Tutorial
This tutorial demonstrates the entire workflow for a simple toggle switch circuit.
You will learn how to:
- Design a circuit using both node-based and code-based methods.
- Simulate the circuit and adjust parameters.
- Generate DNA sequences that match your desired parameters and export them.
1. Designing a circuit¶
Build a single chain¶
First, we'll build a single chain, a sequence of blocks.
Drag and drop a block¶
At the top of the application window, you will see a palette containing various colored blocks. Drag a blue block (promoter) and drop it onto the main area.
Tip
See the guide on circuit design to understand in more detail what each block means.
Select a part¶
Click the newly placed blue block to open a selection panel where you can assign a specific biological part. For this tutorial, choose "PameR".
Connect more blocks¶
When you drag a new block and bring it near an already existing block, the blocks will automatically connect to each other.
- Drag a green block (protein) near the blue block and drop it to connect them.
- Drag a red block (terminator) near the green block and drop it to connect them.
- Select "AmtR" as the part for the green block and "L3S3P31" for the red block.
You have now created a single chain of three blocks: a promoter, a protein, and a terminator.
Note
A "chain" is a sequence of promoters, proteins, and a terminator.
Build another chain with DSL¶
Circuits can also be designed using the Synergetica DSL.
The DSL editor is accessible by clicking the sidebar toggle on the left side of the application.
Check the existing code¶
The following code should already be present in the coding palette. It represents the chain that was just constructed.
- chain:
- type: Promoter
name: PameR
- type: Protein
name: AmtR
- type: Terminator
name: L3S3P31
Note
The node-based editor and the code-based editor are always synchronized.
Copy and paste¶
Copy the code of the existing chain and paste it immediately afterward. The same chain will then appear in the graphical view.
Rename parts¶
Change the names of two parts from "PameR" to "PamtR" and from "AmtR" to "AmeR" (see highlighted lines below):
- chain:
- type: Promoter
name: PameR
- type: Protein
name: AmtR
- type: Terminator
name: L3S3P31
- chain:
- type: Promoter
name: PamtR
- type: Protein
name: AmeR
- type: Terminator
name: L3S3P31
After that, the blocks in the graphical view will automatically update, and blue arrows will appear to indicate the interactions between the blocks.
You have now finished building the toggle switch circuit! 
Note
If there is an interaction between a promoter and a protein in the circuit, an arrow will automatically appear to illustrate that interaction. The arrow starts at the protein and ends at the promoter.
- : Activation (the protein increases the expression of the connected promoter)
- : Repression (the protein decreases the expression of the connected promoter)
In the part selection screen, you can see which parts interact with each other.
2. Running a simulation¶
With your toggle switch circuit in place, it’s time to see how it behaves over time.
Start simulation¶
To start the simulation, click the "Start" button in the lower right corner of the application. This will automatically open the simulation sidebar from the right side and display the results.
The graph shows how the protein (green block) concentration changes over time in this circuit.
Tip
See the guide on genetic simulation to know more about what the graphs and slider values mean biologically.
Adjust parameters¶
Two sliders are displayed, each corresponding to a protein in the circuit and allowing you to adjust the translation intensity.
Try moving each slider and notice that adjusting one slider affects both curves.
Adjust the parameters to achieve the protein concentration you desire.
3. Generating sequences¶
Once the parameters have been adjusted, the last step is to generate the specific DNA sequences to realize your chosen parameters.
Start sequence generation¶
Click the "Run" button in the Generation section at the bottom right of the app to start the sequence generation process.
Synergetica will create optimized DNA sequences corresponding to the circuit parameters you set.
View the results¶
Once generation completes, you can view the results by clicking the "Result" button.
The generated DNA sequences corresponding to each chain will be displayed in the result window.
Tip
See the guide on sequence generation to understand the generation process in more detail.
Export to FASTA¶
By clicking the "Export FASTA" button, you can save these sequences locally in FASTA format.
> mighty-bobcats-pay
GATAGTGACAAACTTGACAACTCATCACTTCCTAGGTATAATGCTAGCACCTCTGAGCGATGTGTGCACGCACCCATGGCAGGCGCAGTTGGTCGTCCGCGTCGTAGTGCACCGCGTCGTGCAGGTAAAAATCCGCGTGAAGAAATTCTGGATGCAAGCGCAGAACTGTTTACCCGTCAGGGTTTTGCAACCACCAGTACCCATCAGATTGCAGATGCAGTTGGTATTCGTCAGGCAAGCCTGTATTATCATTTTCCGAGCAAAACCGAAATCTTTCTGACCCTGCTGAAAAGCACCGTTGAACCGAGCACCGTTCTGGCAGAAGATCTGAGCACCCTGGATGCAGGTCCGGAAATGCGTCTGTGGGCAATTGTTGCAAGCGAAGTTCGTCTGCTGCTGAGCACCAAATGGAATGTTGGTCGTCTGTATCAGCTGCCGATTGTTGGTAGCGAAGAATTTGCAGAATATCATAGCCAGCGTGAAGCACTGACCAATGTTTTTCGTGATCTGGCAACCGAAATTGTTGGTGATGATCCGCGTGCAGAACTGCCGTTTCATATTACCATGAGCGTTATTGAAATGCGTCGCAATGATGGTAAAATTCCGAGTCCGCTGAGCGCAGATAGCCTGCCGGAAACCGCAATTATGCTGGCAGATGCAAGCCTGGCAGTTCTGGGTGCACCGCTGCCTGCAGATCGTGTTGAAAAAACCCTGGAACTGATTAAACAGGCAGATGCAAAATAACCAATTATTGAACACCCTAACGGGTGTTTTTTTTTTTTTGGTCTACC
> cute-camels-wish
GATTCGTTACCAATTGACAGTTTCTATCGATCTATAGATAATGCTAGCGAGCCTCTATTCAAGCATTCTACTATCATGAACAAAACCATTGATCAGGTGCGTAAAGGTGATCGTAAAAGCGATCTGCCGGTTCGTCGTCGTCCGCGTCGTAGTGCCGAAGAAACCCGTCGTGATATTCTGGCAAAAGCCGAAGAACTGTTTCGTGAACGTGGTTTTAATGCAGTTGCCATTGCAGATATTGCAAGCGCACTGAATATGAGTCCGGCAAATGTGTTTAAACATTTTAGCAGCAAAAACGCACTGGTTGATGCAATTGGTTTTGGTCAGATTGGTGTTTTTGAACGTCAGATTTGTCCGCTGGATAAAAGCCATGCACCGCTGGATCGTCTGCGTCATCTGGCACGTAATCTGATGGAACAGCATCATCAGGATCATTTCAAACACATACGGGTTTTTATTCAGATCCTGATGACCGCCAAACAGGATATGAAATGTGGCGATTATTACAAAAGCGTGATTGCAAAACTGCTGGCCGAAATTATTCGTGATGGTGTTGAAGCAGGTCTGTATATTGCAACCGATATTCCGGTTCTGGCAGAAACCGTTCTGCATGCACTGACCAGCGTTATTCATCCGGTTCTGATTGCACAAGAAGATATTGGTAATCTGGCAACCCGTTGTGATCAGCTGGTTGATCTGATTGATGCAGGTCTGCGTAATCCGCTGGCAAAATAACCAATTATTGAACACCCTAACGGGTGTTTTTTTTTTTTTGGTCTACC
Congratulations!
You’ve successfully designed, simulated, and generated sequences for a toggle switch using Synergetica. If you’d like to learn more, check out the Guides section.
Happy designing!