Answered

What is the difference between BoundaryCondition and ConstantAmount?

Constant=true means that the value of a species cannot change during the course of a simulation. It can only be modified at time...

What is the difference between BoundaryCondition and ConstantAmount?

Constant=true means that the value of a species cannot change during the course of a simulation. It can only be modified at time...

12 Monate ago | 0

| accepted

Answered

implement quasi zeroth order kinetic in Simbio

Hi, Whenever you have a discontinuous step change like this in your model, you should include either doses or events at the dis...

implement quasi zeroth order kinetic in Simbio

Hi, Whenever you have a discontinuous step change like this in your model, you should include either doses or events at the dis...

12 Monate ago | 0

Answered

Any simulation speed differences between models loaded with SimBiology() vs sbioloadproject?

I don't expect you to see any noticeable performance impact when simulating a model from the command line, while the same model ...

Any simulation speed differences between models loaded with SimBiology() vs sbioloadproject?

I don't expect you to see any noticeable performance impact when simulating a model from the command line, while the same model ...

12 Monate ago | 0

| accepted

Answered

simbiology problem PK PD modeling

Hi, The problem is that the two variables "time" and "drug" in your data were imported as text instead of numbers. I'm not sure...

simbiology problem PK PD modeling

Hi, The problem is that the two variables "time" and "drug" in your data were imported as text instead of numbers. I'm not sure...

12 Monate ago | 0

Answered

How can I find 4 constants values from and indirect fitting value?

I see that the SimBiology product is tagged for this post, but the attached files are not using SimBiology. I'm one of the devel...

How can I find 4 constants values from and indirect fitting value?

I see that the SimBiology product is tagged for this post, but the attached files are not using SimBiology. I'm one of the devel...

etwa ein Jahr ago | 0

Answered

Why does my .sbproj file can't open on other's computer?

This is expected. Please see the following discussion: https://www.mathworks.com/matlabcentral/answers/500762-loading-simbiolog...

Why does my .sbproj file can't open on other's computer?

This is expected. Please see the following discussion: https://www.mathworks.com/matlabcentral/answers/500762-loading-simbiolog...

etwa ein Jahr ago | 0

| accepted

Answered

How to correctly compile a function containing variables with dimension and call it in SimBiology

Hi, The issue you are seeing is addressed in the "Tip" on the documentation for UnitConversion. The problem is that you are ha...

How to correctly compile a function containing variables with dimension and call it in SimBiology

Hi, The issue you are seeing is addressed in the "Tip" on the documentation for UnitConversion. The problem is that you are ha...

etwa ein Jahr ago | 1

Answered

Issues with doses/variants in parfor loop in SimBiology

First, what version of SimBiology are you using? Prior to R2019b, there was a problem that prevented objects from getting sent t...

Issues with doses/variants in parfor loop in SimBiology

First, what version of SimBiology are you using? Prior to R2019b, there was a problem that prevented objects from getting sent t...

etwa ein Jahr ago | 0

Answered

It is possible to add a constant input term (without reaction rate) for a specie in the diagram view in SIMBIOLOGY?

If I understand your question correctly, it sounds like you want to use a rate rule. If you want to build a rate rule in the dia...

It is possible to add a constant input term (without reaction rate) for a specie in the diagram view in SIMBIOLOGY?

If I understand your question correctly, it sounds like you want to use a rate rule. If you want to build a rate rule in the dia...

etwa ein Jahr ago | 0

| accepted

Answered

error saying "dimentional analysis failed for reaction."

Yes, nanomole is a unit with dimensions of amount, and nanomolar is a unit with dimensions of concentration. Can you share your...

error saying "dimentional analysis failed for reaction."

Yes, nanomole is a unit with dimensions of amount, and nanomolar is a unit with dimensions of concentration. Can you share your...

etwa ein Jahr ago | 0

Answered

SUNDIALS installation in MATLAB

What exactly did you download? Can you provide the website or download link? I'm not sure how we can help you without knowing mo...

SUNDIALS installation in MATLAB

What exactly did you download? Can you provide the website or download link? I'm not sure how we can help you without knowing mo...

mehr als ein Jahr ago | 0

Answered

What is smooth curve?

I'm not sure I fully understand your question. If you're asking what the checkbox labeled "Show smooth curve" does, you can see...

What is smooth curve?

I'm not sure I fully understand your question. If you're asking what the checkbox labeled "Show smooth curve" does, you can see...

mehr als ein Jahr ago | 0

Answered

Namespace and other html / xml information in SimBiology Notes

I would recommend either plain text or XHTML 1.0 as your format. sbmlexport will export both of these to SBML as XHTML 1.0, whic...

Namespace and other html / xml information in SimBiology Notes

I would recommend either plain text or XHTML 1.0 as your format. sbmlexport will export both of these to SBML as XHTML 1.0, whic...

mehr als ein Jahr ago | 1

| accepted

Answered

Loading simbiology models created in MATLAB 2019b in previous version of MATLAB

In general, we cannot guarantee this kind of compatibility (which is called "forward compatibility"). In practice, SimBiology mo...

Loading simbiology models created in MATLAB 2019b in previous version of MATLAB

In general, we cannot guarantee this kind of compatibility (which is called "forward compatibility"). In practice, SimBiology mo...

mehr als ein Jahr ago | 0

| accepted

Answered

How to implement multiple error model?

It depends on whether you are doing nonlinear regression or nonlinear mixed-effects modeling. If you are doing nonlinear regress...

How to implement multiple error model?

