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CLARIOstar Microplate Reader Integration using Scispot GLUE
CLARIOstar Microplate Reader Integration using Scispot GLUE

This article is to help you set up a data connection between your BMG Labtech CLARIOstar Microplate Reader and Scispot

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Written by Satya Singh
Updated over 5 months ago

Overview

This article guides a user through the process of connecting their CLARIOstar Microplate Reader with the Scispot platform. The integration leverages our Scispot agent, a Java application that runs locally on your machine and manages the flow of information from a specified directory to your Scispot account.

Part 1: Setting up the Integration on Scispot

Step 1: Create a Scispot Agent

  1. Navigate to the GLUE application on the left-hand menu of Scispot

  2. Select Agents in the top bar of GLUE

  3. Select Add Agent from on the left side of the screen

  4. Choose a name for the agent you are creating and select your device's operating system to download the appropriate Java application

  5. Select Add Agent to begin the download of the agent application

Step 2: Add Source

The source is the location that will be providing data to be synchronized with Scispot. In this case, it will be your CLARIOstar Plate Reader.

  1. Navigate to GLUE within Scispot

  2. Select Sources in the top bar of GLUE

  3. Select Add Source and under Instruments, select Plate Readers

  4. From the instrument drop down, select the CLARIOstar Plate Reader

  5. Add a name for this instrument in the corresponding field

  6. Select the agent created in Step 1 from the dropdown menu

  7. Select Create Source once this information has been added

Step 3: Add Destination

The destination is the location where the data from the source will be sent.

  1. Navigate to Destinations within Scispot Glue

  2. Select Add Destination and from Data Sources, choose Scispot Labsheets (by default, this means data will save to a file called Agent Files)

  3. Select Scispot Labsheets and select Create Destination

Step 4: Create the Connection

To connect the configured source and destination to each other:

  1. Select Connections in the top bar of GLUE

  2. Select Add Connection in the top right corner of GLUE

  3. Define the source as the created CLARIOstar Instrument source

  4. Define the destination as the created Labsheets destination

  5. Select Create Connection

Part 2: Configuring Data Export from the CLARIOstar Plate Reader

Step 1: Save Data in ASCII Format

  1. Within the BMG Labtech Control Software used to work your CLARIOstar Plate Reader, open the output setting dialogue by using the menu command 'Settings | Data Ouput'

  2. Under Standard Output Settings check the checkbox for 'Save measurement data in ASCII format' if it is not already checked

Step 2: Set the Output Path and File Name for ASCII Files

  1. Once the above checkbox is selected, a 'Define Format for ASCII Export' window will become available

  2. Within this window, select the path for the file directory where ASCII files from the plate reader will be saved; this could be locally on the current device or on directory somewhere on your network. Note that this file directory is the place the Scispot Agent will monitor for the live synchronization of Plate Reader data with Scispot (setup details in Part 3 below)

  3. Setup the filename for the outputted ASCII files - this will be what Scispot uses to name the corresponding Labsheets. Note that the name field does accept variables such as:

    1. <protocol> : Name of the protocol used

    2. <method> : Name of the method used

    3. <1+#> : Assigns consecutive natural numbers to test runs beginning with the value of what is given in the angled brackets (i.e. the example input would cause the values to begin at '1'). The consecutive numbers do restart at the given beginning value when the software is restarted

    4. <date> : The current date

    5. <time> : The current time

      These options can be useful in ensuring that each file created has a unique name.

Step 3: Configure the Output Data Format

  1. Specify the format that the ASCII data will export as under the Data Format tab

Part 3: Connecting Scispot and the Plate Reader Data

Step 1: Configure the Connection

  1. Within GLUE, under the Sources tab, click on your created plate reader under Instruments

  2. Under Configuration, scroll all the way to the bottom to see the field File Watcher Path

  3. Insert a file path into the field; This will be where the agent will watch for file additions and changes. Insert the file path to the directory that you set as the export path for ASCII files from your CLARIOstar Plate Reader in Part 2, Step 2 of this article

  4. Confirm your selection once you have input the appropriate path by selecting Update in the upper right hand corner of the configuration tab

Step 2: Running the Agent

  1. The downloaded Scispot agent file from Part 1, Step 1, is a .zip file containing a Java file that is the Agent application, as well as a batch file containing the command needed to run the agent

  2. Extract these two files from the downloaded .zip file into a directory on the device that will be used for file synchronization - this should be a device that has access to the directory configured as the ASCII file path in Part 2, Step 2

  3. Execute the command contained in the batch file in a terminal to begin running the agent

  4. Your agent is now running! You can make sure it is connected by returning to the GLUE application within Scispot and navigating to the Agents tab. There, your named agent will appear with a green connected logo next to its name

Step 3: Data Sync Begins

  1. The File Watcher will monitor the paths specified in the configuration and sync the files dropped into the folders to Scispot.

  2. The synced files will now appear by default in a Labsheet called Agent Files

  3. Once you have setup your data input format and desired data output with the Scispot team, the platform will automatically run calculations and transformations on the data so that it appears in custom Labsheets and Manifests, ready to be used by your team

Step 4: View the Connection and Data

  1. Now, your folder paths are monitored by the Scispot agent, and whenever any file lands there, it will be sent to Scispot.

  2. To view the status of the connection as well as monitor what files have been synced, from GLUE select Connections and select your CLARIOstar Plate Reader to Labsheets connection - here you can see the transaction logs of file synchronization

  3. Also navigate to the Labsheet called Agent Files to find the uploaded raw files

  4. After setting up your data input format and desired data output, data will now also populate in Labsheets with names corresponding to the file names of each ASCII file as well as corresponding manifests containing the test plate layouts from your plate reader!

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