# Comment: relative to Curto an Morrison, wherein the *.R file was the editable # source code, I'm now switching to the use of JDesigner as my source editor # (model IDE). Thus, for Kowald's SOD models I now provide only the JDesigner # xml file as the model source code. This is my new workflow. library(SBMLR) sod=readSBML(file.path(system.file(package="SBMLR"), "models/SOD2006JD.xml")) summary(sod) out=sim(sod,times=seq(0,1000,1) ) plot(out) #reproduces Fig 2 of JTB 2006 # Note: In RStudio, switch to console and hit return repeatedly to plot (ssic=out[dim(out),2:9]) # set ic to steady state (SOadd <- data.frame(var = "SO", time = 0, value = 1e9,method = "mult")) out=sim(sod,X0=ssic,times=seq(-10,10,.1),events = list(data = SOadd) ) plot(out) # note the SO looks like it dropped, but then why the LOOH go up # Answer, sampling times are too big at 1 sec, need to get to sub millisecs out=sim(sod,X0=ssic,times=seq(-.001,.001,.00001),events = list(data = SOadd) ) plot(out) # now you can actually see the upward spike of SuperOxide, SO
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