Often you will want to investigate how the concentration of a specific component in a mixture impacts the biological system you are studying.
In Synthace, this specifically relates to the Mixture Composition parameter in both the Make Mixtures and Mix Onto elements.
In this tutorial you will learn:
Where to add a numerical, mixture component factor
How to define the concentration levels you want to investigate
How to set a numerical factor as a Quasi-Replicate
How to set a numerical factor as Hard To Change
How to set a numerical factor to sample discretely or a range of values
How to define runs that have the factor set to zero
Defining a numerical mixture component factor
Adding a new numerical mixture component factor.
Build a workflow that defines a set of liquids and provides those liquids to a Make Mixtures element.
Switch the workflow builder into DOE Mode.
Note: only the elements that can have DOE factors applied to their parameters will be interactive and display in colour. If the workflow has not already been added to a Synthace experiment you will be prompted to do so before being able to enter DOE mode.
Select the Make Mixtures element and toggle on the Mixture Compositions parameter. This identifies that you intend to describe these mixtures with DOE factors.
Click the adjacent factor button in the panel to launch the DOE Factor Panel.
Click on the “ADD” button to select a factor type.
Select the “New Factor” Option to open the Factor Definition Panel.
Defining factor properties
Auto-suggestion of factor names
When defining numerical mixture component factors, where the factor name is the Liquid component you want to investigate as a mixture, Synthace will autosuggest the liquid names that were defined in the workflow. This avoids re-entering the same information any mismatching of liquid names.
In this example, three liquids have been defined all with the same stock concentration:
In the Factor Definition Panel, click on the Factor Name entry field and select a liquid name from the dropdown, which includes all the liquids that have been defined in the workflow. In this example Liquid A.
Setting Factor Properties
Select the units for this factor.
Note: the units for your factor must match the units you set for your stock liquid component within your workflow.
Define the levels you want to investigate for your factor. Click on the “Add New Item” button, or press “Enter”, to add additional levels.
To treat this factor as a “Quasi-Replicate”, tick the “Quasi-Replicate” check box. To learn more about quasi-replicating factors, see here.
Note: making a factor a quasi-replicate will disable the sampling control panel as all quasi replicate factors are sampled discretely at the defined levels.
To treat this factor as “Hard to change”, tick the “Hard to change” check box. To learn more about “Hard to change” factors, see here.
Note: making a factor “Hard to change” will disable the sampling control panel as all hard to change factors are sampled discretely at the defined levels.
If you intend to use a space filling design in your experiment, choose whether you want to sample your defined levels discretely or across a range.
Note: if sampling across a range, when calculating the space filling design, only the lowest and highest levels defined will be considered. Any intermediate levels defined here will be disregarded.
When sampling across a range in space filling designs, you can also define the number of runs that you would like this factor to be set to zero.
Note: Sampling three runs at a zero set point means that three of the runs in your calculated space filling design will have Liquid A sampled at 0 mM. This is useful when investigating, for example, a component of interest across a range, while also trying to understand the impact of not having that component in your mixture at all.
Click “Add Factor” to save the factor to your Factor Table, where you will see a summary of the factors’ settings.
Note: Once you have added a numerical mixture component factor, the button in the instance panel will update to say how many factors have been defined in the Mixture Compositions parameter. In most cases, you will be investigating more than one numerical mixture component factor. Click the “Add” button to add and describe one or more factors.
Well done on making it to the end of this tutorial.
To learn how to define a numerical volume factor, click here.
To learn how to define a custom numerical factor, click here.
To learn how to use numerical volume factors in a media optimisation example, click here.
To learn about other factor types, click here.