User:James Chappell /R RK4 Modeling: Difference between revisions
mNo edit summary |
mNo edit summary |
||
| Line 21: | Line 21: | ||
'''Example 1 : Simple Constitutive Expression''' | '''Example 1 : Simple Constitutive Expression''' | ||
<nowiki> | |||
(constitutiveexpression <- function(t, x, parms) { | (constitutiveexpression <- function(t, x, parms) { | ||
| Line 63: | Line 63: | ||
} | } | ||
</nowiki> | |||
</div> | </div> | ||
Revision as of 08:23, 8 July 2009
<html> <style type="text/css"> .firstHeading {display: none;} </style> </html>
James Chappell
Imperial College London Synthetic Biology Lab
RK4
The RK4 tool is a tool that can be used to model ordinary differential equations (ODE). Like other ODE solvers you can output the results of a simulation into graph or tables.
Example 1 : Simple Constitutive Expression (constitutiveexpression <- function(t, x, parms) { #Define the name of the model mRNA <- x[1] protein <- x[2] #Name the response variables – these are the outputs of our model with(as.list(parms),{ dmRNA <- k1 - d1*mRNA dprotein <- k2*mRNA - d2*protein res<-c(dmRNA, dprotein) list(res) })} #Combine these vectors into a list called res times <-seq(0, 1000, length=1001) parms <-c(k1=0.69 , k2=f ,d1=0.23 ,d2=0.012) #Generate a time series over which to solve the equations (1000 in steps of 1) #Set the parameter values in parms y <- xstart <-c (mRNA=1, protein=1) #Set the starting value for response variables output <- as.data.frame(rk4(xstart, times, constitutiveexpression, parms)) plot(output$time, output$protein, ylim=c(0,2000), ylab="protein (molecules)",xlab="time (min)",type="n") }
