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.
Things you'll need
Before you get started you will need an Antha license so that you have access to Antha OS.
Building a Workflow
Opening the Workflow Editor
The Workflow Editor is one of the apps in the app selection menu. Open the Workflow editor by clicking the menu expander icon and selecting the Workflow Editor app.
Searching for Elements
The library of elements can contain many elements. Searching for the one you need is easy. Click the search icon and begin typing the name of the element you are searching for or a keyword that shows up in the description. The elements available will automatically be updated for you as you type.
Adding and Moving Elements
To add an element to the canvas, simply click on the element from the library. If you click on an element multiple times, multiple elements will be added to the canvas. To move an element around, drag the element either by its black bar at the top or the white body of the element.
To remove elements from the canvas, make a box with your cursor around the elements you wish to remove and press the delete key.
To connect two elements together, click and hold the terminal you wish to connect and drag to the corresponding terminal. Terminals which have a compatible connection will be wider than other terminals and rounded on the inner side. This is to make it more apparent that they can be connected. When you are holding and dragging a terminal, all incompatible terminals will be greyed out. Connections can also be seen in the Parameters section and are indicated by the linking icon and the name of the element which the connection is coming from.
To delete an existing connection, select it and press the delete key.
Changing the Workflow Layout
The workflow editor has three layout options to choose from: Compact, Tiered, and Grid.
Zooming In or Out on the Canvas
Sometimes it can be difficult to see all of the elements on the canvas, or you may want to see an element in more detail. To zoom in or out on the canvas, drag left or right on the zooming bar at the bottom of the canvas. You can also zoom by scrolling on your mouse or trackpad.
Clearing the Canvas
If you wish to remove all elements from your canvas, click the "CLEAR" button at from the menu above the canvas. You will be asked to confirm that you want to remove all elements before they are removed.
Exiting the Workflow Editor
To exit the Workflow Editor, or any app, click the X next to the app name at the top of the screen.
Editing the Workflow Configuration
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
Editing Element Parameters
The inputs, outputs, data, and parameters can be changed in the Parameters tab for each element. To edit these details, choose the element you want to modify in the parameters section, and edit accordingly. Some details, like volumes, are changed by editing text, others are a drop down list, and others still are checkboxes.
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.
Finding More Information About Your Elements
Viewing Information about an Element
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.
Viewing Inputs and Outputs of an Element
Hovering your mouse over an element in the canvas will display all of the inputs emanating from the left hand side of the canvas 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. Howevering over each individual input or output will give you details about that specific piece of information.
Viewing the Workflow Inputs
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.
View the Element Code
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.
Uploading, Downloading, and Simulating
Downloading A Workflow
Note: this feature will soon be deprecated and is not recommended.
If you would like to save the details of a job in JSON format, you can do so with the download button. A JSON file with the details of the workflow will be saved to your computer.
Uploading A Workflow
Note: this feature will soon be deprecated and is not recommended.
If you would like to upload a JSON workflow file, you can do so with the upload button button.
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:
- Open Simulation
- 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.
- 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.
Toggling and Clearing the Console
To clear the console, click the "CLEAR" button in the top right hand corner of the console screen. It will remove all of the text from the console but will not affect the workflow.