Purpose 

To provide details about the necessary steps to implement the Roche Cedex Bio adapter 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, .XLSX, or .TXT formatted file with one tab. 
  • If multiple tabs are present, only the first tab will be processed and others will be ignored. 
• Your Roche Cedex Bio 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:
  • Both 5.x and 6.x Software Versions: Order ID* (Entity or Inventory Link)
• Optional columns (examples, but not limited to):
  • Both 5.x and 6.x Software Versions:
    • Kind (Text)
    • Date/Time (Datetime)
    • Test (Text)
    • Sample Type (Text)
    • Unit (Text)
    • Flag (Text)
    • Concentration (Decimal)
    • Rate (Decimal)
    • Priority (Text)
• The values in the “Order ID” columns must refer to unique barcode or name values for an entity or container barcode that already exists in Benchling Inventory or that will be created by the run. 

Applications: 

• This is not supported for Kind = 10 (Archived Calibration Results) or Kind = 20 (Archived Quality Control Results) data. Only Kind 40 or 50 (Archived Sample Results).
• The file’s optional columns may be recorded as results data associated with the entity or container identified in the file. This is all dependent on how the Order ID is named. For example if it is named after a Well Barcode the Order ID column must be configured to be an inventory link. If the Order ID column is named after a Sample it would be an entity link. If it is configured as an inventory link you can configure a snapshot field to compute the contents inside the container. If Well Barcode make sure the barcode in your file is named as follows “PLATE BARCODE:POSITION” i.e. 96WP009:A1
• If you have a >LOQ value in the concentration or Rate column please contact Benchling Support or the respective Benchling point of contact and ask them to configure an “allowable dropdown” within the Results Schema.

Steps within Benchling  

From within Benchling, a user must:

1. Enable the Generic FileWatcher adapter on the tenant [internal admin console]

2. Create a FileWatcher Connection schema

3. Configure a FileWatcher Connection

4. Create a (or select an existing) Result schema to structure the data to be recorded

5. Configure a Run schema to accept data from Roche Cedex Bio and records 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 Result Schema for Roche Cedex Bio data

The Benchling Connect - Roche Cedex Bio adapter uses Benchling’s built-in transform steps to structure the information parsed from the Roche Cedex Bio file export. The data are processed to trigger corresponding Registry, Results, and/or Inventory actions. Instructions below describe creating a new schema of each kind required. If you want to map to an existing schema instead, review the instructions to be sure they are compatible.  

Configure Run Schema for Roche Cedex Bio data

• Create a new Run schema. Select the Benchling FileWatcher connection schema.
  
• Click “next” 
• Click “+” to the right of “Output file configurations” 
• 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 “Create new result schema” then “Copy column headers from file” > “From example file”
  • Copy your data table from an example file and paste in. Assign the detected column headers to their Benchling purposes. 
  • Set data columns to “New result schema field”
  • Click “Create” result schema then name your result schema and click “Next.” 
  • You may need to adjust the data types or add fields

• Click “Create result schema”
• Click “Done”
• 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 example in the first image above, you would choose “2.”

• Under “Configure column mapping” choose to specify either “by column order” or “by column name” (For this specific connector please choose “by column order”)
  • “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. 
• Set the columns to map to their purpose (typically sample name, container or plate barcode, position, or results schema field values). 

• For 5.x Software follow this mapping:

• For 6.x Software follow this mapping:

• Click “Update” and your run is complete. 

• Make sure to set the Delimiter to Tab (“     “)
• 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. 

Revision History

2024/05/10

Initial Version