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Sietse Braakman

MathWorks

Last seen: 4 years ago |  Active since 2017

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Answered
Modeling Anaerobic Digesters in SimBiology
Dear Anna, With the information you provided, I am a little confused as to what you are trying to do with the rate rule. You ca...

4 years ago | 0

Answered
How to assign a rate constant that will change through time into SimBiology model?
Hi Jesse, You can do this using a repeated assignment and the reserved keyword 'time'. E.g.: Add a species 'drug_release' to...

4 years ago | 0

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Answered
Simbiology data fitting program is constantly running nonstop
Hi Jesse, It is not uncommon for estimation programs to take that long. The duration of the fitting process depends on many fac...

4 years ago | 0

Answered
one valid input/output must be specified in simbiology
Hi Kazutaka, I am assuming you are working in MATLAB R2019b or later and that you are trying to run a simulation. From the me...

4 years ago | 1

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Answered
Data fit in simbiology app with a paramater that changes between groups
Hi Quim, Yes, you can do this by creating a species that you 'dose' with your covariate column. You can then assign the value ...

4 years ago | 0

Answered
condition in which one compartment does not affect the mass balance
Hi Kazutaka, In the example you are following along with (https://www.mathworks.com/help/simbio/ug/model-views.html), the PK pa...

4 years ago | 1

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Answered
Dimensional analysis fail for reaction on simbiology
Hi Chi Chun, The dimensional analysis ensures that the units in your model are consistent. However, this requires you to specif...

4 years ago | 1

Answered
Export model to workspace - missing dose
Hi Jacopo, When you export the model to the MATLAB workspace, by right clickin on the model in SimBiology and selecting 'Export...

4 years ago | 0

Answered
Simbiology stimulation reactions in custom PDPK models
Hi Daniel, It sounds like you're mostly there. For each reaction, you can define the stoichiometry (e.g. null -> x) as well as ...

4 years ago | 1

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Answered
In Simbiology, is it possible to run stochastic simulations with Gillespie’s algorithm?
Hi Hassan, You can do this by choosing a stochastic solver. In the user interface, this can be done by going to the 'Simulatio...

4 years ago | 1

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Answered
How to change dose intervals or activate/deactivate dose during simulations in SimBiology?
Hi Hanwen, If I understand you correctly, you could follow one of two routes: use three separate Repeat Doses. One for day 1,...

4 years ago | 1

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Answered
Question about Simbiology Model Publication
Hi Brett, There are multiple ways to do this: You can share the .sbproj file - this is the easiest way for others to use your ...

4 years ago | 0

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Answered
Unable to add an event block to a reaction rate in SimBiology
Hi Jacopo, The parameter you are adding the event function to, ke, is currently "reaction-scoped". If you change the scope of y...

4 years ago | 2

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Answered
using MaximumWallClock in a loop
I am not sure I understand what you mean by "EndTime". There are two things we need to separate here: the wall clock time (the a...

4 years ago | 0

Answered
using MaximumWallClock in a loop
There is no built-in flag but you could exclude any simulation for which the final time step does not equal your stop-time. Let ...

4 years ago | 2

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Answered
Problem with Fit Data in SimBiology
Hi Valentina, Looking at your description of the problem and the files you attached I have a few thoughts on what could be happ...

4 years ago | 0

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Answered
How to do model fitting to sum up two concentration in simbiology
You can create a species ACRG and use a repeated assignment rule to assign the sum of ACRG1 and ACRG2 to ACRG. The repeated assi...

5 years ago | 1

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Answered
Simulation stop criteria for simfunctions and sbiofit
Hi Abed, Interesting questions - Yes, most settings are inherited from the active configset. The most notable exceptions are ...

5 years ago | 1

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Answered
How do I complete a Visual Predictive Check in Simbiology PopPK sbionlmefitsa
Hi Andy, Thank you for the feedback. To support my suggested approach with a more concrete example, we have written a function ...

5 years ago | 0

Answered
Mass balance issues with PBPK model in Simbiology
Hi Andrew, This might be an integration imprecision in the solver due to tolerances that are not strict enough. Have you trie...

5 years ago | 0

Answered
Is there a listing of functions (such as 'trapz') to use in SimBiology explorer?
Hi Andrew, You could use the following: Cmax: max(Central.Drug_Central) Tmax: time(Central.Drug_Central == max(Central.Drug...

5 years ago | 0

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Answered
How do I complete a Visual Predictive Check in Simbiology PopPK sbionlmefitsa
Hi Andy, Please excuse the late reply. Have you looked into using sbiosampleparameters? This function allows you to sample your...

5 years ago | 0

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Answered
Specifying different variants for different groups in 'sbiofit'
Hi Abed, We get this question quite regularly - the best way to do this currently is by using dosing. What you have to do: In ...

5 years ago | 0

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Answered
How to change model parameter value in exported simbiology model?
Hi Rajeev, To clarify - there are two ways I can interpret your question primarily because 'exporting' a SimBiology model can m...

5 years ago | 1

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Answered
Log likelihood is initially high in FOCE but as the iteration proceeds to greater than 3500 the log likelihood reduces and finally ends with error that maximum iteration has been achieved.
Dear Praveen, Generally, parameter estimation is a complicated topic that inherently has a lot of ambiguity. This makes it dif...

5 years ago | 1

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Answered
Does SimBiology provide a PK model with an infusion turned on and off during simulation?
You can dose your model by adding a dose object (e.g. a Repeat Dose) to the species you want to dose. In the image below, the sp...

5 years ago | 0

Answered
Data Extraction from SimBiology Simulations
It looks like you are on Mac OS - the export to Excel uses the function xlswrite, which unfortunately only works on Windows. h...

5 years ago | 0

Answered
Data Extraction from SimBiology Simulations
Hi Andrew, Assuming you are using the SimBiology app, you can do this by right-clicking on the simulation plot and selecting 'E...

5 years ago | 1

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Answered
TissuePartition Function Inclusion into SimBiology PBPK
Hi Andrew, Are you trying to pull out the values of the partition coefficients or the model equations? In general, SimBiology ...

5 years ago | 1

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Answered
Issues fitting ka parameter
Hi Brett, There are three ways you can approach this: by assuming that the dose is reduced by a factor F, such as Peter sugges...

5 years ago | 0

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