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What is the difference between BoundaryCondition and ConstantAmount?
Constant=true means that the value of a species cannot change during the course of a simulation. It can only be modified at time...

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implement quasi zeroth order kinetic in Simbio
Hi, Whenever you have a discontinuous step change like this in your model, you should include either doses or events at the dis...

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Any simulation speed differences between models loaded with SimBiology() vs sbioloadproject?
I don't expect you to see any noticeable performance impact when simulating a model from the command line, while the same model ...

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simbiology problem PK PD modeling
Hi, The problem is that the two variables "time" and "drug" in your data were imported as text instead of numbers. I'm not sure...

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How can I find 4 constants values from and indirect fitting value?
I see that the SimBiology product is tagged for this post, but the attached files are not using SimBiology. I'm one of the devel...

약 1년 전 | 0

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Why does my .sbproj file can't open on other's computer?
This is expected. Please see the following discussion: https://www.mathworks.com/matlabcentral/answers/500762-loading-simbiolog...

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How to correctly compile a function containing variables with dimension and call it in SimBiology
Hi, The issue you are seeing is addressed in the "Tip" on the documentation for UnitConversion. The problem is that you are ha...

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Issues with doses/variants in parfor loop in SimBiology
First, what version of SimBiology are you using? Prior to R2019b, there was a problem that prevented objects from getting sent t...

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It is possible to add a constant input term (without reaction rate) for a specie in the diagram view in SIMBIOLOGY?
If I understand your question correctly, it sounds like you want to use a rate rule. If you want to build a rate rule in the dia...

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error saying "dimentional analysis failed for reaction."
Yes, nanomole is a unit with dimensions of amount, and nanomolar is a unit with dimensions of concentration. Can you share your...

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SUNDIALS installation in MATLAB
What exactly did you download? Can you provide the website or download link? I'm not sure how we can help you without knowing mo...

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What is smooth curve?
I'm not sure I fully understand your question. If you're asking what the checkbox labeled "Show smooth curve" does, you can see...

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Namespace and other html / xml information in SimBiology Notes
I would recommend either plain text or XHTML 1.0 as your format. sbmlexport will export both of these to SBML as XHTML 1.0, whic...

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Loading simbiology models created in MATLAB 2019b in previous version of MATLAB
In general, we cannot guarantee this kind of compatibility (which is called "forward compatibility"). In practice, SimBiology mo...

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How to implement multiple error model?
It depends on whether you are doing nonlinear regression or nonlinear mixed-effects modeling. If you are doing nonlinear regress...

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seqpdist Kimura "method not available for amino acids" even though working with nucleotides
As Geoff points out in the comments, the problem is that several of the default option values don't work for the Kimura distance...

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해결됨


Aquiles y la tortuga
Contaba Zenón en su famosa paradoja que un día Aquiles, el guerrero griego más veloz de la Hélade, se enfrentó a una pequeña tor...

1년 이상 전

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Microarray Analysis Trouble in Analysis
Let me make sure I understand your problem. You are trying to run the following example: https://uk.mathworks.com/help/bioinfo/...

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Simbiology Stochastic solvers non mass action (nonlinear) propensities
Hi, You correctly understand the current constraints of SimBiology's stochastic solver: reactions must use linear, mass action ...

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Restricting output times when calling simfunctions
Yes, if you use tStop = [], then only results at tOutput will be reported.

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Diagnosing simfunction acceleration failure
Hi Abed, There is currently no publicly documented way to get additional debugging information. These situations have historica...

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Stopping simulation early on event
Hi Abed, Interesting question. The only way an event can stop a simulation early is if the event errors. sbiofit would handle s...

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Constant parameter setting throws error, or... if I don't set a parameter to constant, but don't change it, does it stay constant?
Great feedback as always, Jim. As for your immediate questions: "If I leave the parameter variable all the time, but nothing i...

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deleting or removing variant using variant array handle gives unexpected results.
I know it's confusing, and I'll try to explain what's going on. But let me start by saying that the behavior you're seeing is wh...

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Error model with curve-fitting
SimBiology's error models are only available when fitting data to SimBiology models using functions like sbiofit. If you are dir...

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Mass balance issues with PBPK model in Simbiology
One way to confirm that that your model structure is correct is to use SimBiology sbioconsmoiety function to identify conserved ...

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Add multiple doses in ODEsolver
Because doses introduce discontinuities in the solution, you basically need to stop the ODE simulation every time a dose is appl...

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Can I force Matlab to wait 'til it finishes one command to run another?
Hi Jim, The previous responses are correct: The simbiology command returns before the desktop completely loads the project, bec...

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How to handle warnings in SimBiology within series of simulations?
Hi, It's difficult to say for sure whether you can trust the simulation results when you see this warning. I would definitely e...

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Issue with SimBiology - parameters from valid .sbproj not loading
As described here, parameters can be scoped to either the model or to a reaction. The display counts both scopes of parameters, ...

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