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Jeremy Huard

Last seen: 4 dagen ago |  Active since 2014

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Answered
Get information from Unit Conversion
Hi @Elisa, I am curious about why you want to turn off unit conversion. Can you please explain the motivation behind it? As fo...

20 dagen ago | 1

| accepted

Answered
How to modify the values and units of custom parameters in PBPK modeling using simbiology
Dear @红梅, you will need to actively turn on the Unit conversion feature when working with different units. I even recommend to...

20 dagen ago | 0

| accepted

Answered
Using Recursive function to calculate all possible peptide combinations
R2023a introduced the function combinations, which can be used on most datatypes including strings. Your code could then look l...

ongeveer een maand ago | 0

Answered
How to implement constraints (conditions) to the estimation of parameters by fitting?
Hi @Luis B. Walter, one idea would be to actually estimate and , with and have be calculated in the model with an initial ass...

ongeveer 2 maanden ago | 1

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Answered
species go to negative values
I would also recommend to have a look at the Model Debugger for SimBiology. This tool will allow you to define breakpoint condit...

2 maanden ago | 0

Answered
sbiofit ability to estimate the parameter for 3 different cases at the same time
Hi @Mehdi, Currently, when you run this code, you read one sheet and save the experimental data into the variable exp_data, whi...

3 maanden ago | 0

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Answered
Combined Doses in Simfunction
Hi @Mehdi, If you want to use both doses for each simulation run, you will need a cell array of size 1xN, where N is the number...

3 maanden ago | 0

| accepted

Answered
Simbiology interface: only plot time course simulations? or, it is possible to plot, for example, binding curves without leaving the interface?
Hi @Luis B. Walter, the definition of your observables let me think that they will change over time and thus, that they are not...

5 maanden ago | 0

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Answered
How to set a Condition of limitation between two Species ?
Hi @丁, it is recommended to use repeated assignments over algebraic rules whenever a closed-form solution can be implemented. T...

5 maanden ago | 0

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Answered
How to export model as equations
Hi @丁, do you only want to be able to see the ODEs or do you want to export them in a specific format? If you want to visualiz...

5 maanden ago | 0

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Answered
Simbiology program not working
Hi @Yeonsoo, I don't know what you mean when you say you downloaded 'amazon java script program'. But I assume you installed M...

5 maanden ago | 0

Answered
How to randomly sample output times in Simbiology?
Hi @Wang, Since your ultimate goal is to run a GSA on the model output, I would recommend the following: Create parameter outT...

5 maanden ago | 0

Answered
Cannot install libSBML in MATLAB
Hi @Elisa, did you download the binaries or just the src files? You need to download the archive libsbml-x.xx.x-matlab.binarie...

6 maanden ago | 0

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Answered
How to create user-defined unit in SimBiology?
Hi @日曜, I suspect you receive an error when executing the sbioaddtolibrary command because the sbiounit call does not include a...

6 maanden ago | 1

| accepted

Answered
How to set the number of sampling points when simulating using Simbiology APP
Hi @日曜, In the Model Analyzer App you can define the output times for all simulations of your model in its Simulation Settings ...

6 maanden ago | 1

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Answered
Export initial conditions of parameters/compartments/species into workspace
Dear @Justine, there is currently no built-in command line interface to get the initial conditions. However, you could simulat...

7 maanden ago | 0

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Answered
Simultaneously fitting two observed objects
Hi @Bohao, yes, you can accomplish this using fitProblem or the Model Analyzer App. All will need is a different column for eac...

8 maanden ago | 1

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Answered
Unit problems of simbiology model
Dear Bohao, compartments are containers that are typically defined by their volume, so their unit will be e.g. liter, whereas s...

8 maanden ago | 0

| accepted

Answered
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...

9 maanden ago | 0

| accepted

Answered
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...

9 maanden ago | 1

Answered
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); %...

10 maanden ago | 1

| accepted

Answered
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 ...

10 maanden ago | 0

Answered
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...

10 maanden ago | 0

Answered
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 ...

11 maanden ago | 0

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...

11 maanden 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...

ongeveer een jaar ago | 0

Answered
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...

ongeveer een jaar ago | 1

| accepted

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...

ongeveer een jaar ago | 0

Answered
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...

ongeveer een jaar ago | 0

| accepted

Answered
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...

ongeveer een jaar ago | 1

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