On Jul 5, 2013, at 00:41 , Jannetta Steyn wrote: > Hi All > > Thanks for all the comments. I have looked at everything you have pointed > out and this is the situation at the moment: > >> I don't think so. >> In the R script you have >> >> init = c(v_axon_AB=-55,mNa_axon_AB=1,hNa_axon_AB=0,mK_axon_AB=1) >> >> That is not the same as in your Matlab script. To make them the same you > should replace the line with >> >> init = c(v_axon_AB=-55,mNa_axon_AB=0,hNa_axon_AB=1,mK_axon_AB=0) >> >> Using this line gives quite different results. But not the same as Matlab. > > You are right. I have to admit when I referred to equations I referred to > those in the ST function, and not the initialisation and parameter > equations. I fixed the line, but look you said it still doesn't produce the > same results as MatLab. > >> In that case there is probably an inconsistency in the file simulate.m > near the end: >> The last non empty line before the line out = ∑ reads >> >> iLeak_axon = gLeak_axon_AB.*(v_axon_AB-ELeak_axon_AB); >> >> and this doesn't agree with the line >> >> iLeak_axon = ELeak_axon_AB*(v_axon_AB-ELeak_axon_AB); >> >> in the function xdot. > > The correct equation is: > > iLeak_axon = gLeak_axon_AB.*(v_axon_AB-ELeak_axon_AB); > > I think this error was the result of a variable name change at some point > to make the to scripts the same. I have fixed the MatLab script but it is > not making any difference. > >> >> Final question for the OP: if the model is supposed to be dynamic, isn't > it suspicious that Matlab gives a constant result? > > Now this is true ... I'll chat to my MatLab expert about this. I was hoping > that it is not a constant but that it has small variations in the value > that I can't see on the graph. However, I did not know how to check the > values ... another question for my MatLab expert tomorrow. > >> Also, in this block >> >> gNa_axon_AB=300e-3 >> gK_axon_AB=52.5-3 >> gLeak_axon_AB=0.0018e-3 >> >> the middle line looks like a typo for 52.5e-3 and the 3rd line looks very > low -- googling suggests values like (120, 36, 0.3) mS/cm^3, which would be > more consistent with a value around 1e-3. > > Yes you are right. 52.5-3 should be 52.5e-3. I made the change but still no > luck. > > With regards to the value of gLeak_axon_AB, the values I'm using for the > model are from a paper. I tried changing it to what you suggested, but that > seems to result in a constant value of -60.00006
But isn't -60 = ELeak_axon_AB exactly the right steady-state value for the system with both the K and Na channels closed? > > More late night staring ahead for me ... > > Regards > Jannetta > > > -- > > =================================== > Web site: http://www.jannetta.com > Email: janne...@henning.org > =================================== > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd....@cbs.dk Priv: pda...@gmail.com ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.