Table of Contents

Purpose 3

Introduction 3

File Format Requirements Specifications 3

Steps within Benchling 5

Create a Result schema

Configure Run Schema for Biorad CFX96 Real-time System File 5

Revision History 8

Purpose 

To provide details about the necessary steps to implement the Biorad CFX96 Real-time System 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 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 Biorad CFX96 Real-time 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:
    • Well or Sample Description  (Entity or Inventory Link)
  • Optional columns (examples, but not limited to):
    • Conc(copies/uL) (Decimal)
    • Accepted Droplets (Decimal)
    • Positives (Decimal)
    • Negatives (Decimal)
• The values in either the Well or Sample Description column must refer to a unique inventory barcode or entity name that already exists in Benchling or that will be created by the run. 

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 [Connector Name] 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 Biorad CFX96 Real-time System data

The Benchling Connect - Biorad CFX96 Real-time System adapter uses Benchling’s built-in transform steps to structure the information parsed from the file export. The data are processed to capture results against samples or containers. 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 Biorad CFX96 Real-time System data

• Create a new Run schema. Select the Benchling FileWatcher connection schema.
  
• If the result file you’re uploading does not include a column identifying the plate, add a run field so users can enter the plate ID
  • Click “+” to the right of “Run fields” 
  • Name the field “Source Plate”
  • Check the box for Required
  • Change the Definition field to Inventory > 96 Well Plate
• Click Next
• To the right of “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 “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”
• Transform your file by clicking “set transforms”:
  • If your file does not have headers, skip this step. If your file has headers, 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 “9.”
  • If you added a run field for Source Plate, you will need to add a transform to add this information to the file. 
    • Select Type > Add Column
    • Name the new column Source Plate
    • Click Set lookup and choose Source Plate from the “Start from” dropdown
    • Click Continue

• • • Choose Source Plate (96 well plate) from the Lookup attribute
    • Check the box for “Consolidate results into single row”
    • Click Insert

• • Next, merge the well coordinates provided in the file with the plate ID provided by the user
    • Select Type > Merge
    • In Columns to merge type: Source Plate, Well
    • Delimiter should be a semicolon (:)
    • New column name: Well ID
    • Click Done

• 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. 
• Set the columns to map to their purpose (typically sample name, container or plate barcode, position, or results schema field values).
• 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. 

Revision History

• 2024/04 Initial Version