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Jeremy Huard


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MathWorks

34 total contributions since 2014

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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...

4 months 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...

5 months 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 ...

6 months 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...

6 months ago | 1

| accepted

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...

6 months 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...

6 months 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....

11 months ago | 1

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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...

1 year 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...

1 year ago | 0

| accepted

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...

1 year 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 ...

1 year 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...

1 year 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...

1 year 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...

1 year 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...

1 year 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 ...

1 year 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...

1 year 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 ...

1 year 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...

1 year 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...

1 year ago

Answered
Question on specifying input to sbiosimulate
Hi Deepa, there might be different reasons to get this error message. A typical one is when one of the fluxes becomes Inf or Na...

1 year ago | 0

Answered
Finding non-constant species in Simbiology Object
What you get is not a function handle but an heterogenous array of SimBiology objects. This array contains a mix of different co...

1 year ago | 1

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Answered
Question on specifying input to sbiosimulate
There is multiple ways to do this: 1- if you want to run multiple simulations, I recommend to use a SimFunction that will take ...

1 year ago | 1

Answered
Output of sbiosteadystate task
See answer here.

1 year ago | 1

| accepted

Answered
Accessing a variant object
Hi Deepa, you can access the variant content with the dot notation. If your variant is called v, v.Content will be an array of...

1 year ago | 0

| accepted

Answered
How to set up estimation method in sbiofit
Hi Deepa, let me summarize my understanding of your problem and please correct me if I'm wrong: you only have steady state dat...

1 year ago | 0

Answered
How to run the model in SBML file?
Dear Deepa, there is two ways to simulate a model saved in a sbml file: 1. using the SimBiology App You can open the SimB...

1 year ago | 0

| accepted

Submitted


sbioimportBerkeleyMadonna
Imports ODE models in the BerkeleyMadonna(TM) format into a SimBiology(R) model

1 year ago | 1 download |

Answered
Plot StateData at a certain time point in Simbiology
Dear Göran, indeed, you can achieve this by modifying the piece of code contained in the scan plot. Let's say that you want to...

2 years ago | 0

Submitted


Import SBML file with function definitions into SimBiology
Functions to import SBML files containing function definitions into SimBiology.

4 years ago | 2 downloads |

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