Imperial College/Courses/Fall2008/Synthetic Biology (MRes class)/'R' Tutorial/Practical 2: Difference between revisions
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==Exercise 1 (Data frames)== | ==Exercise 1 (Data frames and inputs/ouputs)== | ||
==Exercise 2 (ODE Solver)== | ==Exercise 2 (ODE Solver)== | ||
Revision as of 07:38, 4 December 2008
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Introduction to 'R'
Exercise 1 (Data frames and inputs/ouputs)
Exercise 2 (ODE Solver)
- RK4 solver:
- RK4 documentation
- Interface: rk4(y, times, func, parms, ...)
- Model: Constitutive gene expression
- ODE System:
- d[mRNA]/dt = k_1 - d_1*[mRNA]
- d[protein]/dt = k_2[mRNA] -d_2*[protein]
- ODE System:
- Questions:
- 1.Considering that the half-life for the mRNA and the protein is respectively 3min and 1h. Workout the values of (k_1, d_1, k_2, d_2) so that, at steady state, [mRNA] = 3 and [protein] = 500.
- 2.Using the previously found parameter values, plot on the same graph [mRNA](t) and [protein](t) for t=[0, 5h].
- 3. Parameter scanning: Consider parameter d_2 to vary [-20%, 20%] of its nominal value (10 uniformly spread values). Generate on the same graph the 10 [protein](t) trajectories (t=[0, 5h]).
