Purpose
To provide details about the necessary steps to implement the Echo 525 Transfer Log 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. In cases where ASM models or Benchling ASM converters do not yet exist for an instrument a non-ASM approach is provided instead.
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 Echo 525 Liquid Handler 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:
Source Plate Name
Source Plate Barcode
Source Plate Type
Source Well
Destination Plate Name
Destination Plate Barcode
Destination Plate Type
Destination Well
Destination Well X Offset
Destination Well Y Offset
Sample ID
Sample Name
Transfer Volume
Current Fluid Volume
Actual Volume
Fluid Composition
Fluid Units
Fluid Type
Transfer Status
The values in the Sample ID and Sample Name columns must refer to unique barcode or name values for a plate or container that already exists in Benchling Inventory or that will be created by the run.
Applications:
This process supports importing transfer logs from the Echo 525 Liquid Handler using the Labcyte Echo Cherry Pick application. It is intended for single-run, plate-to-plate liquid handling operations, capturing transfer details including sample identifiers, volumes, and well locations.
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[1]
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 Echo 525 Transfer Log 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 Echo 525 Transfer Log data
The Benchling Connect - Echo 525 Transfer Log adapter uses Benchling’s built-in transform steps to structure the information parsed from the Echo 525 Liquid Handler 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 Echo 525 Transfer Log 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:
“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 “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.
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.