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How do I optimize my simulation and build in appropriate constraints on values?
Hi @Ian, I don't know the original mathematical model but based on the project you shared, I can recommend the following: I re...

más de 2 años hace | 0

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Payload release from ADC in Simbiology
Dear Yosuke, SimBiology supports setting stoichiometry coefficients in reactions. If you use the Model Builder App, you can f...

más de 2 años hace | 1

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Is there a way to combine plots generated in simbiology model analyzer into a single figure to export?
Hi @Rebeca Hannah Oliveira, starting R2023b you can do it programmatically after exporting the figures with: f1 = figure(1); %...

más de 2 años hace | 1

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How to simulate multiple doses and generate only one plot?
Hi @Lo, you can also scan over single dosing parameters such as its amount or even scan over a list of dose objects. There is ...

casi 3 años hace | 0

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How do I fit batch data to a simbiology model?
Hi, you will need first to assign a unique ID to every experiment. It looks like T7 is fixed during every experiment, is this c...

casi 3 años hace | 0

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can simbiology estimate dosage ?
Hi @Lo, yes, absolutely. I see two possibilities: if dosage consists of a single IV bolus at time=0, you can simply estimate ...

casi 3 años hace | 0

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Questions Regarding Sensitivity Analysis for Simbiology (Equation, Value Range)
Hi @Kendric Aaron, I will assume that your question relates to Local Sensitivity Analysis. But please let me know if this is no...

casi 3 años hace | 0

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Simulation error in Simbiology
Hi @Day, can you please share the project file you are using? Assuming you are using the tumor_growth_fitPKPD_completed.sbproj...

alrededor de 3 años hace | 0

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Simbiology program code gave different results from my custom code
Hi @Jesse Chao, the issue comes from the dose template. In the first version your taget is Drug_Central (corresponding to IV bo...

alrededor de 3 años hace | 1

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Simbiology program code gave different results from my custom code
Hi @Jesse Chao, this is difficult to debug without the actual model and data. Would you be able to share them? That said, I n...

alrededor de 3 años hace | 0

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Equilibrate during parameter estimation
Hi @Anu, running sbiosteadystate before each simulation in a fit is not supported. That said, I see two options: If your case...

alrededor de 3 años hace | 0

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error in running a SMBL file with SimBiology
Hi @Youngjae You, the piecewise.m file will need to be either in the Current folder or anywhere on your MATLAB Path for SimBiol...

alrededor de 3 años hace | 1

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Can't remove a custom-made kinetic law using sbioremovefromlibrary
Hi, the easiest way to manage the user-defined library might be from within the Model Builder app: That said, you can still...

alrededor de 3 años hace | 0

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Duplicate model within a project
Hi Natalia, the 'Duplicate model' option in the conctext menu of the project view is indeed not yet available in R2020b. Howev...

alrededor de 3 años hace | 0

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Using simFunction Object in Simbiology when my stoichiometry depends on a model parameter
Hi Mehdi, the stoichiometry of reactions cannot be parametrized unfortunately. But instead of using reactions you can use rate...

alrededor de 3 años hace | 0

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How to define observables units in simbiology Model Builder?
Hi Rebeca, you can define their units in the property editor (far-right panel of Model Builder) once you click on the observabl...

alrededor de 3 años hace | 1

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How to configure SimBiology parameter estimation settings so that two parameters from the same model are actually one and the same?
Hi, the recommendation is to use model-scoped parameters instead of reaction-scoped parameters. Now, let me explain what this...

más de 3 años hace | 1

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How to read multiple .spc files
I would suggest to look at fileDatastore with @tgspcread as ReadFcn argument. You can then : either read all data at once with...

más de 3 años hace | 0

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problem using sortcols()
Even though there is no sortcols function for double matrices, you could transpose A and use the sortrows function before transp...

más de 3 años hace | 0

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Tracking max value during simulation
Hi Abed, the easiest way to keep track of the max of a species during a simulation might be to use an external function (see at...

más de 3 años hace | 0

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Converting from hours to seconds on Simbiology
Hi Rebeca, plots in SimBiology Model Analyzer will use the time unit specified in the program's simulation stop time. So, if y...

más de 3 años hace | 0

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How to assign a transfer rate which changes with time in Simbiology?
Hi, you can use a reaction with mass action kinetics with rate constant k, where k will be defined in a repeated assignment suc...

más de 3 años hace | 1

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Importing XML Simbiology model
Hi Jacopo, this SBML file is indeed not valid according to the SBML validator. One unit definition is missing the 'id' attribut...

más de 3 años hace | 0

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sbiopredictionci return empty result
Hi Jesse, it looks like your model uses an external function calculate_P_A2B_factor. You will need to pass this function to the...

más de 3 años hace | 2

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What is the dotted line in Simbiology model builder, that is not d/dt?
Hi, Could it be that you mean dashed lines? dashed lines indicate that a species is both a reactant and a product of a reactio...

más de 3 años hace | 0

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How to reference compartment value? (Volume)
Hi Felix, you can refer to the volume of a compartment by the name of the compartment in any expression: C in your case. Here ...

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Percentile plot in SimBiology model analyzer
Hi Jess, this built-in plot is currently not available on the command line. But I have attached my own implementation. Hopefu...

más de 3 años hace | 2

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Getting initial estimates for Kp using Calculate partition coefficient function
Hi Bhargavi, I recommend you to have a look at the Generic SimBiology PBPK model and its implementation to see how a MATLAB fun...

casi 4 años hace | 0

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sbiosimulate crashes during ssa simulation of larger sbml models
It is a memory usage issue. Every state variable of this fairly large model is logged at every step when default simulation sett...

casi 4 años hace | 0

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How do I fit PK models to multiple dose datasets using simbiology, specifically using the command line (sbiofit)?
Hi Ross, if the dosing information is included in your dataset (table), then you will be doing pretty much what is done in the ...

casi 4 años hace | 0

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