Jeremy Huard

Last seen: 2 dagen 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...

4 maanden 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: ...

4 maanden ago | 0

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

4 maanden ago | 1

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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 ...

4 maanden 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...

7 maanden 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...

8 maanden ago | 1

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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...

8 maanden ago | 1

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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...

8 maanden 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...

9 maanden 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...

9 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...

10 maanden 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...

10 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...

10 maanden 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...

ongeveer een jaar ago | 0

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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...

ongeveer een jaar ago | 0

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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...

ongeveer een jaar 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...

ongeveer een jaar 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...

ongeveer een jaar 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...

ongeveer een jaar 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...

ongeveer een jaar 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 ...

ongeveer een jaar 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...

ongeveer een jaar 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...

meer dan een jaar 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...

meer dan een jaar 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...

meer dan een jaar 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...

meer dan een jaar 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); %...

meer dan een jaar 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 ...

meer dan een jaar ago | 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...

meer dan een jaar 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 ...

meer dan een jaar ago | 0