Domanda

Is it possible to get the group (that is the subject) number in sbiofit to do a lookup?
If I'm fitting using lsqnonlin, is there a matlab script function that returns the group number? The idea is to allow use of co...

circa 5 anni fa | 3 risposte | 0

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Domanda

Fitting multiple dependent variables with time less than zero
Suppose I have a therapeutic d that modulates an endogenous substance e. I've a pd model of e (for the sake of argument, a cons...

oltre 5 anni fa | 1 risposta | 0

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Domanda

The order of plotted things vs the order of the legend
I'm using patch to show a confidence interval in a matlab plot as a colored region. Assume vectors of time values, tv, and mean...

oltre 5 anni fa | 1 risposta | 0

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Domanda

Is there an object associated with simulate task in the simbiology desktop that contains the name of the task?
I use State_Subplots in "Plots to Generate" in simbiology simulation tasks a lot. "Plots to Generate" allows scripts to be used...

oltre 5 anni fa | 1 risposta | 0

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How To Clear Java Heap Space Memory????
jonathan wrote: "years are passing on this one folks. hello? Mathworks please address this." I'm thinking that maybe eight year...

oltre 5 anni fa | 0

Domanda

nlme fitting error for covariate in popPK model
I select a column (WT) in my dataset as a covariate. When I set up the covariate in the nlme fitting page (interactively, not ...

circa 6 anni fa | 1 risposta | 0

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Domanda

Can I create a variant that captures all current parameter, species and compartment values?
So I'd like to be able to do something like this: sbr = sbioroot; % Get the root object lastn = length(sbr.m...

circa 6 anni fa | 1 risposta | 0

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Domanda

Not finding info on arrays of variant objects
The help page on <https://www.mathworks.com/help/simbio/ref/variantobject.html?searchHighlight=variant%2520array&s_tid=doc_srcht...

circa 6 anni fa | 1 risposta | 0

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Domanda

Better understanding of variants sought (also project files)
If I create a model using the dashboard, including variants(suppose 2, 'var1', and 'var2'), and save the model, the variants are...

circa 6 anni fa | 1 risposta | 0

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Domanda

Could Simbiology simulations have a preload function?
In Simulink, one can write preload scripts that run upon opening a model or upon any number of other actions. In Simbiology...

oltre 6 anni fa | 1 risposta | 0

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How To Clear Java Heap Space Memory????
This error kept me from publishing completed work. That is, Matlab did the analysis, but publish could not complete for the scri...

oltre 6 anni fa | 1

Domanda

Dimensional analysis with math functions flags a warning
I'm getting a warning when I run with dimensional analysis. _ *Cannot perform dimensional analysis for rule 'rule_13' becau...

oltre 6 anni fa | 1 risposta | 1

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Shorthand for sbioselect/set
So I decided to write the code and am embarrassed with how simple it is. But a question arose. Here's the code: function ...

oltre 6 anni fa | 0

Domanda

Shorthand for sbioselect/set
In running simbiology models using scripts, one often wants to change parameter values. For a single parameter (e.g. "p1") we c...

oltre 6 anni fa | 2 risposte | 0

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Domanda

sbioloadproject or sbiosaveproject loses graphical information
If you Google "Why did I become a biologist?" most answers include "I loved science and hated math". One of the key element...

oltre 6 anni fa | 1 risposta | 0

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Variable Stoichiometric Coefficients in SimBiology?
This is an old thread, but I wanted to bounce this off the community. It seems that you can fool the model. If the stoichiomet...

oltre 6 anni fa | 0

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persistent variable precludes simbiology acceleration, how can I keep an array available in memory
Arthur, Thanks! This is good news. As I wrote above, the "persistent" approach seems to me to be more elegant than "global"...

oltre 6 anni fa | 0

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persistent variable precludes simbiology acceleration, how can I keep an array available in memory
Arthur, thanks for your note and this information. I'm confused, though, because when I had persistent variables, the error mes...

oltre 6 anni fa | 0

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persistent variable precludes simbiology acceleration, how can I keep an array available in memory
Another update. After I closed Matlab (or rather, it closed itself preemptively!), I opened it up again. I was able to use the...

oltre 6 anni fa | 0

Domanda

persistent variable precludes simbiology acceleration, how can I keep an array available in memory
In a simbiology model, I use a spline function in a matlab .m function to set the value of a variable parameter. For example, t...

oltre 6 anni fa | 4 risposte | 0

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Domanda

Can I set simbiology repeat assignment rule state to active or inactive using variants?
Using the paradigm similar to that in Dr. Goldspie's insulindemo example, I'm using two rules to set a variable parameter. Let's...

oltre 6 anni fa | 1 risposta | 0

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Vector Variables, Preload, and External matlab functions (in m files) in Simbiology
Arthur, Thank you. One of the things I like about Simbiology is that you have some stuff (like fitting, even nlme fitting)...

oltre 6 anni fa | 0

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Vector Variables, Preload, and External matlab functions (in m files) in Simbiology
Answered one question: I CAN use a user-defined function call to get this information into the model. So if I use function...

oltre 6 anni fa | 0

Domanda

Vector Variables, Preload, and External matlab functions (in m files) in Simbiology
In a previous question, I asked about how to switch between using an ODE-calculated species value, and a forced function fit. I...

oltre 6 anni fa | 3 risposte | 0

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Switching a species between an ode evaluation and a specified function (repeat assignments)
Thanks, Arthur. For others, Arthur's insulindemo example is very helpful: a lot of useful ideas. You can look at how Arthur h...

oltre 6 anni fa | 0

Domanda

Switching a species between an ode evaluation and a specified function (repeat assignments)
Most of the models in Simbiology will be based upon interacting ODEs. Insulin and glucose, in diabetes models, for example. In...

oltre 6 anni fa | 2 risposte | 0

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must I use events for discontinuous functions?
Arthur, this is spot on. I had gotten pretty accurate results by setting the max step-size to 1, but that did lower the numerica...

oltre 6 anni fa | 0

Domanda

must I use events for discontinuous functions?
A previous question asked about input a function of time. A function y = exp(-k*t) was input, with errors. The answer from Mat...

oltre 6 anni fa | 3 risposte | 0

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Dimensional checking in Simbiology
Ricardo, Thanks for your prompt reply. In order: 1)Opening the model in gPKPDsim did indeed allow the simulation. I guess...

oltre 6 anni fa | 0

Domanda

Dimensional checking in Simbiology
I am installing the gPKPDtoolbox as described in the reference below. I'm trying to run an example from the examples that downlo...

oltre 6 anni fa | 2 risposte | 0

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