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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...

約3年前 | 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...

約3年前 | 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, ...

約3年前 | 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...

約3年前 | 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)" ...

3年以上前 | 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...

3年以上前 | 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 ...

3年以上前 | 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...

3年以上前 | 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...

3年以上前 | 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 ...

3年以上前 | 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 ...

3年以上前 | 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 ...

3年以上前 | 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...

3年以上前 | 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...

3年以上前 | 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 ...

3年以上前 | 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...

3年以上前 | 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...

3年以上前 | 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 ...

3年以上前 | 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...

3年以上前 | 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...

3年以上前 | 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...

3年以上前 | 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 ...

3年以上前 | 0

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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...

3年以上前 | 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...

3年以上前 | 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 ...

4年弱前 | 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...

4年弱前 | 0

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

4年弱前 | 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...

4年弱前 | 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...

4年弱前 | 0

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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...

4年弱前 | 1

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