should be expected (with the available data present):

• column part number
• column serial number
• firmware version
• device type
• detection type
• sample identifier
• location identifier
• replicate
• sample amount
• injection ID
• injection time
• injection volume (mL)
• injection source
• acquisition method identifier
• injector position
• data cube label
• retention time (s)
• absorbance (mAU) or fluorescence (RFU) -- based on detector used in experiment
• pump pressure (MPa)

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! 

NOTE: The adapter handles only Liquid chromatography experiments and single sequence runs

OpenLabs CDS Connector Requirements

* This is the version of Agilent OpenLabs CDS with which the data connector has been developed and tested. The data connector may work with other versions of Agilent OpenLabs CDS, but that must be verified by the user.

Revision History

2025/06/27

Initial Version