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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...

6 years 前 | 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...

6 years 前 | 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...

6 years 前 | 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...

6 years 前 | 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...

6 years 前 | 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 ...

6 years 前 | 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>.

6 years 前 | 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...

6 years 前 | 0

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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...

6 years 前 | 0

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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 ...

6 years 前 | 0

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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 ...

6 years 前 | 1

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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...

6 years 前 | 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 ...

6 years 前 | 0

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

6 years 前 | 0

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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...

6 years 前 | 0

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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...

6 years 前 | 0

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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...

6 years 前 | 0

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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...

6 years 前 | 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 ...

6 years 前 | 1

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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 ...

6 years 前 | 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...

6 years 前 | 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...

6 years 前 | 0

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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...

6 years 前 | 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...

6 years 前 | 1

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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...

6 years 前 | 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...

6 years 前 | 0

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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...

7 years 前 | 0

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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...

7 years 前 | 1

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App to convert Simbiology models to .sbproj files
Hi Ivan, The key questions are (1) why do you want to create an EXE app, and (2) what do you really need to accomplish with t...

7 years 前 | 0

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Stochastic simulation with variable volume
As mentioned on <https://www.mathworks.com/help/simbio/ug/stochastic-solvers.html this page>, rules are not currently supported ...

7 years 前 | 0