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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 ...

mehr als ein Jahr vor | 0

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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...

fast 2 Jahre vor | 1

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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 ...

fast 2 Jahre vor | 0

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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 ...

fast 2 Jahre vor | 0

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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...

fast 2 Jahre vor | 0

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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...

fast 2 Jahre vor | 1

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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...

fast 2 Jahre vor | 0

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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...

fast 2 Jahre vor | 0

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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...

etwa 2 Jahre vor | 0

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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 ...

etwa 2 Jahre vor | 0

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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.

etwa 2 Jahre vor | 0

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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...

etwa 2 Jahre vor | 0

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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...

etwa 2 Jahre vor | 0

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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 ...

etwa 2 Jahre vor | 0

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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...

etwa 2 Jahre vor | 0

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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...

etwa 2 Jahre vor | 0

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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...

mehr als 2 Jahre vor | 0

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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...

mehr als 2 Jahre vor | 1

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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 ...

mehr als 2 Jahre vor | 1

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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...

mehr als 2 Jahre vor | 1

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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...

mehr als 2 Jahre vor | 0

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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...

mehr als 2 Jahre vor | 1

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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...

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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...

mehr als 2 Jahre vor | 0

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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...

mehr als 2 Jahre vor | 0

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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)/...

mehr als 2 Jahre vor | 0

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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...

mehr als 2 Jahre vor | 0

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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...

mehr als 2 Jahre vor | 0

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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...

mehr als 2 Jahre vor | 0

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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...

mehr als 2 Jahre vor | 0

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