Imperial College/Courses/Spring2008/Synthetic Biology/Computer Modelling Practicals/Practical 3
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Practical 3
Objectives:
- To explore computationally some simple genetic circuits:
- Genetic Cascade To Be Tuned.
- A genetic oscillator: the Repressilator.
- A mystery device.
Deliverables
- A report is expected by ... (Word or PDF format, sent to XXX@XXX)
- When you find in the text (illustration needed), it means that you will have to provide an image export of your simulation results in your report.
- Instructors: Vincent Rouilly, Geoff Baldwin.
Part I: Genetic Cascade To Be Tuned
In Practical 2, we have explored how gene expression can be controlled (positively or negatively) by other proteins. Here, we start to assemble genetic circuit by connecting genes. The model studied here is a simple genetic cascade, where a Gene_1 produces a protein which repressed the expression of Gene_2. Additionally, you are able to induce the expression of Gene_1 thanks to an inducer.
To start, launch the CellDesigner Application: Double Click on the Icon found on your Desktop. Then follow the instructions below to build the model.
| Model | CellDesigner Instructions |
|---|---|
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Define the topology of the reaction network:
| |
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Following the Law of Mass action, the dynamic of the system is described as: |
|
Questions:
- ...
Additional Resources:
- ...
Part II: Genetic Oscillator: The Repressilator
| Model | CellDesigner Instructions |
|---|---|
|
Define the topology of the reaction network:
| |
|
... |
... |
- Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8. DOI:10.1038/35002125 |
Questions:
- ...
Additional Resources:
- ...
Part III: A mystery device
| Model | CellDesigner Instructions |
|---|---|
|
Define the topology of the reaction network:
| |
|
... |
... |
