Get started
Read the introduction to this series of tutorials, then complete all of the previous tutorials in the series. For more information, click here.
Create a workflow in the builder. To learn how, click here.
Rename the workflow Core elements tutorial 1.2. To learn how, click here.
Select the device on which you want to run your workflow. To learn how, click here.
Select a default plate type. To learn how, click here.
Define your liquids
Open the Elements panel, search for Define Liquids And Plates, then click the element to add it to the canvas.
On the canvas, click the element to open a list of inputs to the element (i.e., a list of things that you can control).
From the Define From input, select Parameters to expose some inputs that you can use to define your liquids.
Specify the names of the liquids
In the Names input, click Add New Item, then specify the name of a liquid. Repeat this step for every liquid that you want to define.
Tip: You can do this very quickly on your keyboard: after you specify the name of a liquid, press the return key to accept the name, press the tab key to select Add New Item, then press the return key again to add a new liquid name field and move your cursor inside.
Tip: Although you must specify a name for each liquid that you want to define, every other input is optional.
Add some tags to the liquids
Use tags to group sets of liquids together. Here, we will specify that Liquid A, Liquid B and Liquid C are Samples, but Liquid D is a Standard.
Specify the tag name first, then the liquids that you want to have that tag.
Tip: You might notice that Synthace will autosuggest the liquid names that you have provided. This means that you do not need to type them repeatedly.
Specify the concentrations of the liquids
In subsequent inputs, you might notice that Synthace will autosuggest the liquid names AND the tag names that you have provided. Use the tag names to apply the same values to groups of liquids. For example, in the following image, we apply the same concentration to every liquid with the Samples tag.
Note: You can select concentration and volume units from a predefined list. If the predefined list does not contain the units that you need, please let us know.
Define some subcomponents
You can also specify the sub-components that the liquids contain. For example, Liquid D, which has the Standard tag, contains some BSA at 10 mg/ml and some Tris-HCl pH 7.5 at 100mM.
Note: Although Liquid D has a relative concentration of 10X (applied to the liquid via the Standard tag), it is composed of 10 mg/ml BSA and 100mM Tris-HCl pH 7.5.
Synthace will track the concentration of any liquid and the concentrations of its sub-components throughout your workflow and calculate the final concentrations for you.
Tip: You can dilute any liquid based on its concentration or the concentrations of its subcomponents (see Core elements tutorial 3.0), normalize any liquid based on its concentration or the concentration of its sub-components (see Core elements tutorial 4.0), and select any liquid based on its concentration or the concentrations of its subcomponents (see Core elements tutorial 8.0).
Select some liquid policies
A liquid policy defines how a liquid handler moves one or more of the liquids in your workflow, such as the aspiration rate, dispense rate and number of premixes.
Add a new entry, specify the liquid (or liquids) for which you want to specify a liquid policy, then click Select A Policy to open the liquid policies library.
Select a liquid policy.
Add some metadata
A piece of metadata is an important nugget of information that you want to add to your liquids (e.g., their batch or lot numbers, or the upstream preparation method that they received).
If you add some metadata to your liquids, Synthace will track that metadata throughout your workflow, and you can select the liquids with the metadata in a similar way to tags.
Auto-allocate the liquids to a plate
Now you have defined four liquids, but not the plates that contain them.
In this tutorial, Synthace will auto-allocate the liquids to the input plate that you specified in the Settings panel earlier.
It will automatically calculate how much of each liquid is required to complete all of the liquid handling steps in the workflow.
Aliquot the liquids to a new plate
Let's instruct a device to transfer a single aliquot of each of these liquids to a new plate.
Open the Elements panel, search for Aliquot, then click the element to add it to the canvas.
We now need to pass the liquids that we defined in the Define Liquids And Plates element to the Aliquot element, so that the Aliquot element knows which liquids to aliquot.
To do so, click and drag the Liquids output from the Define Liquids And Plates element to the Liquids To Aliquot input of the Aliquot element.
Click the Aliquot element, then specify the Aliquot Volume and Replicates.
Tip: To specify the same value for every liquid, use default as the identifier name, then specify the value that you want. To specify a different value for every liquid with a specific tag, use the tag as the identifier (e.g.,
Samples), then specify the value that you want. This overrides the default value. This behaviour is true for most inputs unless stated otherwise.In our example, every liquid will have an aliquot volume of 100ul, every liquid with the
Sampletag will be aliquoted 8 times and every liquid with theStandardtag will be aliquoted 4 times.Specify a Plate Set Name and a Plate Type.
Simulate the workflow
Check that the device that you selected can follow the instructions that you prepared. To learn how, click here.
Preview the execution
After you simulate the workflow, click View Simulation to open the simulation details.
Open the Preview tab, then click through the steps to check that the instructions that Synthace has generated are correct.
While none of the defined liquids were explicitly defined to a plate type, Synthace auto allocated the required volume of each liquid to the specified 12-well trough input plate type defined in the Workflow Settings menu.
Check your work:
To see what your finished workflow to this tutorial should look like simply navigate to the Tutorials and search for Tutorial: 1. Define Liquids and Plates.
Challenges
Let's explore the volume autoscaling feature.
Define three new liquids with a Liquid Name, Liquid Policy, Concentration and Concentration Unit.
Aliquot these liquids three times and review the input plates in the Preview tab.
Increase the number of aliquot Replicates.
Compare the input liquid volumes which have been generated in the input plate: how does this auto-allocation behaviour change depending on the inputPlateType that you select in the Settings panel?