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:...

meer dan 5 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...

meer dan 5 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...

meer dan 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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...

bijna 6 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...

bijna 6 jaar 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 ...

bijna 6 jaar ago | 0

Answered
a training program on PKPD and PBPK
You can find SimBiology PKPD and PBPK resources <https://www.mathworks.com/discovery/pharmacokinetic.html here>.

bijna 6 jaar ago | 0

Answered
How can we use bayesian information in simbiology?
If you want to custom your objective function, you probably cannot use |sbiofit|. Instead, you must write the complete objective...

bijna 6 jaar ago | 0

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Answered
Dimensional analysis with math functions flags a warning
The short answer is that SimBiology does not currently confirm that the inputs to |exp| are dimensionless, but I agree that this...

bijna 6 jaar ago | 0

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Answered
sbioloadproject or sbiosaveproject loses graphical information
Regarding SBML, the Level 3 specs introduce a couple of packages for dealing with graphical representation of models. I haven't ...

bijna 6 jaar ago | 0

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Answered
Use the full range of colours in a colourbar
You are using the HeatMap function from the Bioinformatics Toolbox. By default, this function uses a symmetric colormap. In the ...

bijna 6 jaar ago | 1

| accepted

Answered
microplateplot in matlab r2015b GUI
|microplateplot| expects the containing figure to use the default figure's |uimenu|. If you change the MenuBar property of the f...

bijna 6 jaar ago | 0

Answered
persistent variable precludes simbiology acceleration, how can I keep an array available in memory
This is a timely question. The note about persistent variables being incompatible with acceleration is incorrect. (I think that ...

bijna 6 jaar ago | 0

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Answered
Transit Compartments with Simbiology
Have you seen the documentation example <https://www.mathworks.com/help/simbio/gs/estimate-pk-parameters-using-desktop.html Esti...

bijna 6 jaar ago | 0

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Answered
Can I set simbiology repeat assignment rule state to active or inactive using variants?
You cannot currently use variants to set the Active property of a Rule (or any other object). I agree this is an obvious extensi...

bijna 6 jaar ago | 0

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Answered
Vector Variables, Preload, and External matlab functions (in m files) in Simbiology
Currently, SimBiology only supports scalar quantities for species, compartment, and parameter values. However (as you already di...

ongeveer 6 jaar ago | 0

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Answered
Switching a species between an ode evaluation and a specified function (repeat assignments)
Hi, I would take the approach of adding a repeated assignment rule and setting the BoundaryCondition property to true. In som...

ongeveer 6 jaar ago | 0

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Answered
must I use events for discontinuous functions?
Hi, The only other reserved word is "null", which is used in reactions when there are no reactants or no products. For exampl...

ongeveer 6 jaar ago | 0

Answered
must I use events for discontinuous functions?
Hi Jim, There are several issues in your post that I'd like to address. I'll try to go in the order they appear: (1) must ...

ongeveer 6 jaar ago | 1

| accepted

Answered
assign values from logial vector to a new matrix with the same size
You can use an indexing variable like |D| on both the left and right side of an assignment. If I understand your questions, you ...

ongeveer 6 jaar ago | 0

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