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...

1 year ago | 0

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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...

1 year ago | 0

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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...

1 year ago | 0

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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...

1 year ago | 0

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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...

1 year ago | 0

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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...

1 year ago | 0

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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...

1 year ago | 0

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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 ...

1 year ago | 0

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

1 year ago | 0

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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...

1 year 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...

1 year 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 ...

1 year 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 ...

1 year ago | 1

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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...

1 year ago | 0

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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 ...

1 year 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...

1 year 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...

1 year 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...

1 year 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...

1 year 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...

1 year ago | 0

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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 ...

1 year ago | 1

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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 ...

1 year ago | 0

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Control simbiology model from MATLAB command line
I'm not sure what you mean by "control", but let me try to offer some guidance. You can simulate a model from the command line u...

1 year ago | 1

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Can I trigger/activate a rule using an event in SimBiology?
If I understand correctly, you could get the desired result by replacing the repeated assignment rule |y = f(x)| with |y = min(f...

1 year ago | 0

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Answered
In SimBiology, is there any way to fit multiple data sets to the model with a single set of parameters? How can I do this using Simbiology desktop or coding?
I described a solution to a similar problem <https://www.mathworks.com/matlabcentral/answers/54826-how-to-fit-kinetic-law-parame...

1 year ago | 0

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SymBiology - time delays
SimBiology does not currently support delay differential equations. One workaround is to replace the delay with a more mechanist...

1 year ago | 1

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Answered
matlab cannot find the datainsert function
Hi, I think you need to use <https://www.mathworks.com/help/database/ug/insert.html |insert|> instead of |datainsert|. The Da...

1 year ago | 1

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stoichiometry of cell proliferation
I'm not aware of a centralized list of the validation that is performed before simulating a model. However, the requirements for...

1 year ago | 0

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Answered
redefine mass action kinetics
It's not currently possible to create a custom kinetic law that depends on the reaction's stoichiometry. You will need to manual...

2 years ago | 0

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Answered
Warning that "Simulation with phi=[] could not be completed" occurred during 'Fit Data' task
You can likely ignore this warning. It means that during parameter estimation, the genetic algorithm selected a "bad" set of par...

2 years ago | 1

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