Simulator exercises

The simulator and exercises with it

The Simulator is written in Java, and many web browsers will require you to click to enable it. You may have a warning bar appear at the top of this page that requires you to click to enable the simulator.



Exercise 1

Run the simulator in the 'high mutation rate' setting. Once it has completed, look at the panel on the right hand side that lists the number of bacteria with each genotype. Make a note of how many have the 110 genotype (capable of host invasion) and 111 genotype (which can potentially trigger GBS) and the number that have the original (000) genotype.
Now click 'restart' and then run the simulator in the 'high mutation rate' setting again and compare the results you get from this run to the results you got in the first run?

• Did you get the same results on both runs?
• Why do you think this is?

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Exercise 2

Now you will explore how changing the mutation rate alters the final population. You will need to run the simulator at different mutation rates and keep notes on the differences you observe in order to answer the following questions. Write down your answers before looking at the answers page.

• How does varying the mutation rate affect the proportion of cells capable of host invasion and triggering GBS?
• How does varying the mutation rate affect the diversity of the final population?
• Is running the simulator once at each mutation rate sufficient to answer the above questions?

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Exercise 3

In this exercise you will need to investigate the pattern of mutations closely and consider how the final result is built up by individual mutations. Again you may need to run the simulator multiple times and you should write down your answers before looking at the answers page.

• Do mutations that occur early in the simulation have more or less effect on the population structure than mutations that occur later?
• Look at the populations that the GBS triggering genotypes emerge from. What do you notice about them? Is this always the case?
• Are mutations directional? That is, do they always take the cells closer to the GBS triggering genotype?

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Exercise 4

In this final exercise, you need to think about how realistic the simulator is, and why you would or wouldn't want to use such a tool to investigate the behaviour of phase variation. Again, try to write down your own answers before looking at the answers page.

• How realistic do you think the simulator is?
• How important do you think realism is when using a simulator to understand a system?
• What advantages do you think using a simulation can have over real experiments?

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Next page: Epilogue

Back to start: Simulating hypervariable genome sequences

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