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Jeremy Huard

Last seen: Today Aktiv seit 2014

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Beantwortet
Importing XML Simbiology model
Hi Jacopo, this SBML file is indeed not valid according to the SBML validator. One unit definition is missing the 'id' attribut...

3 Tage vor | 0

| akzeptiert

Beantwortet
sbiopredictionci return empty result
Hi Jesse, it looks like your model uses an external function calculate_P_A2B_factor. You will need to pass this function to the...

etwa ein Monat vor | 2

| akzeptiert

Beantwortet
What is the dotted line in Simbiology model builder, that is not d/dt?
Hi, Could it be that you mean dashed lines? dashed lines indicate that a species is both a reactant and a product of a reactio...

etwa 2 Monate vor | 0

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Beantwortet
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 ...

2 Monate vor | 0

| akzeptiert

Beantwortet
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...

2 Monate vor | 2

Beantwortet
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...

4 Monate vor | 0

Beantwortet
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...

4 Monate vor | 0

Beantwortet
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 ...

4 Monate vor | 0

| akzeptiert

Beantwortet
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...

6 Monate vor | 0

Beantwortet
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...

6 Monate vor | 0

Beantwortet
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...

6 Monate vor | 1

Beantwortet
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...

etwa ein Jahr vor | 0

| akzeptiert

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

etwa ein Jahr vor | 1

| akzeptiert

Beantwortet
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...

etwa ein Jahr vor | 1

Beantwortet
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 ...

mehr als ein Jahr vor | 2

Beantwortet
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...

mehr als ein Jahr vor | 2

| akzeptiert

Beantwortet
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 ...

mehr als ein Jahr vor | 1

Beantwortet
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...

mehr als ein Jahr vor | 0

Beantwortet
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...

mehr als ein Jahr vor | 0

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Beantwortet
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 ...

mehr als ein Jahr vor | 1

| akzeptiert

Beantwortet
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...

mehr als ein Jahr vor | 0

| akzeptiert

Beantwortet
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...

mehr als ein Jahr vor | 2

| akzeptiert

Beantwortet
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...

fast 2 Jahre vor | 1

| akzeptiert

Beantwortet
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,...

etwa 2 Jahre vor | 1

| akzeptiert

Beantwortet
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...

mehr als 2 Jahre vor | 1

Beantwortet
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...

mehr als 2 Jahre vor | 0

| akzeptiert

Beantwortet
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 ...

mehr als 2 Jahre vor | 0

| akzeptiert

Beantwortet
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...

mehr als 2 Jahre vor | 1

| akzeptiert

Beantwortet
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...

mehr als 2 Jahre vor | 1

| akzeptiert

Beantwortet
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...

mehr als 2 Jahre vor | 2

| akzeptiert

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