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Florian Augustin

Last seen: 2 días hace Con actividad desde 2018

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Respondida
Variants in SimBiology debugger
Hi Abed, Yes, you can specify configuration set, doses and variants when starting the debugger. This is currently undocumented,...

20 días hace | 0

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Respondida
Help with Units of species and simulation run error messages
Hi Christos, the SimBiology model uses a custom unit "nmolar". Custom units are currently (R2022b) not bundled with SimBiology ...

22 días hace | 1

Respondida
sbiopredictionci with bootstrap method dealing with data with NaN
Hi Jesse, It looks like you used optimization options for particle swarm optimization when you used lsqnonlin to estimate the p...

alrededor de 1 mes hace | 0

Respondida
selecting and re-assignment of non-existing parameters in SimBiology does not trigger any warning?
Hi, sbioselect returns all objects in the SimBiology model that matches the search query; in your case all model components who...

2 meses hace | 0

Respondida
Errors about the species in different compartments have different unit
Hi, Just to follow up on emjey's comment. The error message indicates that some of your reactions are dimensionally inconsisten...

2 meses hace | 0

Respondida
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...

3 meses hace | 0

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Respondida
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, ...

5 meses hace | 0

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Respondida
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...

5 meses hace | 0

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Respondida
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...

6 meses hace | 1

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Respondida
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...

9 meses hace | 0

Respondida
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...

10 meses hace | 0

Respondida
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...

10 meses hace | 0

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Respondida
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...

10 meses hace | 1

Respondida
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...

11 meses hace | 0

Respondida
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...

alrededor de 1 año hace | 0

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

alrededor de 1 año hace | 1

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Respondida
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...

alrededor de 1 año hace | 1

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Respondida
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...

alrededor de 1 año hace | 1

| aceptada

Respondida
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?...

más de 1 año hace | 1

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Respondida
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 ...

más de 1 año hace | 0

Respondida
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...

más de 1 año hace | 1

Respondida
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...

más de 1 año hace | 0

Respondida
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 ...

más de 1 año hace | 0

Enviada


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

más de 1 año hace | 10 descargas |

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

más de 1 año hace | 0

Respondida
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...

más de 1 año hace | 0

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Respondida
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...

casi 2 años hace | 1

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Respondida
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...

casi 2 años hace | 0

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Respondida
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...

casi 2 años hace | 0

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Respondida
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...

alrededor de 2 años hace | 1

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