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Feeds
Simbiology Previous Initial Parameters
The results of a fit only contain the outputs of the fit itself (for example, parameter estimates). If you want to reproduce tho...
circa 10 ore fa | 0
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...
8 giorni fa | 2
| accettato
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...
11 giorni fa | 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...
25 giorni fa | 1
| accettato
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....
circa un mese fa | 0
| accettato
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...
circa un mese fa | 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...
circa 2 mesi fa | 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 mesi fa | 0
| accettato
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 mesi fa | 0
| accettato
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 mesi fa | 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 mesi fa | 0
| accettato
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 mesi fa | 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 mesi fa | 0
| accettato
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 mesi fa | 0
| accettato
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 mesi fa | 0
| accettato
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 mesi fa | 0
| accettato
Sensitivity analysis in Simbiology
SimBiology does not currently support local sensitivity analysis on models with active events. One potential workaround is to pe...
7 mesi fa | 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 mesi fa | 0
| accettato
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 mesi fa | 0
| accettato
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 mesi fa | 0
| accettato
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 mesi fa | 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 mesi fa | 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 mesi fa | 0
| accettato
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 mesi fa | 0
| accettato
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 mesi fa | 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 mesi fa | 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 mesi fa | 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 mesi fa | 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...
12 mesi fa | 0
| accettato
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 mesi fa | 0
| accettato
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