Purpose
To provide details about the necessary steps to implement the ChemoMetec, NC-View connector for use with the Benchling Connect platform.
Introduction
The ChemoMetec, NC-View connector is a component used in the context of the Benchling Connect platform to parse data from ChemoMetec to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run.
The Benchling Connect, ChemoMetec, NC-View connector is a ‘file-based’ based connector, meaning that it processes CSV exports generated by the ChemoMetec, NC-View. 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, NC-View connector for use with the Benchling platform, there are several steps that need to be followed across both the ChemoMetec, NC-View and Benchling user interfaces.
This guide details the steps to be taken in both applications in order to configure the integration.
Steps within ChemoMetec, NC-View
From within ChemoMetec, NC-View, a user must:
- Configure a CSV export compatible with the Benchling Connect, ChemoMetec, NC-View connector.
- Execute the export of that file from their ChemoMetec, NC-View session.
- Ensure that the file is placed with the watched directory.
Configuring CSV export from NC-View
In the Main Window, following capture of all events:
- Select Create CSV File, in the Tool Bar of the File List
- Configure the columns to be displayed:
-
File information columns
- Name--CM file name: date and run count
- Time--Timepoint for when the CM file was created
- Sample ID--User defined sample ID
- Tags--Tags that have been added to the CM file
- Protocol--Protocol name used when generating the CM file
- Media--Media type (typically Via2-CassetteTM)
- User--Windows username used when generating the CM file
- Operator--Operator name used when generating the CM file
- Approved by--Windows username used for approving the CM file
- Instrument Serial--number of the instrument used for generating the CM file
- Result columns
- Total (cells/ml)--Total cell concentration
- Live (cells/ml)--Live cell concentration
- Dead (cells/ml)--Dead cell concentration
- Viability (%)--Percentage of live cells in the sample
- Diameter (μm)--Median size estimation of the cells
- Aggregates (%)--Percentage of cells in aggregates with five or more cells
- Debris Index--Index of debris events in relation to the cell count.
- Status--Shows OK or warnings such as Foreign object detected or Out of range
Note: The following columns are expected to be export from the NC-View software for NC-View connector compatibility: Name, Time, Sample ID, Viability (%), Live (cells/mL), Dead (cells/mL), Total (cells/mL).
- The output CSV file should then be saved/exported within the file watched directory configured via Benchling Connection
Steps within Benchling
From within Benchling, a user must:
-
Enable the ChemoMetec, NC-View connector on the tenant [internal admin console]
-
Configure a ChemoMetec, NC-View Connection
-
Create a Result schema to structure the data to be recorded
-
Configure a Run schema to accept data from ChemoMetec, NC-View 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 ChemoMetec, NC-View 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 - ChemoMetec, NC-View connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the ChemoMetec, NC-View file export. The data is handled in a two step process; step one from ChemoMetec, NC-View 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 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
The connector then converts the ASM to one of:
sample file .csv - structured such that each row of the file represents a sample
measurement file .csv - structured such that each row of the file represents a measurement
The sample and measurement file can contain the following columns (if available within the data):
- file name
- UNC path
- software name
- ASM converter name
- ASM converter version
- equipment serial number
- product manufacturer
- analyst
- measurement identifier
- measurement time
- sample identifier
- written name
- device type
- detection type
- cell density dilution factor
- viability (cell counter) %
- total cell density (cell counter) 10^6 cell/mL
- viable cell density (cell counter) 10^6 cell/mL
- dead cell density (cell counter) 10^6 cell/mL
- average total cell diameter µm
- cell aggregate percentage %
- debris index
ChemoMetec, NC-View Connector Requirements
Item | Specification |
NC-View | NC-View v1.12* |
Operating System | Windows 10 and 11 only |
Memory | 16 GB RAM or more |
Processor | Intel Core i7 or i9 (9th or 10th generation); 2.5 GHz frequency (clock speed) or more |
Gateway | Benchling Gateway installed on PC, able to communicate on port 443 |
*This is the version of NC-View Software that the Benchling Connector was developed and tested against. Processing exports from other version of the software may be possible, but this would need to be confirmed by the user.
Revision History
2024-09-05
Initial Version
2024/09/18
- Added Github testdata link
2024/11
- Update guide to include handling for Cell Counting ASM-to-CSV to generate measurement file