Until now, offline preparation of input liquids was left in the hands of you, the user. This typically means preparing a “working stock” from an existing master stock solution you may have in the lab. Manually calculating the dilution steps required to prepare these working stock solutions is tedious, time-consuming, and error-prone. With the introduction of the stock solution calculator, this tedious and manual process is a thing of the past.
Workflow Building
All concepts covered here apply to any simulation within the Synthace platform. If you are already familiar with workflow building, then feel free to jump to How to use the Stock Solutions Calculator
In this article, we will take you through the new Stock Solution calculator feature, and how to use it in your own lab. Let’s start off by building a simple workflow for creating a mixture of two liquids. For the purposes of this tutorial, we will:
Define a liquid which will be used as a Diluent
Define two liquids in define liquids and plates and check the box Calculate Required Stocks?.
Prepare 3 mixtures of the two liquids
Review the stock calculator and input liquid creation instructions in the Simulation Details.
This example workflow will be for simulation using a SPT Dragonfly, and generic labware.
Open a new builder page from the Synthace Home page. Set the execution mode and appropriate input plate types for your execution mode. In this example, we will be simulating against the SPT Dragonfly and using High Volume Reservoirs as our input plate type.
Add Define Liquids and Plates, Liquid selection criteria, and Make Mixtures elements to the workflow builder canvas. Connect them as shown below.
Define the diluent “Medium”, with the Concentration = 1 X. This will be the concentration of the input liquid for your protocol.
Define Sub-component concentrations for the medium components Glucose (1 g/l), Amino Acids (1 mM) and Base Medium (1 X).
In the Define Liquids and Plates element define the Liquid Names and Concentration for the following liquids: "Cells" at 100000 cells/ml and "Compound" at 1 mM.
Check the Calculate Required Stocks box for the two liquids "Cells" and "Compound".
Define the Minimum Transfer Volume for your device or execution method in the Liquid Selection Criteria element. In this example, we will set this to 1ul. Optional: set the Maximum Transfer Volume.
In the Make Mixtures element define an output plate for the workflow, letting Synthace optimize the Replicate Grouping. In this example, we will be using the 96-well training plate present in your environment.
Now configure the Make Mixtures element to prepare 1 replicate of the following mixtures (total reaction volume = 1000 ul), using the Let Synthace Optimize Addition Mode. Set Medium as the Diluent to Use by default for all mixtures.
Mixture Component | Mixture - Low | Mixture - High | Negative Control |
Cells | 5000 | 50000 | 50000 |
Compound | 10 nM | 0.156 mM | 0 nM |
DiluentToUse | Medium | Medium | Medium |
To learn how to define mixture compositions, take a look at Mix by Composition.
The workflow is now complete and you are ready to simulate. Click Simulate and view the simulation
How to use the Stock Solutions calculator
With the new Stock Calculator functionality, Synthace will provide additional information to you on the Simulation details page. You will see the reagents list now provides additional information to help you prepare your input liquids.
Reagent Inputs
The Inputs tab provides you with details on the volume requirements. Each liquid has additional information on the volume requirements. You can see the Stock concentration, Target concentration, and Volume.
Open the dropdown menu for liquids with multiple subcomponents to view information on the number of components and instructions on how to prepare this mixture using independent input liquids for each subcomponent. In the case of our Medium, which contained Amino Acids (1 mM), Base Medium (1 x), and Glucose (1 g/l) you will see the Stock, Target, and Volumes of each independent component have been calculated.
For now, Synthace has made some assumptions about component stocks that could be used. Should you wish to define these further i.e. to match stock solutions you already have prepared, simply navigate to the Stocks tab and define your stocks.
Stock Reagents
Define the stock liquid concentrations you will be using in the lab. Changes to these stock concentrations will be reflected in the Inputs tab.
Additional Features
Define additional reagent volume
Do you want to ensure you have extra input liquid volume prepared in advance? Easily increase the total prepared reagent volume of all your liquids by a fixed volume. Simply specify the additional volume in the Extra Volume field.
By specifying that we require 1000 ul extra volume, Synthace has scaled up the Input volume requirement. This functionality can be useful if you are preparing input liquids offline in a different vessel to the one you will use in your automated workflow i.e. a bottle or flask.
Round up reagent volumes
By default, Synthace will calculate the precise volume required for your execution. This can often lead to volume requirements with a high level of precision, making volumes tricky to manually prepare. If you wish you can round up the volumes that Synthace requests to 2 significant figures. Simply switch on the Round Up Volumes toggle to enable the rounding up of input volumes.