The Benchling Connect, Luminex xPONENT data connector is a component used in the context of the Benchling Connect platform to parse data from Luminex xPONENT xMAP Analyzers to an Allotrope Simple Model (ASM) and make that data available within the Benchling UI in the context of a Run.
The Benchling Connect, xPONENT data connector is a ‘file-based’ based data connector, meaning that it processes .csv file exports generated by the Luminex xPONENT 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 Luminex xPONENT data connector for use with the Benchling platform, there are multiple steps that need to be followed across both the Luminex xPONENT and Benchling user interfaces.
This guide details the steps to be taken in both applications in order to configure the integration.
Steps within Luminex xPONENT Software
Executing an assay within the Luminex xPONENT software is referred to as a "Batch".
Prior to running a batch, a user may (optionally) import a sample identifiers.
To retrieve batch data from within Luminex xPONENT a user must:
(i) Generate the .CSV export which is compatible with the Benchling Connect, xPONENT data connector
(ii) Ensure that the file is placed with the watched directory configured via a Benchling Connection.
Importing sample identifiers to Luminex xPONENT batch
The Luminex xPONENT software annotates data based on sample identifiers. Despite being a plate-based instrument, the xPONENT software does not record or report plate identifiers, such as a plate barcode. Therefore for tracking experimental results, it is recommended that the user sample identifiers within the xPONENT batch which correspond to entities registered within Benchling.
To import a list of sample identifiers to a batch, the Import List utility within the Plate Layout view within the Batches tab should be used. The Import List utility expects a .CSV file with columns for: Well, Type, ID, and Dilution; where ID corresponds to the sample identifier.
The file to be upload to the Import List utility can be generated using the Input File Generator within the Benchling Run.
Exporting data from Luminex xPONENT
In order to export data from Luminex xPONENT, the user should follow the instructions for Export the Batch Results (FLEXMAP 3D User Manual, 89-00002-00-622 Rev A, p43).
To do so the user should:
- Navigate to the Results page and select the Saved Batches tab
- Chose the completed batch to export and click Exp Results
- In the Save As dialog box, the user should choose the export destination for the .CSV file
This destination should be folder specified in the Connection configured within Benchling - Click Save
- In the Export Complete dialog box, click "Ok"
Alternatively, an administrator can configure these exports to occur automatically by updating the CSV Options from within the Admin Page. From within the CSV Options the admin should update the following settings:
- Automatically export results CSV file when batch is complete - TRUE
- CSV Export Folder and Automatically Exported Batch Folder - updated to match folder specified in the Connection configured within Benchling
Steps within Benchling
From within Benchling, a user must:
-
Enable the Luminex xPONENT data connector on the tenant [internal admin console]
-
Configure a Luminex xPONENT Connection
-
Create a Result schema to structure the data to be recorded
-
Configure a Run schema for the Luminex xPONENT assay generate file for Import List utility (if desired) and to record 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.
Configuring the Output File Processor - Annotating data via Plate entered as Run field
As noted above, it is recommended annotate experimental data from Luminex xPONENT using sample identifiers recorded within the batch with xPONENT.
However, if the user prefers to associate the data with a plate and well within Benchling, it is possible to do so by annotating the results with information from a plate entered into the Run itself.
In order to use the plate barcode and plate well to associate the well-level measurements contained within the xPONENT file with the appropriate entity in Benchling additional Transform steps must be configured. Note that this method is only appropriate for ingesting xPONENT files with a single plate, if multiple plates are present then the sample identifiers should be entered directly in xPONENT as discussed above.
First an ‘Add Column’ step is needed to capture the barcode of the plate that is entered on the Run. Since this barcode value needs to be repeated for each row of the file, ensure that the ‘Consolidate results into single row’ option is selected.
Next a combination of a ‘Duplicate’ and a ‘Merge’ step are used to combine the plate barcode with the well coordinates from the file, to create a column containing the plate well information in the necessary ‘barcode:well-coordinate’ format. Together the Transform steps would appear as shown below.
Data returned by Luminex xPONENT Data Connector
The Benchling Connect, Luminex xPONENT data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the xPONENT file export. The data is processed in a two step process; step one from xPONENT 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 Multi-Analyte-Profiling 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 data connector then converts the ASM to a well file .csv file, such that each row of the file represents a well of the plate - along with metadata about the experiment
For the Luminex xPONENT, the well file will typically contain the following columns (if available within the data):
- Model Number
- Equipment Serial Number
- Calibration Time <Calibration Test> - repeated for each calibration test performed
- Calibration Report <Calibration Test> - (e.g. "Passed"), repeated for each calibration test performed
- Data System Instance Identifier - identifier for the computer used for analysis
- File Name
- UNC path
- Software Name
- Software Version
- ASM Converter Name
- ASM Converter Version
- Analyst
- Analytical Method Identifier - name of protocol used in analysis
- Method Version - protocol version
- Experimental Data Identifier - xPONENT Batch name
- Container Type
- Plate Well Count
- Measurement Identifier
- Measurement Time
- Sample Identifier
- Location Identifier
- Device Type
- Sample Volume Setting
- Dilution Factor Setting
- Detector Gain Setting
- Minimum Assay Bead Count Setting
- Assay Bead Count Total
- Assay Bead Identifier <Analyte Name> - repeated for each analyte measured performed
- Assay Bead Count <Analyte Name> - repeated for each analyte measured performed
- Fluorescence Median RFU <Analyte Name> - repeated for each analyte measured performed
- Error - List of error message per well (if applicable)
Sample files can be found here.
Configure Run Schema to employ Luminex, xPONENT Connection
The Run schema can be created from the menu under Feature Settings.
As part of the Run schema creation, the user should specify 'Luminex, xPONENT' 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
Luminex xPONENT Data Connector Requirements
| Item | Specification |
| Luminex xPONENT | Luminex xPONENT Software 4.3* |
| Operating System | 64-bit Windows 10 or greater |
| Memory | 8GB RAM |
| Processor |
3.0 GHz Intel Core i5 (or higher) |
| Gateway | Benchling Gateway installed on PC, able to communicate on port 443 |
* This is the version of the xPONENT software with which the data connector has been developed and tested. The data connector may work with other versions of the xPONENT software, but that must be verified by the user.
Revision History
2024/02/27
Initial Version
2024/09/03
Update link to referenced schemas in Github
2024/09/18
Added Github testdata link