Purpose
To provide details about the necessary steps to implement the BD Biosciences, FlowJo connector for use with the Benchling Connect platform.
Introduction
The BD Biosciences, FlowJo connector is a component used in the context of the Benchling Connect platform to parse data from the FlowJo software to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run.
The Benchling Connect, BD Biosciences, FlowJo connector is a ‘file-based’ based connector, meaning that it processes WSP (workspace) exports generated by the FlowJo software. 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 BD Biosciences, FlowJo connector for use with the Benchling platform, there are several steps that need to be followed across both the BD Biosciences, FlowJo and Benchling user interfaces.
This guide details the steps to be taken in both applications in order to configure the integration.
Steps within FlowJo
From within FlowJo software, a user must:
- Configure a WSP export compatible with the Benchling Connect, BD Biosciences, FlowJo connector.
- Execute the export of that file from their FlowJo session.
- Ensure that the file is placed within the watched directory.
Configuring WSP export from FlowJo
To configure the Benchling Connect compatible FlowJo export, a user should:
- Finalize all analysis steps, including adding samples, population gating, population counts/statistics, group creation
- Select File/Save As/Save as Workspace (WSP)
- Save the WSP file in the File Watcher directory configured via Benchling connection
Steps within Benchling
From within Benchling, a user must:
-
Enable the FlowJo connector on the tenant [internal admin console]
-
Configure a FlowJo Connection
-
Create a Result schema to structure the data to be recorded
-
Configure a Run schema to accept data from FlowJo 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 FlowJo 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 - FlowJo connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the FlowJo file export. The data is handled in a two step process; step one from FlowJo 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 Flow Cytometry 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/flow-cytometry
The connector then converts the ASM to one of:
sample file .csv - structured such that each row of the file represents a sample
region file .csv - structured such that each row of the file represents a data region (gate)
compensation file .csv - structured such that each row of the file represents a compensation matrix
population file .csv - structured such that each row of the file represents a population
Output CSV files can contain the following, but may vary depending on the input file.
| Sample File | Region File | Compensation File | Population File |
| Device Identifier | Device Identifier | Device Identifier | Device Identifier |
| Product Manufacturer | Product Manufacturer | Product Manufacturer | Product Manufacturer |
| File Name | File Name | File Name | File Name |
| UNC Path | UNC Path | UNC Path | UNC Path |
| Software Name | Software Name | Software Name | Software Name |
| Software Version | Software Version | Software Version | Software Version |
| ASM Converter Name | ASM Converter Name | ASM Converter Name | ASM Converter Name |
| ASM Converter Version | ASM Converter Version | ASM Converter Version | ASM Converter Version |
| ASM File Identifier | ASM File Identifier | ASM File Identifier | ASM File Identifier |
| Analyst | Analyst | Model Number | Analyst |
| Model Number | Model Number | Data System Instance Identifier | Model Number |
| Data System Instance Identifier | Data System Instance Identifier | Dimension Identifier [constant] -- channel compensated against | Data System Instance Identifier |
| Experimental Data Identifier | Experimental Data Identifier | Dimension Identifier | Experimental Data Identifier |
| Measurement Time | Measurement Time | Compensation Value | Measurement Time |
| Sample Identifier | Sample Identifier | Sample Identifier | |
| Measurement Identifier | Measurement Identifier | Measurement Identifier | |
| Written Name | Written Name | Written Name | |
| Device Type | Device Type | Device Type | |
| Method Version | Data Processing Time | ||
| Data Processing Time | Population Identifier | ||
| Written Name [Population] | Group Identifier | ||
| Data Region Identifier | Written Name [Population] | ||
| Region Type | Data Region Identifier | ||
| X-Coordinate Dimension Identifier -- Channel of x-axis gating | Parent Population Identifier | ||
| Y-Coordinate Dimension Identifier -- Channel of y-axis gating | Count (Counts) | ||
| X-Coordinate | *Population Statistics -- addition of population statistics columns | ||
| Y-Coordinate | |||
Limitations:
While we develop the connector against real world example data, there may be some limitations to the connector. 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!
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FCS files are not currently supported by the FlowJo connector
- Users however can configure their FCS files that correspond to the WSP gating/analysis are attached to the Run
FlowJo Connector Requirements
| Item | Specification |
| FlowJo | FlowJo v10.0.7, v10.8.1, v10.10.0* |
| Operating System | Windows 11 |
| Memory | 4GB of RAM |
| Processor | 1 GHz or faster with 2 or more cores on a compatible 64-bit processor |
| Gateway | Benchling Gateway installed on PC, able to communicate on port 443 |
*This adapter was developed with these FlowJo versions, additional versions may work. If they do not, please reach out to your Benchling Representative to update the compatibility.
Revision History
2025/04
Initial Version