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Feeds
Transfer parameter estimates to model
For item #1, the SimBiologyModelAnalyzer app allows you to create a variant of the parameter estimates (see here for more detail...
3 days ago | 2
| accepted
Encoding conditional assignments in SimBiology
Hi emjey, I see this problem solved in one of two ways: 1) Take advantage of true/false getting converted to 1/0 in mathematic...
7 days ago | 1
How do I fit multiple curves at once, sharing some fitting parameters and floating others?
Are the 6 different analyte concentrations something you want to specify or estimate? Both of these these are possible in SimBio...
21 days ago | 1
| accepted
Different dilution effect on the kinetics of a time course
Hi Luis, Because you don't use units in your model, SimBiology interprets the reaction rates to have dimensions of amount/time....
1 month ago | 0
| accepted
Question re/ matlab.codetools.requiredFilesAndProducts function.
I'd first check the "Certain" field of the pList output to see if these products have been marked as definitely or just possibly...
1 month ago | 0
changes the the simulated mass with changing the absolute and relative tolerance
First, a disclaimer. I'm a SimBiology developer, not a modeler. So I'm most knowledgable about what is technically possible with...
2 months ago | 0
different event functions for the same species
The problem is that you have two conflicting mathematical definitions of Fw. You are trying to set it with both a repeated assig...
3 months ago | 0
| accepted
How do I fix a duplicate name error ?
It's hard to know exactly what's going on without more details. Can you share more details? Ideally, can you share the project a...
3 months ago | 0
| accepted
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...
3 months ago | 0
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 ...
4 months ago | 0
| accepted
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...
4 months ago | 0
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...
4 months ago | 0
| accepted
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.
4 months ago | 0
| accepted
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...
4 months ago | 0
| accepted
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...
4 months ago | 0
| accepted
Sensitivity analysis in Simbiology
SimBiology does not currently support local sensitivity analysis on models with active events. One potential workaround is to pe...
7 months ago | 0
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...
8 months ago | 0
| accepted
Parameter unit setting problem
Hi Bohao, SimBiology's units functionality does not support embedding numeric multipliers like 10^15. And even after you addres...
8 months ago | 0
| accepted
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...
9 months ago | 0
| accepted
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 ...
9 months ago | 0
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...
9 months ago | 3
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...
10 months ago | 0
| accepted
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...
10 months ago | 0
| accepted
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...
10 months ago | 0
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...
10 months ago | 0
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...
10 months ago | 0
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 ...
11 months ago | 0
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...
11 months ago | 0
| accepted
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...
12 months ago | 0
| accepted
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...
12 months ago | 1
| accepted
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