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...

12 månader 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...

ungefär ett år 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...

ungefär ett år 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...

ungefär ett år 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...

ungefär ett år 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...

ungefär ett år 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...

ungefär ett år 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...

ungefär ett år 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...

mer än ett år 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...

mer än ett år 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...

mer än ett år 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...

mer än ett år 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 ...

mer än ett år 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>.

mer än ett år 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...

mer än ett år 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...

mer än ett år 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 ...

mer än ett år 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 ...

mer än ett år 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...

mer än ett år 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 ...

mer än ett år 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...

mer än ett år 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...

mer än ett år 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...

mer än ett år 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...

mer än ett år 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...

mer än ett år 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 ...

mer än ett år 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 ...

mer än ett år ago | 0

Answered
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...

mer än ett år ago | 1

Answered
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...

mer än ett år 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...

mer än ett år ago | 0

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