Answered
Fitting multiple dependent variables with time less than zero
Right now, SimBiology simulations always have to start at zero. So for your problem, you'd have to adjust the data with an offse...

meer dan 2 jaar ago | 0

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Answered
Can more than one model be used for " fit data" in Simbiology
No, SimBiology’s built-in fitting capabilities only support fitting one model to one dataset. If I needed to do this, I would ch...

meer dan 2 jaar ago | 0

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Answered
Getting the following error repeatedly for different error setting other than exponential error in population PK PD modelling in Simbiology.
As a general rule, you will need to address anything that causes an error, while a warning indicates something that may or may n...

meer dan 2 jaar ago | 0

Answered
SimBiology - sundials - ODE solver - CVODE
Hi Mary, It is technically possible to use arbitrary MATLAB functions with SimBiology. So you could in theory create a SimBiolo...

bijna 3 jaar ago | 0

Answered
SimBiology - sundials - ODE solver - CVODE
Hi Mary, You are correct that MaximumNumberOfLogs and MaximumWallClock are SimBiology-specific options. In order to simulate y...

bijna 3 jaar ago | 0

Answered
ODE Events In SimBiology toolbox
Currently (as of R2019a), SimBiology events cannot directly stop a simulation. I usually handle this sort of situation by post-p...

bijna 3 jaar ago | 0

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Answered
Simbiology Sensitivity analysis on dummy variable assigned through a repeatedAssignment Rule
One approach is to analytically differentiate the repeated assignment rule, and figure out how to calculate the desired sensitiv...

bijna 3 jaar ago | 0

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Answered
Tgspcread function error (line 323)
I think this is a bug in how the function tries to find out the size of the SPC file. You will see this error if the file is loc...

bijna 3 jaar ago | 0

Answered
"Too many input arguments" error while running clustergram (Bioinformatics toolbox)
I suspect there is a function in your installation that is "shadowing" some other MATLAB function used by clustergram. I would t...

bijna 3 jaar ago | 0

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Answered
Debugging NaN/Inf right-hand-side values in SimBIology
Hi Abed, There's not currently any documented way to do this sort of debugging. We know that's a pain, so we're working on a de...

bijna 3 jaar ago | 0

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Answered
I Want a one line FASTA!
The fastawrite has a hard-coded limit of 70 characters per line. This follows NCBI recommendations. If you want to incease the m...

bijna 3 jaar ago | 1

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Answered
nlme fitting error for covariate in popPK model
Hi Jim, Here are the answers to your question: 1) SimBiology's covariate model expressions are quite constrained. The problem ...

ongeveer 3 jaar ago | 0

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Answered
Do simfunctions support parameterized dosing?
Yes, parameterized doses are supported with SimFunctions. However, you cannot change the type of parameterization after creating...

ongeveer 3 jaar ago | 0

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Answered
Simbiology: using a dummy species to fit data to a sum of real species with sbiofit
I think your idea is reasonable. I believe the problem is with the rule you added. As written, |addrule| adds an initial assignm...

ongeveer 3 jaar ago | 0

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Answered
Help with code to convert Simbiology sbproj file into gPKPDSim session file in .mat format
Ah, I finally figured out what's going on. The function "which" can only be used to locate files that are in the current working...

ongeveer 3 jaar ago | 0

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Answered
Help with code to convert Simbiology sbproj file into gPKPDSim session file in .mat format
See if your problem is fixed by using two slashes when you define |PathName|. That is, change the line of code to the following:...

ongeveer 3 jaar ago | 0

Answered
how do I assign values to parameters in simbiology model from a .m file?
I'm guessing that some of your parameters are scoped to reactions. First, some background: In SimBiology, <https://www.mathwo...

ongeveer 3 jaar ago | 0

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Answered
I get a mavolcanoplot error and am not sure what it means
I looked at the code for this function. It looks like you are are getting the wrong error message due to a bug in the Bioinforma...

ongeveer 3 jaar ago | 1

| accepted

Answered
How does SimBiology calculate the "lambda" in NCA?
Hi, Currently (as of R2018b), SimBiology's NCA uses linear regression with all of the points weighted equally. I'm guessing t...

meer dan 3 jaar ago | 0

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Answered
Can I create a variant that captures all current parameter, species and compartment values?
You're not overlooking anything. We just need to make variants easier to use. Right now, I would probably do this by making a he...

meer dan 3 jaar ago | 0

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Answered
IS there a simple way to suppress the pop-up figure which is created automatically when calling clustergram()?
Since |clustergram| was designed to visualize data, there is not currently a documented way to keep a figure from appearing. How...

meer dan 3 jaar ago | 0

Answered
Better understanding of variants sought (also project files)
Hi Jim, Variants (and doses) are handled differently than the objects you see listed in the display for a model. As you disco...

meer dan 3 jaar ago | 0

Answered
Not finding info on arrays of variant objects
Hi Jim, Sorry this wasn't clear from the documentation. I think [var1 var2] should have worked. Here are some equivalent ways...

meer dan 3 jaar ago | 0

Answered
'MassAction' versus 'unknown' kinetic law (SimBiology)
Hi Maciej, This is a good question. We do document what SimBiology does <https://www.mathworks.com/help/simbio/ug/libraries.h...

meer dan 3 jaar ago | 1

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Answered
Could Simbiology simulations have a preload function?
Hi Jim, You're not overlooking any functionality. I agree that these would be useful enhancements. I work primarily from func...

meer dan 3 jaar ago | 0

Answered
How can I parameter estimate many unknown parameters in a system of nonlinear ODE?
I see that you mentioned SimBiology in a comment on the previous answer. I'm a developer on that product, so I wanted to share t...

meer dan 3 jaar ago | 0

Answered
Simbiology Unit testing and Version control
The SimBiology GUI does not have any specific functionality for version control or unit testing. However, you can use the genera...

meer dan 3 jaar ago | 0

Answered
Surface Area Calculations in Simbiology
Hi, In SimBiology, compartments can also represent 2-dimensional areas, such as the surface of a cell. I believe the error yo...

meer dan 3 jaar ago | 0

Answered
Simbiology - limits in fitting
If you are using the function |sbiofit| from the command line, you can specify bounds using the |estimatedInfo| input argument a...

meer dan 3 jaar ago | 0

Answered
how to find growth rate constants?
Are you referring to this example? <https://www.mathworks.com/products/demos/simbiology/anti-cancer-model/anti-cancer-model.html...

meer dan 3 jaar ago | 0

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