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...

5 years ago | 3 answers | 0

3

answers

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...

5 years ago | 1 answer | 0

1

answer

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...

5 years ago | 1 answer | 0

1

answer

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...

5 years ago | 1 answer | 0

1

answer

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...

5 years 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 ...

6 years ago | 1 answer | 0

1

answer

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...

6 years ago | 1 answer | 0

1

answer

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...

6 years ago | 1 answer | 0

1

answer

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...

6 years ago | 1 answer | 0

1

answer

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...

6 years ago | 1 answer | 0

1

answer

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...

6 years 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...

6 years ago | 1 answer | 1

1

answer

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 ...

6 years 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...

6 years ago | 2 answers | 0

2

answers

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...

6 years ago | 1 answer | 0

1

answer

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...

6 years 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"...

6 years 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...

6 years 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...

6 years 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...

6 years ago | 4 answers | 0

4

answers

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...

6 years ago | 1 answer | 0

1

answer

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)...

6 years 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...

6 years 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...

6 years ago | 3 answers | 0

3

answers

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...

6 years 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...

6 years ago | 2 answers | 0

2

answers

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...

6 years 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...

6 years ago | 3 answers | 0

3

answers

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...

6 years 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...

7 years ago | 2 answers | 0

2

answers