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Jeremy Huard

Last seen: Today Active since 2014

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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 ...

5 días 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...

6 días 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...

alrededor de 1 mes 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...

alrededor de 2 meses 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 meses ago | 0

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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...

4 meses 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...

4 meses 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...

4 meses 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...

11 meses ago | 0

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

11 meses ago | 1

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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...

11 meses 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 ...

más de 1 año 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...

más de 1 año ago | 2

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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 ...

más de 1 año 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...

más de 1 año 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...

más de 1 año ago | 0

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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 ...

más de 1 año ago | 1

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Answered
Simbiology createSimFunction data access
Hi Mohammad, the method selectbyname allows you to extract the data of a specific state. Alternatively, you can use the attach...

más de 1 año ago | 0

| accepted

Answered
Model diagram in the Simbiology freeze and disappear
(edited: added a more detailed description of the issue) Dear users, We were able to reproduce the issue you reported: Draggi...

más de 1 año ago | 2

| accepted

Answered
Simbiology dose an ode
Hi Bence, you're right, doses can't be applied to species which are defined by rate rules. Their dynamics must be defined by re...

más de 1 año ago | 1

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Answered
Model/Simulation of Drug Release in Graphical SimBio Interface
Hi Greg, we have released video tutorials which cover different topics including model building: SimBiology Tutorials for QSP,...

casi 2 años ago | 1

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Answered
setting of initial conditions simbiology
Dear Kazutaka, is this the example you are using?: PK/PD Modeling and Simulation to Guide Dosing Strategy for Antibiotics If s...

alrededor de 2 años ago | 1

Answered
Export model to workspace - missing dose
Hi Jacopo, doses are indeed included in the model. You can retrieve them using the method getdose. getdose will return all dos...

más de 2 años ago | 0

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Answered
sbiofit example - Fit a One-Compartment Model to an Individual's PK Profile using SimBiology app
Hi Jacopo, I have had a look at your project. There were two things which differed from the programmatic example: you set the ...

más de 2 años ago | 0

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Answered
Is it possible to normalize the output using GUI?
Hi Hassan, in the SimBiology Model Analyzer App you add a step to your program to define and calculate an observable. This new...

más de 2 años ago | 1

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Answered
In Simbiology, how to graphically represent an enzyme production and its activity simultaneously?
Hi Hassan, let me try and summarize to make sure I understood your question correctly: you defined the 'flipping' reaction with...

más de 2 años ago | 1

| accepted

Answered
Dosing in sbiofit example
Hi Jacopo, this is the dose amount used to generate the synthetic data used in this example. But you are right, it should have...

más de 2 años ago | 2

| accepted

Answered
n Transit compartment in 2-compartment PK model in Simbiology
Hi Andy, I have attached a SimBiology implementation of a two compartment model with transit compartments. I hope this helps....

más de 2 años ago | 1

| accepted

Answered
How can I plot only one fitted variable after using sbiofit?
Hi Jim, thanks for this feedback. It would be a good thing to have. Have you had a look at sbiopredictionci? It computes the c...

alrededor de 3 años ago | 0

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Answered
Is it possible to get the group (that is the subject) number in sbiofit to do a lookup?
Hi Jim, the alternative you described, which involves a subject column used as a dose for a dummy species is the best way to ge...

alrededor de 3 años ago | 0

| accepted

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