Imperial College/Courses/Spring2008/Synthetic Biology/Computer Modelling Practicals/Practical 3: Difference between revisions
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'''Questions:''' | '''Questions:''' | ||
* ... | * Using the default kinetics parameters, build the following 3 transfer functions: | ||
** first, between the [inducer] concentration, and the Protein_1 steady-state expression level. Take the inducer level to vary between [0, 10000]. Comment on the behaviour observed (Illustrations) | |||
** second, between the Protein_1 concentration (to be kept constant during the simulations), and the Protein_2 steady-state expression level. Make sure that the range covered by the concentration of Protein_1 helps to explore the full dynamic range of system behaviour. | |||
** third, between the [inducer] concentration, and the Protein_2 steady-state expression level. Take the inducer level to vary between [0, 10000]. Comment on the behaviour observed (Illustrations) | |||
* We want to tune this cascade so that when using our maximal [inducer] concentration we are able to completely shut-down the expression of Protein_2. Suggest 2 independent strategies to achieve that result. | |||
'''Additional Resources:''' | '''Additional Resources:''' | ||
* ... | * [http://genomicsgtl.energy.gov/science/generegulatorynetwork.shtml Gene Regulatory Networks] | ||
* [http://en.wikipedia.org/wiki/Gene_regulatory_network Genetic Networks (from Wikipedia)] | |||
<div style="padding: 0px; width: 710px; color: #2171B7; background-color: #B3CD4E"> | <div style="padding: 0px; width: 710px; color: #2171B7; background-color: #B3CD4E"> | ||
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</font><br> | </font><br> | ||
</div> | </div> | ||
... | |||
<biblio> | |||
#Elowitz2000 pmid=10659856 | |||
</biblio> | |||
{| border="1" cellpadding="10" cellspacing="2" style="width:700px; border:3px green" | {| border="1" cellpadding="10" cellspacing="2" style="width:700px; border:3px green" | ||
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!CellDesigner Instructions | !CellDesigner Instructions | ||
|- | |- | ||
| | | | ||
[[Image:Repressilator_Elowitz_Plasmids.png|300px|Repressilator Elowitz Plasmids]] | |||
| | | | ||
'''Define the topology of the reaction network''': | '''Define the topology of the reaction network''': | ||
* Open a NEW document: File -> New. | * Open a NEW document: File -> New. | ||
[[Image:CellDesigner_Repressilator_Network.png|300px|Repressilator Genetic Circuit]] | [[Image:CellDesigner_Repressilator_Network.png|300px|Repressilator Genetic Circuit]] | ||
|} | |} | ||
'''Questions:''' | '''Questions:''' | ||
* ... | * Focus on the modelling section of the published paper, and build your own 'Repressilator' model in CellDesigner. | ||
* Run a simple sensitivity analysis on each parameter, and suggest some strategies to control the amplitude of the oscillations. | |||
* Do the same to suggest ways to control the frequency of the oscillations. | |||
'''Additional Resources:''' | '''Additional Resources:''' | ||
* ... | * [http://electronics.howstuffworks.com/oscillator.htm How Stuff Works on Oscillators] | ||
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</font><br> | </font><br> | ||
</div> | </div> | ||
... | |||
{| border="1" cellpadding="10" cellspacing="2" style="width:700px; border:3px green" | {| border="1" cellpadding="10" cellspacing="2" style="width:700px; border:3px green" | ||
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* | * | ||
[[Image:CellDesigner_Mystery_Device_Network.png|300px|Mystery Device Network]] | [[Image:CellDesigner_Mystery_Device_Network.png|300px|Mystery Device Network]] | ||
|} | |} | ||
</div> | |||
'''Questions:''' | |||
* Suggest a strategy to characterise this model (Establish clear simulation scenarii to illustrate the properties of this genetic circuit. Tip: The cell designer function related to 'Change Amount' might be handy) | |||
* From your characterisation, how would you call this device ? | |||
* Imagine an application where this genetic device would be useful. | |||
'''Additional Resources:''' | |||
* ... | |||
Revision as of 09:39, 15 January 2008
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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 |
|---|---|
|
Define the topology of the reaction network:
| |
|
Following the Law of Mass action, the dynamic of the system is described as: |
|
Questions:
- Using the default kinetics parameters, build the following 3 transfer functions:
- first, between the [inducer] concentration, and the Protein_1 steady-state expression level. Take the inducer level to vary between [0, 10000]. Comment on the behaviour observed (Illustrations)
- second, between the Protein_1 concentration (to be kept constant during the simulations), and the Protein_2 steady-state expression level. Make sure that the range covered by the concentration of Protein_1 helps to explore the full dynamic range of system behaviour.
- third, between the [inducer] concentration, and the Protein_2 steady-state expression level. Take the inducer level to vary between [0, 10000]. Comment on the behaviour observed (Illustrations)
- We want to tune this cascade so that when using our maximal [inducer] concentration we are able to completely shut-down the expression of Protein_2. Suggest 2 independent strategies to achieve that result.
Additional Resources:
Part II: Genetic Oscillator: The Repressilator
...
- Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8. DOI:10.1038/35002125 |
| Model | CellDesigner Instructions |
|---|---|
|
|
Define the topology of the reaction network:
|
Questions:
- Focus on the modelling section of the published paper, and build your own 'Repressilator' model in CellDesigner.
- Run a simple sensitivity analysis on each parameter, and suggest some strategies to control the amplitude of the oscillations.
- Do the same to suggest ways to control the frequency of the oscillations.
Additional Resources:
Part III: A mystery device
...
| Model | CellDesigner Instructions |
|---|---|
|
Define the topology of the reaction network:
|
Questions:
- Suggest a strategy to characterise this model (Establish clear simulation scenarii to illustrate the properties of this genetic circuit. Tip: The cell designer function related to 'Change Amount' might be handy)
- From your characterisation, how would you call this device ?
- Imagine an application where this genetic device would be useful.
Additional Resources:
- ...
