In the previous tutorials, we saw how we can use liquid properties, such as concentration and sample metadata to select liquids. By doing so we were able to control liquid handling behaviour for subsets of a set of samples. We will now explore how sample metadata persists across individual workflows and how we can use it to make complex data-driven decisions across multiple workflows i.e. a process.
To do so, we will:
Update the liquids defined in Define Plasmid DNA to describe additional metadata values for the plasmid DNA liquids.
Define the Promoter Type and Inducer required for the regulation of protein production for the plasmids.
The Promoter Type will be either Inducible or Constitutive.
The Inducible plasmids require an Inducer for protein expression.
For this example, the Inducer will be either IPTG or Arabinose - two commonly used small-molecule inducers in protein expression protocols. We will perform an addition of the required Inducer based on the Promoter Type AND the Inducer Type in order to demonstrate how the Select element can be used to build AND logic to control liquid handling.
Get started
If you have not read the introduction to this series of tutorials, read this article.
Create a copy of the workflow that you created in Core elements tutorial 12.2. To learn how, click here.
This tutorial will modify the liquid definitions in this workflow and use liquids generated from the generated liquids in downstream processes.
Rename the copy Core elements tutorial 12.3. To learn how, click here.
Define additional metadata in transformation workflow
Add required metadata to liquid definitions
Add metadata column for Promoter Type to the plasmid DNA definitions. Describe some promoter types as Inducible and the rest as Constitutive.
Repeat this process to add a metadata column for Inducer and specify either IPTG or Arabinose as the Inducer.
Example: A file for this liquid definition can be found here.
Once you have defined the additional sample metadata, re-simulate the workflow.
Retrieve plates from previous simulations and inoculate
Open a new instance of the Workflow Builder and add a Define Liquids and Plates element. Rename to
Retrieve Recovery Plate. Define and plate from a previous simulation and retrieve the Recovery Plate from the heat shock transformation workflow.Add another Define element, rename it to
Define Growth Mediaand define the growth media we will use for culturing the transformed cells in. Here we have defined LB.Aliquot 490 ul to a plate called
induction_plate. Connect the Liquids from Define Growth Media to Liquids to Aliquot.Connect Liquid Count from Retrieve Recovery Plate to Replicates of the Aliquot element.
Define the antibiotics you need for culturing your transformed cells.
Mix 5 ul of each antibiotic as required.
Tip: Revisit Core elements tutorial 12.2 if you are unsure how to achieve this. An example of this workflow is shown below.
Incubate all cultures for 2 hours at 37 °C.
Mix liquids according to metadata
Define the two inducer compounds, IPTG and Arabinose.
Use Select to select all the cultures with the Inducible promoter type and IPTG as the inducer from the Incubated Liquids. Set the Selection Condition to ALL.
Rename this Select element to
Select IPTG Inducible. This will select liquids that are Inducible AND induced by IPTG.Mix 5ul of IPTG onto the Selected Liquids.
Repeat this process on the Unselected Liquids for the arabinose addition. Name the Select element
Select Arabinose Inducible.Append the Mixed Liquids from the IPTG and Arabinose addition, plus the Unselected Liquids from the Selection Arabinose Inducible elements together and Incubate for 6 hours at 37 °C.
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 recovery media is aliquoted to a destination plate and the cultures from the recovery plate are added to the media. Antibiotics are then added and the cultures are incubated. Inducers are then added to the respective locations and the cultures are incubated again.
Downloads
We hope that this tutorial has been helpful!
If you got stuck anywhere, or you want to check that you did everything right, compare your workflow to the following example.
The example is in a file that you need to download. To download it, right-click the button, then select Save as.
After you download the file, complete the following steps.
Challenge
In Core elements tutorial 12.2 we expanded the set of selection criteria to include an additional antibiotic - tetracycline. Can you do the same here to account for alternative inducer compounds?