Answered
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...

1 year ago | 0

| accepted

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...

1 year ago | 0

Answered
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...

1 year ago | 0

| accepted

Answered
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...

1 year ago | 1

| accepted

Answered
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...

1 year ago | 1

| accepted

Answered
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...

1 year ago | 0

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

1 year ago | 0

Answered
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...

1 year ago | 0

| accepted

Answered
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...

1 year ago | 0

| accepted

Answered
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...

1 year ago | 1

| accepted

Answered
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...

1 year ago | 0

| accepted

Answered
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...

2 years ago | 2

| accepted

Answered
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...

2 years ago | 0

| accepted

Answered
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 ...

2 years ago | 0

| accepted

Answered
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...

2 years ago | 2

Answered
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...

2 years ago | 0

Answered
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...

2 years ago | 0

Answered
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 ...

2 years ago | 0

| accepted

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...

2 years ago | 0

Answered
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...

2 years ago | 0

Answered
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...

2 years ago | 1

Answered
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...

2 years ago | 0

| accepted

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

2 years ago | 1

| accepted

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...

2 years ago | 1

Answered
Feed Simbiology analyser custom ODE's
Hi Leo, you will have to create a SimBiology model before using the Model Analyzer App. That said, you can use rate rules and ...

3 years ago | 2

Answered
How to perform sequential fitting in Simbiology
Hi 悦吴, you can indeed do this with the following steps: 1. fit PK data with a Fit program 2. right-c...

3 years ago | 2

| accepted

Answered
exporting data from simBiology model analyser
For completeness: This question was answered in the following thread: insulindemo_changing the value of body weight. Also, I ...

3 years ago | 1

Answered
Simbiology: intratumoral volume
Hi Kelly, compartments have a 'Constant' property that can be set to false to allow the volume to change during the course of a...

3 years ago | 0

Answered
How can I define a time-dependent (species) reaction rate for an model in SimBiology?
Hi Puru, I would recommend you to create a reaction null -> A with a custom reaction rate defined by the quadratic equation. I...

3 years ago | 0

| accepted

Answered
Is it possible to create custom (species-specific) conversion factors in Simbiology?
Hi Shalla, In this case, the easiest way is to : import your experimental data as a table add a column that divides the dose ...

3 years ago | 1

| accepted