Answered
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...

ungefär ett år ago | 0

Answered
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...

mer än ett år ago | 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...

mer än ett år ago | 1

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Answered
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...

mer än ett år ago | 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...

mer än ett år ago | 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...

mer än ett år ago | 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...

mer än ett år ago | 0

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Answered
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...

mer än ett år ago | 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...

mer än ett år ago | 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...

mer än ett år ago | 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...

nästan 2 år ago | 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...

nästan 2 år ago | 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...

nästan 2 år ago | 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...

nästan 2 år ago | 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...

nästan 2 år ago | 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...

nästan 2 år ago | 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...

nästan 2 år ago | 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...

ungefär 2 år ago | 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...

ungefär 2 år ago | 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 ...

ungefär 2 år ago | 0

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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...

ungefär 2 år ago | 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...

mer än 2 år ago | 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...

mer än 2 år ago | 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 ...

mer än 2 år ago | 0

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Answered
Implementing Gillespie's Algorithm.
While this post is about understanding Gillespie's algorithm, it might be interesting for anyone landing on this page to know th...

mer än 2 år ago | 0

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How should I modify the rate rule using Symbiology so that it works?
This is an old question but an answer could still benefit others who bumped into the same issue. The key piece of the error mes...

mer än 2 år ago | 0

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How do I resolve, error in resample ?
Hi Ramya, many of the simulations generated with this code contains only one data point. sbioensemblestats tries first to synch...

mer än 2 år ago | 1

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Administer simultaneously different doses to different compartment in Simbiology
Hi Zinnia, yes, you can administer different doses with different targets at the same time during a simulation. You can do this...

ungefär 3 år ago | 0

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Log-uniform sampling for global sensitivity analyses
Hi Abed, This option was added to sbiosobol in the latest release R2021b. Best regards, Jérémy

ungefär 3 år ago | 1

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Answered
How to compare equations of two simbiology models?
Hi, One way to compare the equations of two models is to load the models in the MATLAB workspace, generate the equations with g...

ungefär 3 år ago | 1