Question

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...

ongeveer 5 jaar ago | 3 answers | 0

Question

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...

meer dan 5 jaar ago | 1 answer | 0

Question

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...

meer dan 5 jaar ago | 1 answer | 0

Question

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...

meer dan 5 jaar ago | 1 answer | 0

Answered

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...

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...

meer dan 5 jaar ago | 0

Question

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 ...

bijna 6 jaar ago | 1 answer | 0

Question

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...

ongeveer 6 jaar ago | 1 answer | 0

Question

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...

ongeveer 6 jaar ago | 1 answer | 0

Question

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...

ongeveer 6 jaar ago | 1 answer | 0

Question

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...

ongeveer 6 jaar ago | 1 answer | 0

Answered

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...

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...

ongeveer 6 jaar ago | 1

Question

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...

meer dan 6 jaar ago | 1 answer | 1

Answered

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 ...

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 ...

meer dan 6 jaar ago | 0

Question

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...

meer dan 6 jaar ago | 2 answers | 0

Question

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...

meer dan 6 jaar ago | 1 answer | 0

Answered

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...

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...

meer dan 6 jaar ago | 0

Answered

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"...

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"...

meer dan 6 jaar ago | 0

Answered

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...

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...

meer dan 6 jaar ago | 0

Answered

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...

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...

meer dan 6 jaar ago | 0

Question

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...

meer dan 6 jaar ago | 4 answers | 0

Question

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...

meer dan 6 jaar ago | 1 answer | 0

Answered

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)...

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)...

meer dan 6 jaar ago | 0

Answered

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...

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...

meer dan 6 jaar ago | 0

Question

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...

meer dan 6 jaar ago | 3 answers | 0

Answered

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...

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...

meer dan 6 jaar ago | 0

Question

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...

meer dan 6 jaar ago | 2 answers | 0

Answered

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...

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...

meer dan 6 jaar ago | 0

Question

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...

meer dan 6 jaar ago | 3 answers | 0

Answered

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...

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...

meer dan 6 jaar ago | 0

Question

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...

meer dan 6 jaar ago | 2 answers | 0