It depends on whether you are doing nonlinear regression or nonlinear mixed-effects modeling. If you are doing nonlinear regress...

mehr als ein Jahr ago | 0

| accepted

Answered

seqpdist Kimura "method not available for amino acids" even though working with nucleotides

As Geoff points out in the comments, the problem is that several of the default option values don't work for the Kimura distance...

seqpdist Kimura "method not available for amino acids" even though working with nucleotides

As Geoff points out in the comments, the problem is that several of the default option values don't work for the Kimura distance...

mehr als ein Jahr ago | 0

| accepted

Solved

Aquiles y la tortuga

Contaba Zenón en su famosa paradoja que un día Aquiles, el guerrero griego más veloz de la Hélade, se enfrentó a una pequeña tor...

mehr als ein Jahr ago

Answered

Microarray Analysis Trouble in Analysis

Let me make sure I understand your problem. You are trying to run the following example: https://uk.mathworks.com/help/bioinfo/...

Microarray Analysis Trouble in Analysis

Let me make sure I understand your problem. You are trying to run the following example: https://uk.mathworks.com/help/bioinfo/...

mehr als ein Jahr ago | 0

Answered

Simbiology Stochastic solvers non mass action (nonlinear) propensities

Hi, You correctly understand the current constraints of SimBiology's stochastic solver: reactions must use linear, mass action ...

Simbiology Stochastic solvers non mass action (nonlinear) propensities

Hi, You correctly understand the current constraints of SimBiology's stochastic solver: reactions must use linear, mass action ...

mehr als ein Jahr ago | 1

| accepted

Answered

Restricting output times when calling simfunctions

Yes, if you use tStop = [], then only results at tOutput will be reported.

Restricting output times when calling simfunctions

Yes, if you use tStop = [], then only results at tOutput will be reported.

mehr als ein Jahr ago | 0

| accepted

Answered

Diagnosing simfunction acceleration failure

Hi Abed, There is currently no publicly documented way to get additional debugging information. These situations have historica...

Diagnosing simfunction acceleration failure

Hi Abed, There is currently no publicly documented way to get additional debugging information. These situations have historica...

mehr als ein Jahr ago | 0

| accepted

Answered

Stopping simulation early on event

Hi Abed, Interesting question. The only way an event can stop a simulation early is if the event errors. sbiofit would handle s...

Stopping simulation early on event

Hi Abed, Interesting question. The only way an event can stop a simulation early is if the event errors. sbiofit would handle s...

mehr als ein Jahr ago | 0

| accepted

Answered

Constant parameter setting throws error, or... if I don't set a parameter to constant, but don't change it, does it stay constant?

Great feedback as always, Jim. As for your immediate questions: "If I leave the parameter variable all the time, but nothing i...

Constant parameter setting throws error, or... if I don't set a parameter to constant, but don't change it, does it stay constant?

Great feedback as always, Jim. As for your immediate questions: "If I leave the parameter variable all the time, but nothing i...

mehr als ein Jahr ago | 0

| accepted

Answered

deleting or removing variant using variant array handle gives unexpected results.

I know it's confusing, and I'll try to explain what's going on. But let me start by saying that the behavior you're seeing is wh...

deleting or removing variant using variant array handle gives unexpected results.

I know it's confusing, and I'll try to explain what's going on. But let me start by saying that the behavior you're seeing is wh...

mehr als ein Jahr ago | 1

| accepted

Answered

Error model with curve-fitting

SimBiology's error models are only available when fitting data to SimBiology models using functions like sbiofit. If you are dir...

Error model with curve-fitting

SimBiology's error models are only available when fitting data to SimBiology models using functions like sbiofit. If you are dir...

mehr als ein Jahr ago | 0

| accepted

Answered

Mass balance issues with PBPK model in Simbiology

One way to confirm that that your model structure is correct is to use SimBiology sbioconsmoiety function to identify conserved ...

Mass balance issues with PBPK model in Simbiology

One way to confirm that that your model structure is correct is to use SimBiology sbioconsmoiety function to identify conserved ...

mehr als ein Jahr ago | 0

| accepted

Answered

Add multiple doses in ODEsolver

Because doses introduce discontinuities in the solution, you basically need to stop the ODE simulation every time a dose is appl...

Add multiple doses in ODEsolver

Because doses introduce discontinuities in the solution, you basically need to stop the ODE simulation every time a dose is appl...

mehr als ein Jahr ago | 0

| accepted

Answered

Can I force Matlab to wait 'til it finishes one command to run another?

Hi Jim, The previous responses are correct: The simbiology command returns before the desktop completely loads the project, bec...

Can I force Matlab to wait 'til it finishes one command to run another?

Hi Jim, The previous responses are correct: The simbiology command returns before the desktop completely loads the project, bec...

mehr als ein Jahr ago | 1

| accepted

Answered

How to handle warnings in SimBiology within series of simulations?

Hi, It's difficult to say for sure whether you can trust the simulation results when you see this warning. I would definitely e...

How to handle warnings in SimBiology within series of simulations?

Hi, It's difficult to say for sure whether you can trust the simulation results when you see this warning. I would definitely e...

mehr als ein Jahr ago | 1

| accepted

Answered

Issue with SimBiology - parameters from valid .sbproj not loading

As described here, parameters can be scoped to either the model or to a reaction. The display counts both scopes of parameters, ...

Issue with SimBiology - parameters from valid .sbproj not loading

As described here, parameters can be scoped to either the model or to a reaction. The display counts both scopes of parameters, ...

mehr als ein Jahr ago | 1

| accepted