Answered
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 ...

9 months ago | 0

Answered
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.

9 months ago | 0

Answered
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...

10 months ago | 0

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Answered
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...

10 months ago | 0

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Answered
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 ...

10 months ago | 0

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Answered
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...

11 months ago | 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...

11 months ago | 0

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Answered
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...

12 months ago | 0

Answered
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...

12 months ago | 1

Answered
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 ...

12 months ago | 1

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Answered
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...

1 year ago | 1

Answered
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...

1 year ago | 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...

1 year ago | 1

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Answered
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...

1 year ago | 0

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Answered
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...

1 year ago | 0

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Answered
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...

1 year ago | 0

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Answered
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)/...

1 year ago | 0

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Answered
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...

1 year ago | 0

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Answered
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...

1 year ago | 0

Answered
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...

1 year ago | 0

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Answered
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...

1 year ago | 0

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Answered
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...

1 year ago | 0

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Answered
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 ...

1 year ago | 0

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Should plasma membrane be its own compartment?
Yes, I think the simplest approach would be to create separate compartments for each location where you need to consider that sp...

1 year ago | 0

Answered
Different units in the same Simbiology model
I would recommend against mixing mass-based units and mole-based units for species participating in the same reaction. In such c...

1 year ago | 2

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Answered
Status 429 with message "Too Many Requests" in response to NCBI URL
As described here, you are seeing the error because NCBI limits the number of queries from a particular IP address to 3 per seco...

1 year ago | 0

Answered
eGPU set up for Simbiology calculation
No, SimBiology does not currently have any built-in support for GPU calculations. I suggest profiling to see what code is takin...

1 year ago | 0

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Answered
What toolboxes are useful to run with SimBiology?
I recommend simulating your model within SimBiology (that is, using SimBiology's ODE solvers rather than exporting your equation...

1 year ago | 0

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Answered
Apply Parallel Computing to Simbiology
Hi Jesse, The simplest fix would be to change 'ProgressPlot',true to 'ProgressPlot',false. The issue is that you're trying to c...

1 year ago | 2

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Answered
Command in Script for Data Comparison
Hi, Are you using the functions sbiofit or sbiofitmixed? If so, you will find RMSE, AIC, and BIC as properties on the first out...

1 year ago | 1

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