ChemoMetec NucleoView Configuration Guide

Purpose 

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

Introduction

The Benchling Connect, ChemoMetec NucleoView data connector is a component used in the context of the Benchling Connect platform to parse data from ChemoMetec NucleoCounter NC-200 cell counter to an Allotrope Simple Model (ASM) and make that data available within the Benchling UI in the context of a Run.

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

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

Steps within ChemoMetec, NucleoView

The user  should perform measurements following the instructions provided in the NucleoView NC-200 Software User’s Guide provided by ChemoMetec (PN 991-0204, Rev 1.14).

The user is expected to enter Sample ID values within the NucleoView UI that conform to entity identifiers within Benchling, either existing entity IDs or entities they wish to register upon processing of results. This behavior can be enforced by selecting “Sample ID Always Required” under the Options → General menu within the NuceloView UI.

As part of the measurement process, the user should ensure that:

(i) Generate the Results File compatible with the Benchling Connect, NucleoView data connector

(ii) Ensure that the file is placed with the watched directory configured via a Benchling Connection.

The Results File is a .CSV file that should be generated automatically as part of the measurement. The location to which the Results File  is saved can be updated under the Options → Folders menu within the NuceloView UI.

Steps within Benchling 

From within Benchling, a user must:

1. Enable the ChemoMetec NucleoView data connector on the tenant [internal admin console]

2. Configure a ChemoMetec NucleoView Connection

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

4. Configure a Run schema to accept data from ChemoMetec NucleoView and records Results

For steps 1 - 2, please reference the Benchling Connect Installation Guide for details related to creating and installing a Gateway and configuring a Connection.

Create Results Schema for NucleoView data

The Benchling Connect - ChemoMetec NucleoView connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the ChemoMetec file export. The data is processed in a two step process; step one from ChemoMetec NucleoView export to the .json based ASM, and step two from the ASM .json to a .csv files available for ingest to Benchling.

These data are structured using the Allotrope Cell Counting ASM data model. Details about the this ASM schema can be found here:

https://github.com/Benchling-Open-Source/allotropy/tree/main/src/allotropy/allotrope/schemas/adm 

For the ChemoMetec NucleoView, the file will typically contain the following columns (if available within the data):

• ASM converter name
• ASM converter version
• Model Number
• Equipment Serial Number
• File name
• Software Name
• Software Version
• Analyst
• Measurement Identifier
• Measurement Time
• Sample Identifier
• Device Type
• Detection Type
• Sample Volume Setting
• Viability (cell counter)
• Total Cell Density (cell counter)
• Viable Cell Density (cell counter)
• Dead Cell Density (cell counter)
• Average Total Cell Diameter
• Cell Density Dilution Factor

Sample files can be found here.

In order to create the Result schema directly from NucleoView sample data, the Result schema can be configured as part of the Run schema creation (discussed below).

Configure Run Schema to employ NucleoView Connection

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

As part of the Run schema creation, the user should specify ‘Chemometec NucleoView' 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

Example NucleoView Data

Refer to the example files in the repository below if you would like to test this configuration pattern with demonstration data. 

https://github.com/Benchling-Open-Source/allotropy/tree/main/tests/parsers/chemometec_nucleoview/testdata

ChemoMetec NucleoView Data Connector Requirements

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

Revision History

2024/04/15

Initial Version

2024/09/03

Update link to referenced schemas in Github

2024/09/18

Added Github testdata link