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Arthur Goldsipe

MathWorks

Last seen: Today |  Active since 2011

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Answered
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 dag ago | 0

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Answered
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...

13 dagen ago | 0

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Answered
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...

13 dagen 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...

16 dagen ago | 0

Answered
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...

16 dagen ago | 0

Answered
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 ...

ongeveer een maand ago | 0

Answered
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...

ongeveer 2 maanden ago | 0

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Answered
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...

2 maanden ago | 0

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Answered
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...

2 maanden ago | 1

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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, ...

3 maanden 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...

3 maanden ago | 0

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Answered
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)" ...

4 maanden ago | 0

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Answered
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...

4 maanden ago | 1

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Answered
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 ...

5 maanden ago | 0

Answered
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...

5 maanden 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...

5 maanden ago | 1

Answered
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 ...

7 maanden 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 ...

7 maanden ago | 0

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Answered
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 ...

8 maanden ago | 0

Answered
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...

8 maanden 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...

8 maanden 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 ...

8 maanden 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...

8 maanden ago | 0

Answered
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...

8 maanden ago | 0

Answered
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 ...

8 maanden ago | 0

Answered
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...

8 maanden 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...

8 maanden 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...

9 maanden ago | 1

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Answered
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 ...

9 maanden 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...

9 maanden ago | 0

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