# Sietse Braakman

### MathWorks

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**Feeds**

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...

mer än 3 år ago | 0

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...

mer än 3 år ago | 0

| accepted

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...

mer än 3 år ago | 0

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...

mer än 3 år ago | 1

| accepted

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 ...

nästan 4 år ago | 0

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...

nästan 4 år ago | 1

| accepted

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...

nästan 4 år ago | 1

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...

nästan 4 år ago | 0

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 ...

nästan 4 år ago | 1

| accepted

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...

nästan 4 år ago | 1

| accepted

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,...

ungefär 4 år ago | 1

| accepted

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 ...

ungefär 4 år ago | 0

| accepted

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...

ungefär 4 år ago | 2

| accepted

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...

mer än 4 år ago | 0

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 ...

mer än 4 år ago | 2

| accepted

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...

mer än 4 år ago | 0

| accepted

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...

mer än 4 år ago | 1

| accepted

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 ...

mer än 4 år ago | 1

| accepted

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 ...

mer än 4 år ago | 0

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...

mer än 4 år ago | 0

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...

mer än 4 år ago | 0

| accepted

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...

mer än 4 år ago | 0

| accepted

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 ...

nästan 5 år ago | 0

| accepted

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...

nästan 5 år ago | 1

| accepted

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...

nästan 5 år ago | 1

| accepted

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...

ungefär 5 år ago | 0

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...

ungefär 5 år ago | 0

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...

ungefär 5 år ago | 1

| accepted

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 ...

ungefär 5 år ago | 1

| accepted

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...

ungefär 5 år ago | 0

| accepted