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Arthur Goldsipe

MathWorks

Last seen: Today Active since 2011

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Answered
A variable is specified by more than one assignment rule
It sounds like you have an ill-defined problem with an algebraic loop. Specifically, A_Total is a function of a, but a is a func...

7 days ago | 0

Answered
Data fit to observables
Hi Justine, I just tried this in R2023b, and I was able to select an observable in the mapping for the response. I'm attaching ...

15 days ago | 0

| accepted

Answered
Fitting model on a Debian machine
If you want to fit a SimBiology model using a command-line function, you can directly call sbiofit (or sbiofitmixed). This is ex...

15 days ago | 0

Answered
Modeling Mitochondria Voltage depending on the Sodium/Potassium Pumps results in Algebraic loops Error.
Can you share your model? That would allow me to offer more specific advice. (If you're not comfortable posting it publicly, ple...

19 days ago | 0

| accepted

Answered
How can I add stoichiometry value in simbiology model builder 2023b ?
I believe your question is similar to this one. Please see the accepted answer there.

20 days ago | 0

| accepted

Answered
Dimensional analysis issue because of the function 'log' in the rule
Since your expression is dimensionally correct, you can safely ignore this warning. Note that is an informational warning (as o...

28 days ago | 0

| accepted

Answered
Using simFunction Object in Simbiology when my stoichiometry depends on a model parameter
The error you report is intended to communicate that SimBiology does not allow the following the following combination of condit...

1 month ago | 0

| accepted

Answered
Sensitivity analysis in Simbiology
SimBiology does not currently support local sensitivity analysis on models with active events. One potential workaround is to pe...

4 months ago | 0

Answered
Apply fmincon nonlinear parameter inequality constraints into SimBiology for parameterization
The estimation program in the SimBiology Model Analyzer app uses the command-line function sbiofit. Unfortunately, this function...

5 months ago | 0

| accepted

Answered
Parameter unit setting problem
Hi Bohao, SimBiology's units functionality does not support embedding numeric multipliers like 10^15. And even after you addres...

5 months ago | 0

| accepted

Answered
Categorical covariates in parameter estimation
Do you want to do nonlinear regression or nonlinear mixed effects (NLME)? The feature Joe mentions in his comment only applies t...

6 months ago | 0

| accepted

Answered
How to solve this error
(Copying answer from comments.) The problem was that one value of DV1 was 0, so the resulting weight was infinite. One thing I ...

6 months ago | 0

Answered
Fit simbiology model to cmax or AUC data
One option would be to add Cmax to your model as an observable. Then, you can include Cmax in your fit the same way you fit to a...

6 months ago | 3

Answered
Change in simulation output with changing in the units of stop time
If you have constructed your model correctly, I expect the results of the two simulations to be equivalent but not numerically i...

7 months ago | 0

| accepted

Answered
Failure of dimensional analysis for a rule
When you enable dimensional analysis (or unit conversion) in SimBiology, fractional exponents can only be applied to dimensionle...

7 months ago | 0

| accepted

Answered
Dimension of the species
In SimBiology, a species is intended to represent a entity (like a protein or some other chemical) that exists in a physical com...

7 months ago | 0

Answered
unit dimensional analysis problems
If your reactions are using mass action kinetics, then the units you report for "kf" are not correct. For the first reaction, th...

7 months ago | 0

Answered
Dimensional analysis fail for reaction on simbiology
It looks like this was answered in a comment on the question. I'll paste it here for completeness: The first term of the rate r...

7 months ago | 0

Answered
How do I open or convert a .sbproj.zip file in Simbiology?
An .sbproj file is a specially formatted .zip file. So perhaps whatever you're using to download the file recognized it as such ...

8 months ago | 0

Answered
Why isn't Stoichiometry Math working in Simbiology?
It sounds like you are trying to import an SBML file that uses the stoichiometryMath element defined in SBML level 2. Unfortunat...

8 months ago | 0

| accepted

Answered
Error when calculating AUC in simbiology
In case anyone runs into a similar issue and is looking for the answer, I looked at Brett's model and made a few recommendations...

9 months ago | 0

| accepted

Answered
Modeling dissociation using Hill function provides misleading results
Similar questions come up periodicaly. I suggest looking at my previous responses here and here. The bottom line is that both o...

9 months ago | 1

| accepted

Answered
How to overcome the error "Unrecognized field name \stopTimeUseConfigset\." when simulating a simbiology model on a previous Matlab version?
SimBiology doesn't currently support opening newer projects in older versions. (This is called forward compatibility.) In fact, ...

9 months ago | 0

| accepted

Answered
Simbiology in app model simulation
I think the problem comes down to the way that calculate_KTC depends on time. This function has a maximum around a time of 1. If...

10 months ago | 0

| accepted

Answered
Adding erf(x) to a rule in Simbiology
You can call almost any MATLAB function within your rules (or in any expression in SimBiology). So, the expressoin "y = erf(x)" ...

10 months ago | 0

| accepted

Answered
Unable to locate and load .mat file after compiled into standalone file in App Designer
I suspect the problem is that you need to include in your app additional supporting function files that are required by the SimF...

11 months ago | 1

| accepted

Answered
Unites of the transfer rates
Did you enable UnitConversion for your model? If not, then you will need to manually update your entire model to use consistent ...

11 months ago | 0

Answered
Occasionally when creating a SimFunction, SimBiology returns a failure to compile error, what causes this?
Hi Craig, My guess is that this is some sort of bug. But it's hard to say definitively without reproduction steps. If you can c...

11 months ago | 0

| accepted

Answered
error message - Unrecognized function or variable ‘rec’.
Your NCA program is erroring because of problems with the first row in your data. If you change that first ID from 0 to 1, and t...

12 months ago | 1

Answered
Adding equations as a function of time
I suspect the problem is with "Time". SimBiology requires you to reference time as "time" (all lowercase). If that doesn't fix ...

1 year ago | 0

| accepted

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