Introduction
The Benchling Connect, Bio-Rad Bio-Plex Manager data connector is a component used in the context of the Benchling Connect platform to parse data from Bio-Rad 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, Bio-Plex Manager data connector is a ‘file-based’ based data connector, meaning that it processes .XML file exports generated by the Bio-Plex Manager 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 Bio-Plex Manager data connector for use with the Benchling platform, there are multiple steps that need to be followed across both the Bio-Plex Manager and Benchling user interfaces.
This guide details the steps to be taken in both applications in order to configure the integration.
Steps within Bio-Plex Manager Software
The following steps should be performed by the user within the Bio-Plex Manager Software.
Prior to performing experiment:
- Update Sample Identifiers (optional)
- Update the Plate Identifier (recommended)
- Note: It is expected that all wells share the same plate identifier in the instrument file (i.e. one plate per instrument file)
At conclusion of the experiment
- Generate the .XML export of experiment data.
- Ensure the .XML file is place within the watched directory configured via the Benchling Connection.
Updating Sample Identifiers within Bio-Plex Manager Software
For tracking experimental results, it is always recommended that the user provide at the point of data collection sample identifiers that correspond to entities registered within Benchling.
The Bio-Plex Manager software does not provide a utility for importing sample identifiers using a text file. Instead sample identifiers may be copy/pasted into the Description column within the tables for Standards, Controls, and Sample information within the Protocol Settings menu. Note that these three sample types are handled as separate tables within Bio-Plex manager, so the identifiers for each need to be entered into each separate table.
Updating Plate Identifier within Bio-Plex Manager Software
In all cases, it is strongly recommended that the user provide a plate identifier which corresponds to a plate currently (or to be) registered within Benchling. This is true regardless of whether the user has opted to enter sample identifiers in the previous step.
Upon initiation of the experiment, the user should enter the plate identifier within the Plate ID in the Run Protocol dialog. Complete instructions for the Run Protocol dialog are provide in the Bio-Plex Manager User Guide (p. 121).
Generating XML export of experimental data
Following the Document Export Options as detailed on p.198, the user should specify the Content of the export as the “Bio-Plex XML”, and specify the directory to which this file should be saved. This location should match the directory specified in the Connection configured within Benchling.
The user is recommended to have the XML file generated automatically at the conclusion of the instrument run by selecting this option within the Advanced Run Settings.
Steps within Benchling
From within Benchling, a user must:
-
Enable the Bio-Rad Bio-Plex Manager data connector on the tenant [internal admin console]
-
Configure a Bio-Plex Manager Connection
-
Create a Result schema to structure the data to be recorded
-
Configure a Run schema for the Bio-Plex Manager assay: to generate a sample list (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.
Data returned by Bio-Rad Bio-Plex Manager Data Connector
The Benchling Connect, Bio-Plex Manager data connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the Bio-Plex Manager file export. The data is processed in a two step process; step one from Bio-Plex Manager .XML 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 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 Bio-Plex Manager , the well file will typically contain the following columns (if available within the data):
- Product Manufacturer
- Equipment Serial Number
- Firmware Version
- File Name
- UNC path
- Software Name
- Software Version
- ASM Converter Name
- ASM Converter Version
- Analyst
- Analytical Method Identifier - name of protocol used in analysis
- Experimental Data Identifier - original Bio-Plex Manager filename (.rbx or .srbx)
- Container Type
- Plate Well Count
- Measurement Identifier
- Measurement Time
- Sample Identifier
- Sample Role Type
- Description
- Location Identifier
- Well Plate 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 Bio-Rad Bio-Plex Connection
The Run schema can be created from the menu under Feature Settings.
As part of the Run schema creation, the user should specify 'Bio-Rad Bio-Plex' 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
Bio-Rad Bio-Plex Manager Data Connector Requirements
| Item | Specification |
| Bio-Plex Manager | Bio-Rad Bio-Plex Manager Software 6.2* |
| Operating System | 64-bit Windows 10 or greater |
| Memory | 4GB 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 Bio-Plex Manager software with which the data connector has been developed and tested. The data connector may work with other versions of the Bio-Plex Manager software, but that must be verified by the user.
Revision History
2024/03/14
Initial Version
2024/09/04
Add link to referenced schemas in Github
2024/09/18
Added Github testdata link