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**Content Feed**

Possible ways to test SimBiology model robustness

The closest thing I can think of off the top of my head is cross-validation. Maybe you want to take a look at this page and see ...

7 dagen ago | 0

How to add noise in SimBiology analyzer app

Hi, I can't think of a way to add noise using just the SimBiology Model Analyzer app. I think you will need to export the data ...

12 dagen ago | 0

| accepted

Reaction continues even after the concentration is below zero in Simbiology

I answered a similar question here. As I mention there, there's currently no way to completely prevent negative numbers in all c...

21 dagen ago | 0

| accepted

Simbiology plot problem when using global solvers

Can you share the project or provide some other way for us to reproduce what you're seeing? That would help us definitely say wh...

ongeveer een maand ago | 1

How to introduce a delay in a simbiology model?

SimBiology does not directly support delays. One approach would be a more mechanistic model of the delay. For exampe, you might...

ongeveer een maand ago | 0

How can I estimate PD parameters for two - compartment model?

I looked at the project you attached in the comments. I didn't see any obvious problems. Your parameter estimates are within a f...

ongeveer een maand ago | 0

| accepted

Creating a 3-D bar graph with parameter sensitivities with respect to all model species

I'm guessing the configset is not configured for sensitivity analysis. You probably need to do something like the following befo...

2 maanden ago | 0

| accepted

How to plot categorical data to compare with SimBiology simulation result?

If I understand your question, you're primarily asking how to extract the simulation results at a specific time (for example, 5 ...

2 maanden ago | 0

Excluding C and N terminus from Isoelectric calculation

I think you want to set the N_term and C_term entries to 7.0 rather than 0.0, since 7.0 is the the "neutral" pK value.

3 maanden ago | 0

Can we estimate different variance of the error model for different data set in NLME Simbiology?

I don't completely understand your workflow, but my guess is that this is not possible today with the NLME methods provided in M...

3 maanden ago | 0

| accepted

SimBio: Running Stochastic SSA Simulation of SBML imported model

First, a little background on why you're seeing this behavior. SBML does not indicate whether a particular reaction follows mass...

4 maanden ago | 0

| accepted

Any progress on relaxing the constraints on species units?

I'd love to pick your brain about exactly what you need and expect from such functionality! Which is to say that today species ...

4 maanden ago | 0

| accepted

dose dependence in simbiology model

I think the answer depends on how, mathematically, you want to model dose-dependent absorption. You can easily create various PK...

4 maanden ago | 0

Error while validating MEX Setup

Hi, This is a warning, not an error. You can still use SimBiology. But if you install a supported compiler, you should see fitt...

5 maanden ago | 0

How to consider steady state concentration of biomarker in Simbiology

The SimBiology app does not currently provide any direct way to automatically fit steady state data. However, if I'm correctly u...

5 maanden ago | 0

make a data plot

This looks to me like a horizontally oriented box plot. You can easily create such plots using boxchart or boxplot. Since you wa...

5 maanden ago | 1

How do I use global solver to estimate parameters in SimBiology R2021A

I would not read too much into this message. It simply explains why the optimization stopped when it did. In and of itself that ...

5 maanden ago | 1

| accepted

Work with ODE model system in Simbiology

Not silly at all. That's a pretty common question. The easiest and most direct way to convert such a model over to SimBiology is...

6 maanden ago | 1

Is volume capacity required to fit PK data in simbiology?

Let me first make sure I understand your question. I think you want to estimate the volume of peripheral and central compartment...

6 maanden ago | 0

Model fitting using different data sets in SimBiology

Would it be possible for you to upgrade to R2021b? There's a new feature in that release that would make it much easier to do wh...

7 maanden ago | 1

| accepted

How to assess to the simulation data after the parameter estimation in Simbiology

Hi Jesse, You can get access to the SimData results used in the plot method by calling the fitted method (described here). If y...

7 maanden ago | 0

| accepted

Simulation of tissue drug concentration profile with Kp values

If you are looking for an example of how to incorporate tissue partition coefficients into a PBPK model, then perhaps you can us...

7 maanden ago | 0

| accepted

How to set boundary conditions for a reaction to occur in SimBiology?

Hi, Take a look at this answer I shared. It's from several years ago, but the information is still accurate. Some additional ti...

8 maanden ago | 0

| accepted

Invalid assignment syntax or parse error for event function (Simbiology)

Hi, Events can only assign a value to a component, not to an expression. So your assignment ((syn_CT.PD1_PDL1+syn_CT.PD1_PDL2)/...

8 maanden ago | 0

| accepted

How to customize built-in optimization functions in SimBiology without using MATLAB code?

If I understand your question correctly, you are asking how to customie the cost (or objective) function when using a fit progra...

8 maanden ago | 0

| accepted

why PSI values are diffrent when nlmefit using ode45 solver compared to when it uses analytical solution?

The reason the results from nlmefit differ significantly is because your ODE solution is not equivalent to your analyitical solu...

9 maanden ago | 0

Scanning Simbiology variants in Matlab for virtual population simulations

There are lots of ways you could do this. And you certainly could use variants. But I personally would do this by creating a Sim...

9 maanden ago | 0

| accepted

How do I generate a rectangular pulse for an input species in Simbiology?

I would not use rules to implement discontinuous changes in a SimBiology model. The ODE solver should be restarted whenever ther...

9 maanden ago | 0

| accepted

Error: expected the time data (independent variable) of the data input argument to be finite

This error means that your time data is invalid because it contains non-finite values. Look for infinite or NaN (not a number) v...

9 maanden ago | 0

| accepted

use simbiology for radiation dosimetry

SimBiology is primarily designed to model reactions of species in compartments. It can be used to model other problems that are ...

9 maanden ago | 0