This lesson is aimed at beginner Antha OS users.
About this tutorial
This lesson contains information about the basic features of the plate prep task. To learn how to edit Plate Layout template files, see the editing plate layouts lesson.
Things you'll need
Before you get started you will need an Antha license so that you have access to Antha OS.
What you'll learn
- What the Plate Prep task view is and what features it offers.
- How to physically prepare an input plate based on the instructions given by the Plate Prep task view
- How to download a plate
- How to upload a plate file
- How to find plates in the inventory
- Understanding the colour-coding
Walkthrough of the Plate Prep Task
The Plate Prep task view is accessed by clicking on the Plate Prep icon in the timeline of the Dashboard View of a selected job.
When you open the Plate Prep task view, you are presented with your first auto-generated plate. If there are any input plates added by the system, they will show up first in blue. In this particular example, there are not yet any input plates because we need to upload a plate layout file. To do this, click the blue "edit plates" button.
Then click the grey "upload plates from file or inventory".
In this view, you can either drag your plate file onto the upload area or you can click the blue text to upload the file from your file browser.
Once you upload your file, you will be prompted to submit a name and barcode for the new plate. After you've filled in this information, click "confirm" to continue.
Your newly uploaded plate should be visible on the left. Repeat these upload steps for any additional plates. If you are satisfied with the plates, press the yellow "Confirm plate prep" button to go back to the plate view.
You will be prompted to confirm that you want to re-simulate your workflow. This step is important to make sure that the plate you've uploaded is valid and will work with the other components in your custom workflow. Click "Confirm" to continue.
If your job re-simulates successfully, you will be brought back to the plate view where you will see your newly uploaded plate. Once you are satisfied with all of your plates click "Confirm Plate Prep" again.
A dialog will appear asking you to name and barcode your plate if you haven't done so already. Click the blue text which reads "click here" to name and barcode your plate.
Once you are satisfied with the names and barcodes of your plate, press "save" to continue.
Click "confirm" to confirm your plate layouts and return to the dashboard.
How to Physically Prepare an Input Plate Based on the Instructions Given by the Plate Prep Task View
The most useful part of the Plate Prep view is using it as a guide for physically preparing the input plates you'll need for your your job. With the visual cues offered by the Plate Prep view, making up your plate is fast and simple.
Knowing the Contents of a Well
To find out what the contents of your input plate are supposed to be, you can click on individual wells, a single row, or a single column to highlight its contents. By doing so, the volume will appear in the selected well and the content details will be highlighted.
Here is what it looks like when a well is highlighted...
...a column is highlighted...
...and a row is highlighted.
The contents of a plate are colour-coded based on how the liquids are handled by the liquid handling robot.
How to Download a Plate
There are three places where you can download the plate layout file: The Type IIS Construct Assembly Protocol card, the Workflow Information Sidebar (which is shared between the Job Queue and the Dashboard) or within the Plate Prep task of an existing job.
Getting the Template Files Through the Type IIS Construct Assembly Protocol Card
The templates for all of the files compatible with the Antha OS environment, including the plate prep layout, can be found in the Type IIS Construct Assembly Protocol card.
To access the Type IIS Construct Assembly Protocol card, select the "Protocol" tab at the top of the app and click the "get started" button in the "Type IIS Construct Assembly" card.
Within the protocol card there is a link for downloading a .zip of template files. Click on the yellow text reading "Download the template files" to download this .zip archive.
Once the file has downloaded, unzip the archive to access the files.
Within the unzipped folder you will find three template files: A sample .json bundle file, a sample .gdx design file, and a sample .csv plate file.
Open the .csv plate file to begin editing.
Getting an Existing Plate Layout File from the Dashboard or the Job Queue
You can modify the input plate in the Dashboard or the Job Queue by downloading the auto-generated input plate, editing it, and re-uploading it.
Scroll down on the Workflow Details sidebar until you see "Plate files." Click on the input plate (the one with the blue icon).
Open the downloaded file and save to a memorable location
Getting the Template File in the Plate Prep Task of your Workflow
You can also modify the input plate in the Plate Prep Task View by downloading the auto-generated input plate, editing it, and re-uploading it.
From the Dashboard of a selected Job, click on the Plate Prep task.
Choose a plate for which you would like to download the plate layout file. Click the word "Download" above the plate image.
Your plate layout will be downloaded as a .csv file which you can edit and upload elsewhere.
How to Find Plates in the Inventory
If you would prefer to load a plate which already exists in your inventory, you can do so by searching for it by its barcode in the inventory. To do this, click the blue "edit plates" button and select "Upload plates from file or inventory." Then simply select the "Search by barcode" area and enter the barcode of the plate you wish to import.