Jeremy Huard

Last seen: Today | 2014년부터 활동

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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...

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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...

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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...

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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...

2개월 전 | 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...

2개월 전 | 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...

3개월 전 | 0

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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...

3개월 전 | 1

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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 ...

3개월 전 | 1

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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...

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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...

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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...

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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...

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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...

6개월 전 | 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); %...

7개월 전 | 1

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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 ...

7개월 전 | 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...

7개월 전 | 0

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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 ...

8개월 전 | 0

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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...

8개월 전 | 0

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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...

11개월 전 | 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...

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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...

11개월 전 | 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...

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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...

12개월 전 | 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...

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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...

12개월 전 | 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...

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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...

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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...

대략 1년 전 | 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...

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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...

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Jeremy Huard

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