Arthur Goldsipe

MathWorks

Last seen: 3 dagar ago | Active since 2011

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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 ...

15 dagar 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...

16 dagar 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...

22 dagar 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 ...

3 månader 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 ...

3 månader 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 ...

3 månader 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...

4 månader 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...

4 månader 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 ...

4 månader 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...

4 månader 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...

4 månader 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 ...

4 månader 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...

4 månader 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...

4 månader 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...

5 månader 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 ...

5 månader 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...

5 månader 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...

5 månader ago | 0

Answered
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 ...

6 månader ago | 0

Answered
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...

6 månader ago | 0

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

6 månader 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...

6 månader ago | 0

Answered
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...

7 månader 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...

7 månader 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...

8 månader 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 ...

8 månader ago | 0

Answered
Simbiology reaction stoichiometry: R + E ==> P + E, or the simpler R ==> P?
I don't expect this choice to make any numerical difference. For most situations, I consider it a stylistic choice (for example,...

9 månader ago | 0

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Answered
Pooled data fit of multiple data sets from different model parameters
If I understand correctly, you can do this in the Model Analyzer app. You just need to merge the two data sets into a single dat...

9 månader ago | 0

Answered
Computer freeze results in invalid zip error for simbiology model
Change the extension of the backup files to .sbproj, and then you should be able to (try to) open them in SimBiology. If you wan...

10 månader ago | 1

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Answered
SimBiology parameter estimation for a series of single dose-response data
I think the problem is that you need to add a grouping variable to your DOSEdata and your CONCdata. As the code is currently wri...

10 månader ago | 0

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