Arthur Goldsipe

MathWorks

Last seen: Today | Aktiv seit 2011

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Beantwortet
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 Tage vor | 2

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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 Tage vor | 1

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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 Tage vor | 1

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Beantwortet
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....

etwa ein Monat vor | 0

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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...

etwa ein Monat vor | 0

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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...

etwa 2 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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

7 Monate vor | 0

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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 Monate vor | 0

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Beantwortet
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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 3

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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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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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 Monate vor | 0

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Beantwortet
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 Monate vor | 1

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