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...

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...

15 days ago | 1

| accepted

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...

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...

19 days 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...

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...

29 days 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 ...

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 ...

1 month ago | 1

| accepted

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...

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...

1 month ago | 1

| accepted

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,...

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,...

2 months ago | 1

| accepted

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 ...

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 ...

3 months ago | 0

| accepted

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...

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 months ago | 2

| accepted

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...

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...

5 months 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 ...

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 ...

5 months ago | 2

| accepted

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...

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...

5 months ago | 0

| accepted

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...

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 months ago | 1

| accepted

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 ...

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 ...

8 months ago | 1

| accepted

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 ...

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 ...

9 months 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...

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...

10 months 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...

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...

10 months ago | 0

| accepted

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...

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...

10 months ago | 0

| accepted

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 ...

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 ...

12 months ago | 0

| accepted

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...

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...

12 months ago | 1

| accepted

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...

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...

1 year ago | 1

| accepted

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...

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...

1 year 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...

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...

1 year 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...

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...

1 year ago | 1

| accepted

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 ...

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 ...

1 year ago | 1

| accepted

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...

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...

1 year ago | 0

| accepted

Answered

reproducing sensitivities from MATLAB GUI

A typical use case for this question is when calculating a sensitivity on species C, where species C is a linear combination of ...

reproducing sensitivities from MATLAB GUI

A typical use case for this question is when calculating a sensitivity on species C, where species C is a linear combination of ...

1 year ago | 0

Answered

Is there an object associated with simulate task in the simbiology desktop that contains the name of the task?

Hi Jim, These are good questions. Currently, there is no way to access the task name from the desktop, or from MATLAB. One so...

Is there an object associated with simulate task in the simbiology desktop that contains the name of the task?

Hi Jim, These are good questions. Currently, there is no way to access the task name from the desktop, or from MATLAB. One so...

1 year ago | 0

| accepted

Answered

How do I calculate a confidence interval for a simulation from a PK model?

Since R2017b, SimBiology has two functions to calculate confidence intervals. At the time this question was asked, these functio...

How do I calculate a confidence interval for a simulation from a PK model?

Since R2017b, SimBiology has two functions to calculate confidence intervals. At the time this question was asked, these functio...

1 year ago | 1

| accepted

Answered

How to assign to a SimBiology model a parameter value (known and constant) changing for each data in the dataset for a non-linear mixed effect estimation?

Hi Anne, As of 2018b, there is no easier way to achieve this, other than the method described by Arthur above. We are aware tha...

How to assign to a SimBiology model a parameter value (known and constant) changing for each data in the dataset for a non-linear mixed effect estimation?

Hi Anne, As of 2018b, there is no easier way to achieve this, other than the method described by Arthur above. We are aware tha...

1 year ago | 0

Answered

Infinite StandardError with sbiofit

Fitting problems like the one Hussein describes tend to be difficult to troubleshoot online, especially when the model/data cann...

Infinite StandardError with sbiofit

Fitting problems like the one Hussein describes tend to be difficult to troubleshoot online, especially when the model/data cann...

1 year ago | 0

| accepted