User:Tom Adie/CS2: Difference between revisions

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*2. Using the previously found parameter values, plot on the same graph [mRNA](t) and [protein](t) for t{{Equals}}[0, 5h].
*2. Using the previously found parameter values, plot on the same graph [mRNA](t) and [protein](t) for t{{Equals}}[0, 5h].
''Concentrations at time t can be found using a step function as below:
ODE <- function(k1,d1,k2,d2,mrna,protein,t) {
for (i in 1:t) {
protein <- protein+k2*mrna-d2*protein
mrna <- mrna+k1-d1*mrna
}
cat("        t =",t,"\n")
cat("  [mRNA] =",mrna,"\n")
cat("[Protein] =",protein,"\n")
}
ODE(0.69,0.23,2,0.012,0,0,300)
        t = 300
    [mRNA] = 3
[Protein] = 485.8966
this uses the parameters from above to output the values of [mRNA] and [Protein] at time t (where t is in minutes). Saving the values of t, [mRNA] and [Protein] after every step into concatenated lists, then saving those as a data set, would give me something to graph... But this doesn't use rk4!''
*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{{Equals}}[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{{Equals}}[0, 5h]).
|}}
|}}

Revision as of 08:01, 9 December 2008

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MRes Case Study 2

R Exercise 2 (ODE Solver)

Intro

Links:

Inputs:

  • Wavelength
  • Intensity
  • Stimulation time (pulse length)

Outputs:

  • Viability of cells (bearing in mind YtvA pathway triggers stress response)
  • PoPs
References
  1. One
  2. Two
  3. Three
  4. Four
  5. Five

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