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Jeremy Huard

MathWorks

Last seen: 22 days ago Active since 2014

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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 ...

2 months 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...

2 months ago | 1

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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 ...

3 months 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...

3 months 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...

3 months ago | 0

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 ...

3 months 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...

3 months ago | 0

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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...

3 months ago | 1

| 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...

5 months ago | 1

| accepted

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,...

8 months 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...

1 year 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...

1 year 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 ...

1 year ago | 0

| accepted

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...

1 year 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...

1 year 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...

1 year 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....

1 year 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...

2 years 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...

2 years ago | 0

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Answered
Doripenem PKPD simbiology example: How to execute monte carlo simulation with off diagonal covariance values?
Hi Daniel, you're right, in this example all parameters are independent of each other. If you want to include correlations, y...

2 years ago | 1

Answered
How to simulate simbiology model using array of doses?
In your code, dose_sc and dose_iv contain both all doses in your model. You should specify the name of a SC or IV dose that is ...

2 years ago | 1

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Answered
Performing infusion experiment in Simbiology desktop
Hi Rajeev, whether you choose a repeated dose or a scheduled dose has rather to do with the schedule of your drug regimen. Both...

2 years ago | 1

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Answered
How to create custom error model in Simbiology
Hi Praveen, the error model you suggested looks like a combined error model. But from your equation I don't see whether you exp...

2 years ago | 0

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Answered
75 errors arise from simulation of Biomodels model.
The error message is pretty clear though. It says that some variables used in reaction rates are not defined. Actually the troub...

2 years ago | 1

Answered
Simulation makes no sense
By the way, I think had changed the glucose injection to 0.3 instead of 0.003 mainly to make easier to spot the event. But if y...

2 years ago | 0

Answered
Simulation makes no sense
Hi Juan Carlos, as Pax suggested in his answer to your previous question, this model does not contain units, so you can't make ...

2 years ago | 1

Answered
SimBiology getConfigSet does not recognise model object
Hi Alvaro, sbioloadproject will return a struct that contains your model(s). This should work: s = sbioloadproject('RandomNet...

2 years ago | 1

Answered
How to upload KEGG file to Simbiology so I can start analyzing.
Hi Juan Carlos, KEGG files can't be imprted into SimBiology as is. You will need to convert them into SBML files first. There ...

2 years ago | 0

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Answered
In Simbiology, should the categorical variables be assigned as group variable or covariate in the dataset?
Group variable defines an index for a subject/experiment. In your dataset, ID is a group variable. Gender and age can be both co...

2 years ago | 0

Solved


Make the vector [1 2 3 4 5 6 7 8 9 10]
In MATLAB, you create a vector by enclosing the elements in square brackets like so: x = [1 2 3 4] Commas are optional, s...

2 years ago

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