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Florian Augustin

Last seen: Today Active since 2018

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Answered
How to modify the plotting layout after sbiopredictionci
Hi Jesse, it sounds like the helper function selectivePlotCI from this MATLAB Answers post could help. The function selectivePl...

22 Tage ago | 0

| accepted

Answered
simbiology duplicates sbml id tokens when "duplicate" is used
Hi Jim, Thank you for reporting this bug. A fix is included in R2022a Update 3. The releases R2021b Update 4, R2021a Update 7, ...

2 Monate ago | 0

| accepted

Answered
sbml export does not appear to export modifiers
Hi Jim, SimBiology interprets a list of modifier species in an SBML document as catalysts. When importing a reaction with speci...

2 Monate ago | 0

| accepted

Answered
Time-dependent Growth Rate of Species in Model
Hi Marco, you may be able to use SimBiology Events to switch between reaction rates. The general idea would be as follows: Def...

3 Monate ago | 1

| accepted

Answered
During SSA simulation of sbml model using sbiosimulate, observables are not saved.
Hi Torkel, The model in the SBML file defines assignment rules, which are imported into SimBiology as repeated assignment rules...

7 Monate ago | 0

Answered
Import XML File to Simbiology
Hi Aditi, The SBML model in the supplemental material of the paper you are citing imports without error on my computer in MATLA...

7 Monate ago | 0

Answered
Using 'time' in observable expressions
Hi Abed, when evaluating expressions of observables, SimBiology first tries to determine whether the result is a scalar value o...

8 Monate ago | 0

| accepted

Answered
Can anyone help me in fitting a SVEAIHR epidemic model to the observe data please?
Hi Sonam, Following up on Steven's comment, here are a few general links that may be helpful for how to fit models to data in S...

8 Monate ago | 1

Answered
MPGSA questions regarding plot visualizations and log-distributed sampling
Hello Abed, You can use the name-value pair Parameters in the plot or histogram methods to selectively visualize GSA results. Y...

9 Monate ago | 0

Answered
Pre-equilibrating models when performing global sensitivity analyses
Hi Abed, You can chain a steady-state analysis and a global sensitivity analysis. For this you first have to run sbiosteadystat...

10 Monate ago | 0

| accepted

Answered
Formatting for 'addobservables'
Hi Shaun, expressions of SimBiology observables can only reference names of components on the model, or functions on the Matlab...

11 Monate ago | 1

| accepted

Answered
How to organize plot of sbiosobol results
Hello Jesse, You can use the name-value arguments "Parameters" and "Observables" of the plot and bar functions to specify which...

11 Monate ago | 1

| accepted

Answered
Simulate different dosing amounts with a schedule dose
Hello, parameterized schedule doses are currently not supported (Matlab release R2021b), only repeat doses can be parameterized...

11 Monate ago | 1

| accepted

Answered
Export scan's results to excel using MacOS
Hello, You should be able to export the simulation results on Mac as well as on Windows. Which version of Matlab are you using?...

etwa ein Jahr ago | 1

| accepted

Answered
How to align diagram blocks, species, etc.?
Hi, Unfortunately, the alignment tools are not available in the SimBiology Model Builder app in Matlab R2020b. Alignment tools ...

etwa ein Jahr ago | 0

Answered
Global sensitivity analysis: Can the first order effect be greater than the total order effect?
Hi, You are right that first order Sobol indices are always smaller than or equal to the corresponding total order Sobol indic...

mehr als ein Jahr ago | 1

Answered
Exporting SimBiology model with custom units
Hi, Thank you for reporting this issue. There is a bug in sbmlexport, it should be able to export your custom unit. We are loo...

mehr als ein Jahr ago | 0

Answered
Export SimBiology HTML and diagram
Hi, as of SimBiology (R2021a) exporting the model to HTML is only supported in the SimBiology Model Builder app. Functionality ...

mehr als ein Jahr ago | 0

Submitted


Global Sensitivity Analysis for SimBiology
Compute Sobol indices and perform a multiparametric global sensitivity analysis (MPGSA) of model responses.

mehr als ein Jahr ago | 13 downloads |

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Answered
Parameter transformation in sbiofitmixed
Hi Ben, An alternative idea would be to compute a confidence interval for the fixed effects (for example, estimatedValue + [-1....

mehr als ein Jahr ago | 0

Answered
Handling incorrect parameter values in sbiofit and sbiofitmixed
Hello Czakó, Unfortunately, it is currently not possible to stop model simulations in SimBiology programatically. A better erro...

mehr als ein Jahr ago | 0

| accepted

Answered
Combine two models in simbiology, where one of them is a species.
Hi Sudharsana, It sounds like the copy-paste tool in the graphical user interface for SimBiology could help in your case. To op...

mehr als ein Jahr ago | 1

| accepted

Answered
Mathematical calculation required for how matlab simbiology performs local sensitivity analysis for a set of ODEs in simbiology model analyzer. (https://www.mathworks.com/help/simbio/ug/perform-sensitivity-analysis-for-tumor-growth.html)
Hi Darshna, Here is a link with some information for how to interpret the sensitivity (time/bar) plots. The reported values, an...

mehr als ein Jahr ago | 0

| accepted

Answered
Percentage perturbation in Simbiology Local Sensitivity Analysis (https://www.mathworks.com/help/simbio/ug/perform-sensitivity-analysis-for-tumor-growth.html)
Hi Darshna, the sensitivities you are referring to are local derivatives. SimBiology integrates a system of differential equati...

mehr als ein Jahr ago | 0

| accepted

Answered
Unit testing on Simbiology created model
Hi Andrew, That's an interesting project you are investigating! Below are a couple thoughts on how you could go about testing b...

etwa 2 Jahre ago | 1

| accepted

Answered
In Simbiology, how to analyze sensitivity analysis?
Hi, SimBiology supports different ways to analyze sensitivities. Here is a documentation page with an overview and links to dif...

mehr als 2 Jahre ago | 0

| accepted

Submitted


Model Debugger for SimBiology
The Model Debugger for SimBiology lets you analyze model responses, model structure, and expressions during simulations.

mehr als 2 Jahre ago | 5 downloads |

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Answered
Simulating multiple model parameterizations using scenarios and simfunctions
Hi Abed, The short answer why you see the error message is that the SimFunction is being created with one dose input, and it is...

fast 3 Jahre ago | 0

Answered
parfor error for global SA Morris method using SimBiology
Hi, It looks like you are running into an issue that the SimBiology model is not copied to the workers natively. In MATLAB vers...

etwa 3 Jahre ago | 3

| accepted

Answered
Computed parameter in Simbiology
Hi Rajeev, You could call the function getequations on your model, getequations(m1). This gives you a printout of the values. I...

etwa 3 Jahre ago | 0

| accepted

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