Answered
Saving a model after UnitConversion in SimBiology
Based on your reply, I now understand that you'd like to update a model in SimBiology, so that you can simulate it correctly wit...

9 years ago | 0

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Answered
Saving a model after UnitConversion in SimBiology
Hi, I'd like to make sure I understand your question. Tell me if this is accurate: When you simulate your model in SimBiology...

9 years ago | 0

Answered
How to fit a SimBiology model with data generated in different experimental conditions
Hi, Your question is conceptually similar to <http://www.mathworks.com/matlabcentral/answers/301890-dummy-variables-in-simbio...

9 years ago | 0

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Answered
Can anyone please tell me how to use dosage for "fit parameter" task in simbiology?
Hi, It's fine if you don't have a concentration measurement at a dosing time. If that's the case, you just need to put |NaN| ...

9 years ago | 0

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Adding parameters while programmatically setting up a SimBiology model
Hi Scott, You've already found one solution: Set ParameterVariableNames. However, I wanted to provide another solution and gi...

9 years ago | 0

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Error using blastncbi (line 433) - I am not able to connect the ncbi blast server using the bioinformatics toolbox
This error occurs because NCBI changed their servers from using HTTP to HTTPS. You can fix this problem by downloading a patch f...

9 years ago | 0

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Answered
Dear Matlab community, I have a question about simbiology app in MATLAB
The answer depends on what you mean by "a fit." If you are performing nonlinear regression, then you can specify bounds. See <ht...

9 years ago | 0

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SimBiology Parameter Estimation: How to use 2 different data sets to generate parameters?
Hi Jonathan, SimBiology supports this sort of task (estimating a single set of model parameters by simultaneously fitting a m...

9 years ago | 1

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Answered
I can't seem to get the simbiology toolbox installed
Hi, SimBiology is a MathWorks product that is built on top of MATLAB. In other words, you will need to install MATLAB to use ...

9 years ago | 0

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How to output concentrations if species dimension is 'substance'.
Hi Colin, Today (as of R2016b), you must decide to represent a species either in amount or in concentration. There is no dire...

9 years ago | 0

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Answered
Can I run a sensitivity analysis in Simbiology if I have a compartment that changes size?
Hi, <https://en.wikipedia.org/wiki/Finite_difference_method Finite differencing> is a method for approximating derivatives. L...

9 years ago | 1

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Answered
Can I run a sensitivity analysis in Simbiology if I have a compartment that changes size?
Hi, As of R2016b, SimBiology does not support sensitivity analysis on models with non-constant compartments. The most straigh...

9 years ago | 1

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using 3rd party optimization toolbox with simbiology
Hi, Are you using optimization methods to estimate model parameters that best fit a model to data? I'm going to assume so for...

9 years ago | 0

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fitting dde compartment model
Hi, You can solve delayed differential equations in MATLAB using the function |dde23|. You can find more information and exam...

9 years ago | 0

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How to retrieve specific compartment in Simbiology model by name?
Hi, We made the |sbioselect| function for things like this, and even for more general kinds of searching. In this case, you c...

9 years ago | 0

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Answered
dimensional analysis problems with simbiology mass action kinetics units
I think the problem is with the units on your forward rate constant. I think you forgot a set of parentheses and ended up multip...

9 years ago | 0

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Answered
How to zoom a graph in simbiology without changing the DE associated with the graph? I want to zoom the concentration of only one species among the various species plotted on the same graph against time.
Personally, I would split the results into two separate plots, one for insulin and one for the others. If you really want insuli...

9 years ago | 0

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Are algebraic rules available outside simbiology?
Hi, Yes, you can include algebraic constraints with your differential equations when solving them in MATLAB using solvers lik...

9 years ago | 0

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Simbiology: How to use a species calculated by a repeated rule in downstream reactions
Hi, If you don't want a species to be modified by reactions that it participates in, you need to set the |BoundaryCondition| ...

9 years ago | 0

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Simbiology initial condition failed
I think this is likely an overly aggressive error check, and I removed it from SimBiology in R2016b. So one fix would be to upgr...

9 years ago | 1

Answered
Retrieve number of identities after alignment of two amino acid sequences
If I understand correctly, |showalignment| doesn't actually do the alignment. Instead, you pass the alignment information in as ...

9 years ago | 2

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Answered
dummy variables in simbiology
Hi, Currently (as of R2016a), the data in a fit task can only affect a model via dosing. So I think you could do what you wan...

9 years ago | 0

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Answered
Setting number of clusters on clustergram object
I'm not an expert with clustering, but I don't think clustergram was designed with this sort of functionality in mind. I think y...

9 years ago | 0

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How to assign to a SimBiology model a parameter value (known and constant) changing for each data in the dataset for a non-linear mixed effect estimation?
Hi Micaela, Currently, the only information that can be fixed and different for each subject is the dosing. As a workaround, ...

9 years ago | 0

Answered
How do I fix this error in SImbiology?
You're referencing files and projects that we don't have access to. In the future, please consider attaching any files that coul...

9 years ago | 0

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How do I load the Simbiology project onto Matlab so I can edit the code?
The command you typed loaded the project into the MATLAB workspace. The model is usually stored in a variable called |m1|. You c...

9 years ago | 0

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Answered
Is it possible to combine pooled and unpooled parameter fitting in SimBiology 4.3 (R2013a)?
As of R2014b, the SimBiology command-line offers the capability to simultaneously estimate "pooled" and "unpooled" parameters (t...

9 years ago | 0

Answered
How to obtain exponential equation parameters from Simbiology fit of IV bolus pharmacokinetic data?
If your goal is to estimate the coefficients of a poly-exponential and their corresponding error estimates, then I think it's ea...

9 years ago | 0

Answered
Simbiology Desktop Activate Reaction Using Event
Hi, Events cannot directly change the Active property. However, you can accomplish the same simulation result by creating an ...

9 years ago | 1

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Answered
Best way to use compartment capacity as reaction parameter.
Hi Colin, You don't need to create a parameter named Volume. You can refer to the capacity (that is, volume) of a compartment...

9 years ago | 0

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