Risposto
Is specifying objective fuction for multiple variables in SimBiology possible?
It depends on what you mean by "possible." :-) If you're using a fit program in the SimBiology Model Analyzer app or the functio...

oltre un anno fa | 0

| accettato

Risposto
How to add programmatically (using command line) add a program to a simbiology model?
This is not currently possible but is something we would consider adding in a future release. Until then, you will need to creat...

quasi 2 anni fa | 0

| accettato

Risposto
Incorrect units in simple reaction in SimBiology?
This is a bug in SimBiology. SimBiology checks that all species participating in a reaction have dimensionally consistent units....

quasi 2 anni fa | 0

| accettato

Risposto
Estimating Parameter That Satisfies Minimal Efficacy
Here's a high-level description of how I'd do this in the Analyzer App: Create and run a simulation program that determines the...

quasi 2 anni fa | 1

Risposto
Time after last dose
I haven't read the article, so I don't know how the TAD parameter is used. I'm assuming you need to know TAD during the simulati...

quasi 2 anni fa | 0

| accettato

Risposto
Automatic generation of SimBiology code from GUI
There is not currently any shipping functionality to do this. However, this is something we've been thinking about for a future ...

quasi 2 anni fa | 0

| accettato

Risposto
Specifying a cost function to optimize a simbiology model response to plausible ranges
Fearass and I had a chat about this. I figured out that the cost function is essentially a modification of some of squares of re...

quasi 2 anni fa | 1

| accettato

Risposto
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 ...

quasi 2 anni fa | 0

Risposto
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 ...

quasi 2 anni fa | 0

| accettato

Risposto
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...

quasi 2 anni fa | 0

| accettato

Risposto
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...

quasi 2 anni fa | 1

| accettato

Risposto
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...

circa 2 anni fa | 0

Risposto
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...

circa 2 anni fa | 0

| accettato

Risposto
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...

circa 2 anni fa | 0

| accettato

Risposto
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 ...

circa 2 anni fa | 0

Risposto
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.

circa 2 anni fa | 0

Risposto
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...

circa 2 anni fa | 0

| accettato

Risposto
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...

circa 2 anni fa | 0

| accettato

Risposto
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 ...

circa 2 anni fa | 0

| accettato

Risposto
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...

circa 2 anni fa | 0

Risposto
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...

oltre 2 anni fa | 0

| accettato

Risposto
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...

oltre 2 anni fa | 0

Risposto
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...

oltre 2 anni fa | 1

Risposto
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 ...

oltre 2 anni fa | 1

| accettato

Risposto
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...

oltre 2 anni fa | 1

Risposto
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...

oltre 2 anni fa | 0

Risposto
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...

oltre 2 anni fa | 1

| accettato

Risposto
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...

oltre 2 anni fa | 0

| accettato

Risposto
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...

oltre 2 anni fa | 0

| accettato

Risposto
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...

oltre 2 anni fa | 0

| accettato

Carica altro