Answered
How to overcome the error "Unrecognized field name \stopTimeUseConfigset\." when simulating a simbiology model on a previous Matlab version?
SimBiology doesn't currently support opening newer projects in older versions. (This is called forward compatibility.) In fact, ...

1 year ago | 0

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Answered
Simbiology in app model simulation
I think the problem comes down to the way that calculate_KTC depends on time. This function has a maximum around a time of 1. If...

1 year ago | 0

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Adding erf(x) to a rule in Simbiology
You can call almost any MATLAB function within your rules (or in any expression in SimBiology). So, the expressoin "y = erf(x)" ...

1 year ago | 0

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Unable to locate and load .mat file after compiled into standalone file in App Designer
I suspect the problem is that you need to include in your app additional supporting function files that are required by the SimF...

1 year ago | 1

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Unites of the transfer rates
Did you enable UnitConversion for your model? If not, then you will need to manually update your entire model to use consistent ...

1 year ago | 0

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Occasionally when creating a SimFunction, SimBiology returns a failure to compile error, what causes this?
Hi Craig, My guess is that this is some sort of bug. But it's hard to say definitively without reproduction steps. If you can c...

1 year ago | 0

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Answered
error message - Unrecognized function or variable ‘rec’.
Your NCA program is erroring because of problems with the first row in your data. If you change that first ID from 0 to 1, and t...

1 year ago | 1

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Adding equations as a function of time
I suspect the problem is with "Time". SimBiology requires you to reference time as "time" (all lowercase). If that doesn't fix ...

1 year ago | 0

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Answered
The fluctuation of the content of a species between negative and positive
Can you share the model? As Jacopo mentions in the comment above, this is likely due to the difficult of solving the underlying ...

1 year ago | 0

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Simbiology with compartments of different volume
I think this is because of the volume scaling of the reaction rate. I suggest calling getequations on your model, and seeing if ...

1 year ago | 0

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How to extract the atomic coordinates of a specific amino acid from a pdb file
What is your definition for the location of lysine amino acid? The reason I ask is that a PDB file contain information about the...

1 year ago | 1

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Answered
Is there a way to turn off the slider in simbiology text boxes? They are ugly and worse than useless if you are using the text boxes for labels.
Is this problem specific to annotation blocks? If so, that's a known bug that I think was introduced in R2022b. It's on our rada...

1 year ago | 0

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Answered
Adding two different dose regimes to achieve full dose scheme
I opened the project you attached, and I do see that both doses get applied. Note that I increased the simulation stop time to ...

1 year ago | 1

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Answered
Adding and configuring events
Events are not restricted to specific times. They can also be used for something like this. The event trigger might look somethi...

1 year ago | 0

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What does a dashed line in simbiology mean?
The dashed line in the diagram indicates a species that is a catalyst. More specifically, it means the species appears as both a...

1 year ago | 0

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Simulate chemical reactions: how to include one polymerization step which consists of x reactions with identical rate constants?
I think SimBiology is most suited to modeling each degree of polymerization as a separate species. Building and simulating will ...

1 year ago | 0

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Is there any built-in code in MATLAB that calculates phi-psi angles in pdb file as the bio.pdb module in biopython does?
Yes, take a look at the ramachandran function. It's primarily designed to show these angles in a Ramachadran plot, but it has op...

1 year ago | 0

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Answered
How to rectify "arrays have incompatible sizes for this operation error" in this code: (Bioinformatics-related)
Let me just start by sharing the fixed code. (I also fixed a bug in the first for loop.) ubq=getpdb('1UBQ'); for i=1:numel(ubq...

1 year ago | 0

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Answered
How does Matlab calculate mean squared error in sbiofit?
The MSE could be Inf for several reasons. My guess is that you have a poorly posed fitting problem. Did you see any warning mess...

1 year ago | 1

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Simbiology example expression in the Tumor growth model
Hi, We chose to model the tumor weight this way so that it would be possible to perform local sensitivity analysis using tumor ...

1 year ago | 0

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Answered
How can I calculate the Hessian matrix for fit results with sbiofit (SimBiology)?
I can't think of an easy way to calculate the Hessian matrix. The objective function is not analytical (since it involves approx...

1 year ago | 0

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how to do sensitivity analysis
Hi, It's not currently possible to use an observable as a sensitivity analysis input or output. One workaround is to perform se...

1 year ago | 0

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Are ADDL (additional doses) and II (interval) nlme columns supported in Simbiology datasets for model fitting?
When you actually perform the fit, you typically want one row in your data that describes each distinct dose event. (It is also ...

1 year ago | 0

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Is it possible to deactivate all reactions within a compartment in SimBiology?
I think the getBlock function will give you the information you need to determine whether a reaction is inside a compartment. It...

1 year ago | 0

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/tmp/.e6fa-d450-cf2c-87f9.tmp Invalid cross-device link
MathWorks recently published a bug report about this.

1 year ago | 0

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How to extract value of Sobol index from the Sobol index plot generated in Matlab ?
In your comment, what do you mean by the "global sensitivity analysis tool"? Do you mean you are running a global sensitivity a...

1 year ago | 0

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Creating a reaction that combines multiple individual species together in Simbiology
Hi, Your question doesn't yet completely make sense to me, so I can't yet give a direct answer. But I'll try to provide an indi...

1 year ago | 0

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Answered
sbiosimulate Not Releasing Memory
My guess is that this memory usage is somehow associated with SimBiology models that are still in memory. If you want to reclaim...

1 year ago | 1

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Answered
how to re-assign parameter value assigned in an active variant in SimBiology?
sbiosimulate(modelObj) will simulate using only active variants. If you set all your variants to inactive, then you should simul...

2 years ago | 0

Answered
selecting and re-assignment of non-existing parameters in SimBiology does not trigger any warning?
I can think of several ways to answer your question, depending on exactly how you want to handle this situation. sbioselect can ...

2 years ago | 0