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Jeremy Huard

Last seen: 6 days ago |  Active since 2014

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Answered
Parameter Estimation for a System of Differential Equations
You could also consider using SimBiology which provides parameter estimation capabilities for ODE systems. Here is a short vide...

1 month ago | 0

Answered
Lognormal distribution parameters mu and sigma
You can find a good description of how to specify the lognormal distribution parameters µ and σ from the mean m and variance v: ...

1 month ago | 0

Answered
Copy Figure in high quality
Since R2020a exportgraphics and copygraphics can help for this task. All options to export graphics are summarized here: Compa...

1 month ago | 1

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Answered
Parameter estimation with constraints
Hi @Luis B. Walter, algebraic rules do not support inequalities. They are meant to define an equation in the form f(x) = 0 and ...

1 month ago | 0

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Comment supprimer ou modifier la loi cinétique abstraite dans les bibliothèques ?
Bonjour @Vladimir Kovalev, vous parlez d'une loi cinétique personalisée? Vous pourriez me décrire comment vous la créez? En li...

4 months ago | 0

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Advanced matlab function autocompletion based on previous input
Hi @Augusto Mazzei, the autocompletion defined in the function signature JSON file does not have to be static. For example, th...

5 months ago | 1

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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...

6 months ago | 1

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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...

6 months ago | 0

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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...

6 months ago | 0

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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...

7 months 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...

7 months ago | 0

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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...

8 months 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...

8 months ago | 0

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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...

10 months 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...

10 months 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...

10 months 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...

10 months ago | 0

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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...

10 months ago | 0

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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...

11 months 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...

11 months ago | 1

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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 ...

11 months 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...

12 months 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...

1 year ago | 1

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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...

1 year ago | 0

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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...

1 year ago | 0

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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...

1 year ago | 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); %...

1 year ago | 1

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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 ...

1 year 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...

1 year 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 ...

1 year ago | 0

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