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How to solve this error
(Copying answer from comments.) The problem was that one value of DV1 was 0, so the resulting weight was infinite. One thing I ...

1 year ago | 0

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Fit simbiology model to cmax or AUC data
One option would be to add Cmax to your model as an observable. Then, you can include Cmax in your fit the same way you fit to a...

1 year ago | 3

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Change in simulation output with changing in the units of stop time
If you have constructed your model correctly, I expect the results of the two simulations to be equivalent but not numerically i...

1 year ago | 0

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Failure of dimensional analysis for a rule
When you enable dimensional analysis (or unit conversion) in SimBiology, fractional exponents can only be applied to dimensionle...

1 year ago | 0

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Dimension of the species
In SimBiology, a species is intended to represent a entity (like a protein or some other chemical) that exists in a physical com...

1 year ago | 0

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unit dimensional analysis problems
If your reactions are using mass action kinetics, then the units you report for "kf" are not correct. For the first reaction, th...

1 year ago | 0

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Dimensional analysis fail for reaction on simbiology
It looks like this was answered in a comment on the question. I'll paste it here for completeness: The first term of the rate r...

1 year ago | 0

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How do I open or convert a .sbproj.zip file in Simbiology?
An .sbproj file is a specially formatted .zip file. So perhaps whatever you're using to download the file recognized it as such ...

1 year ago | 0

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Why isn't Stoichiometry Math working in Simbiology?
It sounds like you are trying to import an SBML file that uses the stoichiometryMath element defined in SBML level 2. Unfortunat...

1 year ago | 0

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Error when calculating AUC in simbiology
In case anyone runs into a similar issue and is looking for the answer, I looked at Brett's model and made a few recommendations...

1 year ago | 0

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Modeling dissociation using Hill function provides misleading results
Similar questions come up periodicaly. I suggest looking at my previous responses here and here. The bottom line is that both o...

1 year ago | 1

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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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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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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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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 ...

2 years 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...

2 years ago | 1

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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...

2 years ago | 0

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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 ...

2 years ago | 1

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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...

2 years 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...

2 years 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 ...

2 years 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...

2 years ago | 0

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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...

2 years ago | 0

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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...

2 years ago | 1

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