The Workflow Editor
The Workflow Editor is a platform for intermediate Antha users to create custom element workflows, which increase the flexibility and complexity of the experimental or data tasks you wish to automate.
The Editor provides you with the ability to connect elements together such that the output of one element may be used as the input for the next. In doing so the range of behaviour that can be achieved from an automation platform can be expanded to increase throughput in a laboratory setting.
About this tutorial
In this tutorial you will be walked through the key features of the Workflow Editor and how to use it. This tutorial will focus on the Editor as a whole and not on details of the individual elements, how they work, or how to use them specifically. To learn how to use specific elements in the workflow editor take a look at the relevant sections within our Antha Case Studies
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
The different areas within the Workflow Editor:
- The Workflow Details area
- The Element Library and Search Tool sidebar
- The Workflow Space
- The Workflow Space toolbar
- The Workflow Properties sidebar
- Parameters tab
- Configuration tab
- Upload/Download workflow files
The Workflow Editor areas
Within the Workflow Editor there are several key areas that you will access. The following sections will take you through these areas one by one describing what they do and how they can be used.
The Workflow Details area is located in the top right of the Workflow Editor and has a blue background.
This area provides two pieces of information for the user.
- The name of the workflow you are working on. This name will appear in the Job Queue for this workflow as the primary means of identification if you need to find this workflow again in the future. The name will also be used as the file name when you download the workflow properties file (bundle file).
- The estimated time it would physically take to run your workflow (calculated after simulating a workflow)
Element Library sidebar
The Element Library sidebar lists all of the Antha elements available to you in alphabetical order. The library can be searched using the search bar located immediately above the list of elements.
In order to add one of these elements to the Workflow Space, locate the element you want and use a single mouse click on that element to add it to the Workflow Space.
There are many options available to the user here. You can:
- Load a single instance of an element
- Load multiple instances of an element
- Load multiple different elements that run in parallel
- Load multiple instances of the same/different element that are wired up together into a workflow.
The Workflow Space is used to manage Antha elements and to interactively link them together into workflows if required.
In the following figures we will use an element called AccuracyTest as an example but will not go into detail of how this element works or what it does. Firstly a single mouse click on the AccuracyTest element from the Element Library side bar will produce a specific instance of this element in the Workflow Space.
The Workflow Space now provides more information to use about the workflow we have started to assemble. Hovering your mouse over the AccuracyTest element card in the Workflow Space will display all of the inputs emanating from the left hand side of the Workflow Space into the element card. Likewise all of the outputs from this element leave the element card to the right hand side of the Workflow Space.
The input and output streams are colour coded to the parameter types (e.g. string, volume, concentration, DNA sequence, etc.) To see what each of the colours represent you can click on the inputs info tab which will open a dialogue box with a type key and examples of the data types these may be.
Parameters of the same types can be wired together between two different elements such that the output of one element becomes the input for the next. For more detailed information on how to wire elements together take a look at the Antha Case Studies.
Element specific information can be accessed through the small code or info icons at the top of the element card in the Workflow Space.
Clicking on the code icon (<>) will reveal the Anthalang code that sits behind the scenes of the element and determines how the inputs are converted to the relevant outputs for that element.
Likewise, clicking on the info icon opens up a dialogue box with three tabs displaying more general information about what that element does and what each input or output element does.
Workflow Space toolbar
The Workflow Space toolbar contains a range of clickable tools allowing the user to:
- Clear the Workflow Space
- Clicking on the Clear tool bar button will reset the Workflow Space, removing all elements permanently.
- The layout buttons allow the user to organise their elements in the workspace by either vertically overlapping, vertically non-overlapping or horizontally non overlapping.
- Set zoom options of the Workflow Space
- The zoom buttons will increase or decrease the zoom of the Workflow Space only.
- Clone or Delete Antha elements
- Elements can be cloned or deleted by highlighting the desired elements in the Workflow Space by either clicking on them or drawing a box around multiple elements followed by clicking on either the clone or delete button in the tool bar.
- Simulate workflows
- The simulate button runs an in silico simulation of your workflow against the parameters set for each of the elements in the workflow and against the selected automation platform to check for any run time errors or device related conflicts. A successful simulation is necessary in order to be able to physically run a workflow.
- View the console and clear the console.
- The console button allows the user to display or hide the console where any simulation results or errors are displayed. The clear console button will erase any messages currently in the console.
Workflow Properties sidebar
The Workflow Properties sidebar is where the user can customise their workflow. For example, whilst the Aliquot element will always produce aliquots, the Workflow Properties area allows the user to set the specific parameters for this instance of the element making it unique from others.
The user can also specify some system settings here such as plate types, device types or alter the driver specified deck layout.
Bundle files containing the user specified workflow properties can be uploaded or downloaded for future use or sharing by clicking on the import/export buttons.
Parameters side bar
The Parameters side bar will at first appear empty with a note to the user that "This workflow has no elements yet".
Once an element has been selected and appears in the Workflow Space, the Parameters side bar will be populated with a collapsable menu to access the parameter options for that instance of that element. If multiple elements are being run in the workflow a numbered key to map elements to their instance of parameter values can be visualised by a number in a green tab.
For more detailed information on how to edit parameter settings take a look at the Antha Case Studies.
Configuration side bar
The Configuration tab allows the user to define higher level system preferences rather than element level preferences. There are several options available to the user here:
- Plates (Input plate sample layout)
To learn more detail about the Configuration tab in the Workflow Properties side bar take a look at the About Configuration documentation
Simulating a workflow
Once all your parameters and workflow preferences have been set the next step is to run an in silico simulation to make sure there are no errors in parameter inputs or configuration conflicts.
To do this you simply click on the Simulation button in the Workflow Space tool bar. This will automatically open the Console showing you the progress of the Simulation. If there are no errors then you will be presented with many options:
- See simulation details
- This button will take you too a dashboard of the simulated job which will walk you through the physical steps to set up your experiment. To learn more about the dashboard take a look at the Dashboard documentation.
- View execution graph
- The execution graph will present an interactive graphical representation of all the liquid handling steps that will be carried out in your workflow. To learn more about the execution graph take a look at the Graph View documentation.
- Download data files
- Protocol data files available for download will be shown here.
- Download outputs.json
- outputs.json is a file which contains all of the final outputs for your workflow and can be analysed for tracing purposes.
What should I learn next?
Now you know how to use the Workflow Editor to prepare custom workflows we would suggest that you next learn how to use the Dashboard to walk you through the physical set up of your experiment.