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# Arthur Goldsipe

### MathWorks

Last seen: Today Con actividad desde 2011

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

alrededor de 3 horas hace | 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...

alrededor de 3 horas hace | 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 días hace | 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 días hace | 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...

7 días hace | 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...

16 días hace | 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 ...

17 días hace | 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...

23 días hace | 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...

24 días hace | 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 ...

alrededor de 2 meses hace | 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...

alrededor de 2 meses hace | 0

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2 meses hace | 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...

2 meses hace | 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...

3 meses hace | 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...

3 meses hace | 1

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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...

4 meses hace | 0

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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 ...

4 meses hace | 0

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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,...

5 meses hace | 0

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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...

5 meses hace | 0

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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...

6 meses hace | 1

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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...

6 meses hace | 0

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How to solve issue with loading project on simbiology (index exceeds number of array elements).
I don't think there's anything you can do as an end user. But I'm a developer on SimBiology, and I'd like to see if we can do an...

6 meses hace | 0

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Integration tolerance not met in simbiology project
Without reproduction steps, I can't be sure what's going on. I recommend reading this page on Troubleshooting Simulation Problem...

7 meses hace | 0

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Build-in unit conversion in SimBiology
Short answer: You can see the relationship between two by using the function sbiounitcalculator, which shows you that 1 day is ...

7 meses hace | 0

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Running parallel using build in 10-core GPU and 16-core neural Engine in MacBook Air M2
You can use run the Intel version of many releases of MATLAB on an M2 Mac just fine. I'm a SimBiology developer with an M1Pro Ma...

7 meses hace | 0

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Is specifying objective fuction for multiple variables in SimBiology possible?
It depends on what you mean by "possible." :-) If you're using a fit program in the SimBiology Model Analyzer app or the functio...

7 meses hace | 0

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How to add programmatically (using command line) add a program to a simbiology model?
This is not currently possible but is something we would consider adding in a future release. Until then, you will need to creat...

7 meses hace | 0

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Incorrect units in simple reaction in SimBiology?
This is a bug in SimBiology. SimBiology checks that all species participating in a reaction have dimensionally consistent units....

7 meses hace | 0

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Estimating Parameter That Satisfies Minimal Efficacy
Here's a high-level description of how I'd do this in the Analyzer App: Create and run a simulation program that determines the...

7 meses hace | 1

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Time after last dose
I haven't read the article, so I don't know how the TAD parameter is used. I'm assuming you need to know TAD during the simulati...

7 meses hace | 0