Florian Augustin

Last seen: Today | Active since 2018

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

2 months ago | 7 downloads |

Answered
pcsk9Model example model showed different number of parameters between command and workspace
Hi Jesse, the model component CholesterolIntakeDiet is a reaction-scoped parameter and needs to be referenced by it's "qualifie...

1 year ago | 0

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Submitted

Feature Ranking for SimBiology
Rank importance of parameters in a SimBiology model for parameter estimation.

2 years ago | 2 downloads |

Submitted

Bayesian Parameter Estimation for SimBiology
Bayesian parameter estimation to fit SimBiology models to data using a constant (Gaussian) error model.

2 years ago | 2 downloads |

Answered
Why the color of bar plot of elementary effects is so light?
Hi, There is a way to change the color, but I would like explain those bar plots a little. They color-code a histogram of the s...

2 years ago | 1

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Answered
How to plot a single answerName with confidence intervals for model predictions?
Hi Valentina, maybe the function selectivePlotCI from this MATLAB Answers post could help. With this function, you can select w...

2 years ago | 1

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

2 years ago | 0

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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 ...

2 years ago | 1

Answered
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...

2 years ago | 0

Answered
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 years ago | 0

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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 years ago | 0

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...

2 years ago | 0

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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 years ago | 0

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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 years ago | 0

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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...

2 years ago | 1

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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...

2 years ago | 0

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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...

3 years ago | 0

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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...

3 years ago | 0

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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...

3 years 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...

3 years 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...

3 years ago | 0

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

3 years ago | 1

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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...

3 years ago | 1

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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...

3 years ago | 1

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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?...

3 years ago | 1

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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 ...

3 years ago | 0

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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...

3 years ago | 2

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...

3 years 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 ...

3 years ago | 0

Submitted

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

3 years ago | 10 downloads |

Florian Augustin

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