Editing a Plate Layout Template File
This lesson is for all users of the Antha OS system who wish to know more about how to edit an input plate layout file.
About this tutorial
This tutorial will teach you about the plate layout file structure and how you would edit it such that by uploading either in the Configuration tab of the Workflow Editor or via Plate prep you can specify the layout of your samples in a chosen plate type. If your specified plate layout already exists in the inventory then there is no need to provide a plate layout file, you can search for the plate in the inventory to specify your sample layout that way instead.
Things you'll need
Before you get started you will need an Antha license so that you have access to Antha OS. It would also help, but is not a necessity, to read through these reference documents:
- Using the Workflow Editor
- About Simulation and Reports
- About Dashboard
- About Plate Prep
- Uploading files
What you'll learn
In this tutorial you will learn:
- How to download a plate layout template file
- The structure of a plate layout template file
- How to specify the plate type your samples will be in
- How to specify the location of your samples in your chosen plate
How to download a plate layout template file
There are three places that you can download a plate layout template file from:
- The Dashboard
- Plate prep
- Job Queue
From either Dashboard or the Job Queue you can download a plate layout template file simply by clicking on any of the Plate files for that job. In Plate Prep there is a Download button at the top right of every plate schematic.
Sample layout table format
The sample layout table lets you give a number of pieces of information regarding your samples, e.g. plate type, well position, liquid type, volume of sample, volume unit, concentration and concentration unit. You can download an example plate layout file here
The first column of the table is used for specifying the plate type that your samples are in and the well positions in that plate.
The second column defines the solution/sample that is in that well position. The header for this column is optional and is used to give the plate a name when uploaded to an existing workflow. However, if you give it a name when prompted during upload, it will overwrite the name given in the file.
The third column lets you set the liquid type for that sample. This will define how that liquid will be treated. For example enzymes are viscous solutions therefore we treat them like they are glycerol so that they are pipetted slowly etc.
The next two columns allow you to set the volume of the solution that is in the well and the volume unit.
The last two columns are not currently used in this release of Antha but in future releases will be implemented. They will allow you to define the solution concentration and the units of concentration. However, whilst these columns are not yet used the cells in the Conc column must not be empty and require at least a 0 or a number in here.
Specifying plate type
In order for you to specify the type of plate your samples are in you simply have to enter the name of the plate type in cell A1 of the plate layout template file. (Column 1 header).
Antha has a plate library that describes the plate dimensions for an automation platform to interpret. Antha uses specific identifiers (names) for different plates but also the type of riser that plate is on.
Specifying sample location
Specifying your sample location is now as simple as reformatting the template table to specify where your samples are on the plate.
You may have the situation where you have a plate that only contains your DNA samples and nothing else. If this is the case then you could alter the plate layout file to look like this:
Antha will recognise the fact that you are missing the other samples required for this workflow and will create a new plate for you with the remaining samples with auto allocated positions.
How to upload a new plate layout file
The only thing left for you to do is to upload the new plate layout file so that Antha knows you want to specify your sample locations yourself. To learn about how to upload plate layout files take a look at the Uploading Files documentation.