Elasticity Coefficients with SimBiology Toolbox
in [Matlab]
|
Prev: Recognizing a key hit while running
Next: Is there a manual on reading Matlab segmentation fault stack traces?
From: Pascal Schulthess on 10 May 2010 10:12 Hi Arthur, thanks for your answer! It's good to know that I did everything as it was intended to be handled. So, yeah me :) And I know it's a lot more difficult to implement steady state analysis for every possible model out there than doing it for those easy textbook models. But I think you guys will find a satisfying solution. Cheers, Pascal "Arthur Goldsipe" <REMOVE.Arthur.Goldsipe(a)REMOVE.mathworks.com> wrote in message <hs1mtt$aq$1(a)fred.mathworks.com>... > Hi Pascal, > > I'd like to clarify how SimBiology uses 'SpeciesInputFactors', and make sure this is really what you mean by response coefficient. If you specify x as a SpeciesOutput and y as a SpeciesInputFactor, then SimBiology will calculate the sensitivity of species x (at some time t) with respect to the *initial amount* of species y. Hopefully, this is what you mean, since a perturbation in species y at time t shouldn't affect x at time t, but I just wanted to make sure. > > Unfortunately, SimBiology does not yet calculate steady states. (In general, a model could be oscillatory or chaotic and so not even have steady states!) However, we know that in many cases steady states are well-defined, and this is definitely a feature we've been thinking about for the future. > > In the interim, I think your best option is to set the stop time of the simulation to something that will approximate your steady state. Then, the approximate steady-state sensitivities will be the final row of the matrix R (where R is the second output from getsensmatrix). > > Good luck! > -Arthur > > "Pascal Schulthess" <hello(a)pascalschulthess.de> wrote in message <hs14qg$6pn$1(a)fred.mathworks.com>... > > Hi Pramod, > > > > thanks for the help and sorry for my late answer. > > > > What I meant by is response coefficient is the sensitivity of a species to small perturbations in another species (dx/dy). I discovered that I can calculate this with: > > > > spe = sbioselect(model,'Type','species'); > > set(configsModel.SensitivityAnalysisOptions,'SpeciesInputFactors', spe); > > set(configsModel.SensitivityAnalysisOptions,'SpeciesOutputs',spe); > > simModel = sbiosimulate(model,configsModel,[],[]); > > [T, R, snames, ifacs] = getsensmatrix(simModel); > > R2 = squeeze(R); > > > > This gives my the continuous sensitivity of every species to every other species. But now I'm struggling with the steady state response. Is there a way to calculate R2 at steady state? > > > > Thank so much! > > > > Pascal |