Purpose 

To provide details about the necessary steps to implement the Cedex HiRes Connector for use with the Benchling Connect platform.

Introduction

Connectors allow Benchling to read a file generated by an instrument and take inventory actions in Benchling or record measurements. Benchling connectors use Allotrope Simple Models (ASM) where possible. This guide provides a non-ASM approach to Connect instruments with Benchling until ASM models or Benchling ASM converters exist. 

Connector guides describe the required file format, Benchling configuration steps, and outcomes supported by the connector.  The connector is specific to a single file format and a single type of assay. Your file must meet the requirements described below to be compatible with the instructions that follow. If it does not, it may be possible to adjust your file and the steps to support your instrument’s file format or it may not. Please reach out to your Benchling representative or support@benchling.com for assistance. 

File Format Requirement Specifications: 

• Your export file must be a .CSV or .XLSX formatted file with one tab. 
  • If multiple tabs are present, only the first tab will be processed and others will be ignored. 
• Your Cedex HiRes file contains a single data table that either:
  • Starts with column headers in row 1 and data in the following rows.
  • Starts with headers that are a consistent length. I.e. we can always remove the first n rows and after doing so the data table will begin in cell A1.

• Your data table contains columns (exact names can differ) including:
• Required* columns:
  • Sample identifier*

*The values in the Sample identifier column must be an entity or container in Benchling

• Optional columns (examples, but not limited to):
  • Avg Area,, Avg Perimeter, Avg Diameter, Avg Compactness etc.
  • Data set name, Reactor identifier, Dilution, Sample volume, Sample draw Time, Date finished, etc.. 

Applications:

Record Data:

• The file’s optional columns may be recorded as results data associated with the entity or container identified in the file.
• What the connector will do: Record results data for the selected columns against a sample or container.

Steps within Benchling 

From within Benchling, a user must:

1. Enable the Generic FileWatcher adapter on the tenant [internal admin console - for non Benchling employees, please reach out to Benchling Support for assistance]

2. Create a FileWatcher Connection schema

3. Configure a FileWatcher Connection

4. Create (or select an existing) Custom Entity Registry or Container schema to represent the entity the results will be captured against

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

6. Configure a Run schema to accept files from the specified filewatcher folder and record Results

For steps 1 - 3, please reference the Benchling Connect Installation Guide for details related to creating and installing a Gateway and configuring a Connection.

Create Registry and Result schemas

The Benchling Connect - Cedex HiRes connector uses Benchling’s built-in transform steps to structure the information parsed from the Cedex HiRes file export. The data are processed to trigger result capture. 

If you do not already have a Registry schema created for Timepoint Samples and a Result schema created for the Cedex HiRes, these should be created before moving on.  Please refer to the Registry schema creation and Result schema creation help articles, as needed.

Configure Run Schema for Cedex HiRes

• Create a new Run schema. 
  • Help articles outlining each step of creating and configuring a run can be found here.
• Select the Benchling FileWatcher connection schema.
  
• Click next then next to “Output file configurations” click + 
• Set a custom name and select: 

• “Register and/or update entities” 
• “Transfer samples” 
• “Record results”

• Under “Result schema” select the results schema you would like to use or
  • For each schema field, choose Use column from output file, then select Done
  • Optional: If a result schema does not already exist, use “Create new result schema” 
• If your file does not have headers, skip this step. If your file has headers, click “set transforms:
  • Select Type > Extra headers
  • In the “Row number of column header” box, type the row number where the data table begins. In the above image for example you would choose “9.”
• Under “Configure column mapping” choose to specify either “by column order” or “by column name”
  • “By column order” assigns the columns to their purpose based on position so if column header names change the run will still work. Additional columns not specified will be ignored. 
  • “By column name” assigns the columns to their purpose based on exact match to the column header name. Columns not exactly matched will be ignored. 

• Click “Update” and your run is complete. 
• Create a connection to the FileWatcher into which files from this instrument will be saved and add the run you created to your Notebook Entries and templates to select and process the file to take the corresponding actions in Benchling. 

Configure Run Schema to employ CEDEX HiRes Connection

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

As part of the Run schema creation, the user should specify 'CEDEX HiRes' 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

Revision History

• 2024/04 Initial Version

Appendix

Full requirements to be attached to SOWs with non-ASM connectors included. 

General Connector Caveats

• The data described above will be recorded as raw data in a new or existing registry or results schema formatted as described.
• Analysis or transformation of any data within the file is not included in the connector itself and will be handled as a separate workstream leveraging Insights, Analyses, or Notebook  features such as tables. 
  • As part of an Implementation Project, effort to manipulate, analyze, validate, verify, or transform data after it is recorded to the raw results schema is separate and additional to connector configuration effort. Any such effort must be accounted for independently or addressed by the Customer independently.
• Benchling Connectors that rely on Benchling’s native file processing features are not specific to an instrument and software version combination. They are specific to a particular file format and use case. 
• Files that are similar to but not expressly supported by the requirements described above may still be able to be supported by native Benchling functionality with adjustments to the above instructions. For such cases, additional scoping is required to confirm feasibility and effort. Additional Implementation Project time will be required to adjust configurations to accept such formats. 

Cedex HiRes Caveats

• Customer’s Cedex HiRes file must be formatted as described above. 
• Customer may create and transfer new Registry entities alone or may do those steps and record results. Other actions such as creating entities without transferring or transferring without creating new entities are not supported by this connector.