Question

Namespace and other html / xml information in SimBiology Notes

Simbiology notes allows (requires?) one to use html for nicely formatted notes. For normal documentation use, where there will b...

3 months ago | 1 answer | 0

Question

Constant parameter setting throws error, or... if I don't set a parameter to constant, but don't change it, does it stay constant?

In another thread, I asked about using subject- (group- in SimBiology) dependent parameter values to allow fitting of one part o...

5 months ago | 1 answer | 0

Answered

Icons for pinned SimBiology(R) graphics

Repeating as a partial answer: As to the last point, found this: Simbiology / Preferences / Indicators Show indicator when a ...

Icons for pinned SimBiology(R) graphics

Repeating as a partial answer: As to the last point, found this: Simbiology / Preferences / Indicators Show indicator when a ...

5 months ago | 0

| accepted

Question

Icons for pinned SimBiology(R) graphics

When building models graphically usign the dashboard, one can pin graphical elements. This prevents inadvertently messing up a c...

5 months ago | 1 answer | 0

Question

deleting or removing variant using variant array handle gives unexpected results.

If I have a variable that contains a SimBiology parameter object, and I change it, the object reflects that change: par1 = addp...

6 months ago | 1 answer | 0

Question

Can I force Matlab to wait 'til it finishes one command to run another?

I have a script that loads a SimBiology model using the simbiology() command. Then I try to get a handle for the model simbiol...

6 months ago | 1 answer | 0

Answered

Is it possible to get the group (that is the subject) number in sbiofit to do a lookup?

One last thing. I tested using the group to set parameters. Works fine. So a repeat assignment rule is just pv = setparvalu(...

Is it possible to get the group (that is the subject) number in sbiofit to do a lookup?

One last thing. I tested using the group to set parameters. Works fine. So a repeat assignment rule is just pv = setparvalu(...

7 months ago | 0

Question

sbiofitmixed/ nlmefit and weighting two dependent variables

I am fitting a trial with two output measurements (for now). These are CONC1 and CONC2. Supposing that they have very differen...

7 months ago | 0 answers | 0

Answered

Is it possible to get the group (that is the subject) number in sbiofit to do a lookup?

Jérémy Glad if the ideas help. I enjoy the interactions with you, Arthur, Pax, and others on your team. I just want to clarif...

Is it possible to get the group (that is the subject) number in sbiofit to do a lookup?

Jérémy Glad if the ideas help. I enjoy the interactions with you, Arthur, Pax, and others on your team. I just want to clarif...

7 months ago | 0

Question

How can I plot only one fitted variable after using sbiofit?

I'm fitting a model to a dataset. I have two variables I'm fitting simultaneously: the therapy, and the quantity of an endogeno...

7 months ago | 2 answers | 0

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...

7 months 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...

9 months 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...

10 months 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...

1 year 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...

1 year ago | 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...

1 year 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 ...

1 year 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...

1 year 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...

1 year 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...

1 year 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...

1 year ago | 1 answer | 0

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...

2 years ago | 1 answer | 0

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 ...

2 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...

2 years 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...

2 years 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...

2 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"...

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"...

2 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...

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...

2 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...

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...

2 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...

2 years ago | 4 answers | 0