The Execution Graph
This lesson is for all users of the Antha OS system who wish to know more about how the Execution Graph is used.
About this tutorial
This tutorial will introduce the Execution Graph to you, how to access it, the information you can get from it and how to use it.
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:
What you'll learn
In this tutorial you will learn:
- What the Execution Graph is
- How to access the Execution Graph
- The different areas of the Execution Graph
What is the Execution graph
The Execution Graph is an interactive graphical representation of the physical liquid handling steps required to perform your workflow.
The Execution Graph displays a lot of useful information such as:
- The volumes of solutions being pipetted
- Source and destination wells
- Names of solutions or mixtures
- The deck position for where a well will be located
- The number of pipetting actions
The Execution graph is extremely useful for checking and identifying any potential errors in your workflow before you run the physical experiment and therefore gives you the opportunity to rectify any problems with your workflow.
It is also a very useful tool for helping to visualise and understand the exact liquid handling steps of an element and can therefore guide you in your choice of element when unsure.
How to access the Execution Graph
There are two routes to being able to access the Execution Graph dependent on the route by which you are running your workflow, either through the Protocol Card or through the Workflow Editor.
If you are running your workflow via the Protocol Card then the only way to access the Execution Graph is through the "mix task button" in the Dashboard.
If you are running your workflow via the Workflow Editor then you have two different routes to the Execution Graph.
- A button presented in the Console after a successful simulation
- Via the Dashboard by the "mix" task button as above
Execution Graph Layout
The Execution Graph page has three key areas:
- The Execution Graph toolbar
- The Execution Graph Window
- The Timeline sidebar
The Execution Graph toolbar
The Execution Graph toolbar allows you to alter the graphical representation of your physical liquid handling steps. There are several tools here for you to use:
- This will reset the graphical representation in the Execution Graph Window when a subset of wells have been selected. Clicking here will reset the view such that all greyed out wells become visible.
- The Label toggles will toggle the display of either well names, well contents or arrow labels in the Execution Graph Window.
- The layout styles options allow the user to change the way the wells are positioned within the Execution Graph Window in order to clarify the process. All display options allow you to interact with the graph and drag wells within the display to new positions to various degrees. The Physical option is a static representation of the device deck layout that you simulated against such that wells can not be moved.
Arrow Label options.
- The arrow label options allow you to change the information that is displayed along the arrows between wells in the Execution Graph Window. for instance the volume of solution being transfered or the time it takes for a liquid handling step. The colour and display style of the arrow will change to reflect a different label option.
- The timeline controls allow you to play through your simulation to see the order in which your liquid handling steps will take place. This is often useful to get a feel of what the elements or workflows you have simulated will do.
- The parameters button allows you to be able to edit the parameters that were chosen to simulate against your workflow such that you can trigger a resimulation and see the results updated instantly in graph view.
- The View options allow you to toggle between zooming in and out of the Execution Graph Window or changing the Meta percentage. The meta percentage alters the parameters in the physics engine used to make the wells interactive and how you can move them within the Execution Graph Window.
The Execution Graph Window
The Execution graph window gives you a graphical representation of all the physical liquid handling steps involved in your workflow.
It shows you several pieces of information:
- Which wells are considered source wells (blue) or destination wells (purple)
- The well position within its plate
- The plate location on the automation platform deck you simulated against
- The contents of the wells
- The volume being transferred from one well to another. The label presented along the arrow and the arrow style can be changed using the Arrow Label options from the toolbar
- A key showing a cumulative plot of the arrow labels. e.g. the number of times a specific volume is transferred. The key automatically updates to represent the Arrow Label option that is selected from the toolbar
By clicking on any well in the Execution Graph Window only that well and any other wells that precede it in provenance will be displayed. All other wells will be greyed out. This often simplifies the view when complex workflows are being run such that you can get a better grasp of what is happening in a single instance of the workflow.
The Arrow Label key will also be updated to now only show the cumulative scores for the current selection.
The Execution Graph Timeline sidebar
The Execution Graph Timeline shows all the liquid handling steps (aspirations and dispenses) in a chronological order.
You are shown which well and plate (deck position) a sample is being aspirated from and then where it is being dispensed.
Using the Timeline controls in the Execution Graph toolbar will let you play through the timeline allowing you to keep track of what is happening to your samples. All steps will be greyed out but will appear as that step has been completed. This process also mimics the same effect within the Execution Graph Window with wells becoming visible once that step has proceeded.
As with selecting subsets of wells, whilst playing through the timeline you will notice the cumulative graph keeping track of all the liquid handling steps.