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...

6 years 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...

6 years 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...

7 years 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...

7 years 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...

7 years 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...

7 years 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...

7 years 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...

7 years 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...

7 years 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...

7 years 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 ...

7 years 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...

7 years 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...

7 years 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...

7 years 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:...

7 years 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...

7 years 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...

7 years ago | 1

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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...

7 years 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...

7 years 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...

7 years 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...

7 years 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...

7 years 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...

7 years 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...

7 years 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...

7 years 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...

7 years 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...

7 years 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...

7 years 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...

7 years ago | 0

Answered
SimBiology Desktop Fitting using Concentration and response time profiles
The SimBiology documentation includes <https://www.mathworks.com/help/search.html?qdoc=sbiofit+type%3Aex several examples> that ...

7 years ago | 0