In most experimental protocols it is important to explicitly specify the order in which actions are executed. Even when steps can be performed in parallel, it might be desirable to perform them sequentially to guarantee that actions are performed consistently. To control the order in which certain steps are performed in your protocol, try using the Synchronize element.
Notice here that a different workflow has been built in comparison to the one in Core elements tutorial 10.1 to achieve the same type of basic assay, but with different plate layouts and control of execution order. This highlights the flexibility of Synthace and the Core Elements in providing you with a way to build workflows that best suits your style of expression.
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 10.2. 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.
Dilute standard, then aliquot samples and dilutions
In this example, a standard is serially diluted and then aliquoted in replicates, along with a set of undiluted samples. This is a common step in protein or DNA quantification protocols, such as a Bradford or a Picogreen Assay. Preparing dilutions can take a significant amount of time, so it’s desirable to only start aliquoting the samples once all the dilutions are performed. This guarantees that both the dilutions and the samples incubate on the final plate for a similar amount of time.
In the workflow builder, you have already defined your Standard, diluent and samples liquids, as well as specified how to make dilutions. For more information on how to use the Define Liquids and Plates or how to specify dilutions, click here.
Add 3 elements to your canvas: 1x Synchronize, 1x Append and 1x Aliquot.
Connect the Dilutions parameter from the Dilute element to the Liquids A input parameter of the Synchronize element.
Connect the Liquids parameter from the Define Liquids and Plates element to the Liquids B input parameter of the Synchronize element.
To aliquot both the dilutions and the samples, the liquids need to be appended. To do so, use the Append element. Connect the Liquids A output parameter from the Synchronize element to the Liquids A input parameter of the Append element. Liquids are outputted from the Synchronize element in order, which means that Liquids A corresponds to your diluted liquids. For more information on how to use Append, click here.
Connect the Liquids B output parameter from the Synchronize element to the Liquids B input parameter of the Append element. Liquids B corresponds to your samples.
Now that we have a single set of liquids, they can be aliquoted together. Connect the Liquids output from the Append element to the Liquids To Aliquot input of the Aliquot element.
Specify the Aliquot Volume, Replicates, Plate Set Name and the Plate Type parameters in the Aliquot element.
Note: To apply a parameter value to all input liquids use the default identifier, as in the example above. To apply a parameter value to a specific liquid then provide the liquid name, or alternatively use a tag to apply a parameter value to a group of liquids. This behaviour is true for most parameters unless stated otherwise.
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.
You can see that dilutions are prepared, and only once they have been completed, they are aliquoted to the final plate, along with the undiluted samples.
Check your work:
To see what your finished workflow to this tutorial should look like simply navigate to the Tutorials and search for Tutorial: 10. Building basic assays.
Challenges
Imagine you now want to prepare two sets of dilutions (one dilution by factor, and another by concentration range), and you want one to be executed after the other. After that, you want all liquids to be aliquoted to a third plate using the same aliquot element. How would you build this workflow?