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**Content Feed**

Question

When will sbmlimport support sbml level 3?

Would be useful to know. I believe 2020b only supports level 2, correct? Has anyone else run into having to use an sblm level ...

9 months ago | 1 answer | 0

### 1

answerQuestion

Semicolons in SimBiology species names: just characters, or functionally active?

I was looking at Sven Mesecke's implementation of the Renin Angiotensin Aldosterone System model of Lo et al. 2011. (For those ...

1 year ago | 1 answer | 0

### 1

answerQuestion

Any simulation speed differences between models loaded with SimBiology() vs sbioloadproject?

The question is in the title. I haven't seen much difference in numerical efficiency between the same model opened in sbioloadpr...

1 year ago | 1 answer | 0

### 1

answerQuestion

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...

2 years ago | 1 answer | 0

### 1

answerQuestion

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...

2 years ago | 1 answer | 0

### 1

answerIcons for pinned SimBiology(R) graphics

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

2 years 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...

2 years ago | 1 answer | 0

### 1

answerQuestion

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...

2 years ago | 1 answer | 0

### 1

answerQuestion

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...

2 years ago | 1 answer | 0

### 1

answerIs 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(...

2 years 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...

2 years ago | 0 answers | 0

### 0

answersIs 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...

2 years 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...

2 years ago | 2 answers | 0

### 2

answersQuestion

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...

2 years ago | 3 answers | 0

### 3

answersQuestion

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...

2 years ago | 1 answer | 0

### 1

answerQuestion

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...

2 years ago | 1 answer | 0

### 1

answerQuestion

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...

2 years ago | 1 answer | 0

### 1

answerHow 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...

2 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 ...

3 years ago | 1 answer | 0

### 1

answerQuestion

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...

3 years ago | 1 answer | 0

### 1

answerQuestion

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...

3 years ago | 1 answer | 0

### 1

answerQuestion

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...

3 years ago | 1 answer | 0

### 1

answerQuestion

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...

3 years ago | 1 answer | 0

### 1

answerHow 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...

3 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...

3 years ago | 1 answer | 0

### 1

answerShorthand 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 ...

3 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...

3 years ago | 2 answers | 0

### 2

answersQuestion

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...

3 years ago | 1 answer | 0

### 1

answerVariable 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...

3 years ago | 0

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"...

3 years ago | 0