Arthur Goldsipe

MathWorks

Last seen: 1 day ago | Active since 2011

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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...

2 days 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...

11 days ago | 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 ...

12 days ago | 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...

18 days 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...

19 days ago | 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 ...

2 months ago | 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...

2 months ago | 0

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

2 months 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...

2 months ago | 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 months 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...

3 months ago | 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...

3 months ago | 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 months ago | 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 months 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...

5 months ago | 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...

5 months 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...

6 months ago | 0

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Answered
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 months ago | 0

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Answered
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...

6 months ago | 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 ...

6 months ago | 0

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Answered
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...

6 months ago | 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...

6 months ago | 0

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Answered
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 months ago | 0

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Answered
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 months ago | 0

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Answered
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 months ago | 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 months ago | 0

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Automatic generation of SimBiology code from GUI
There is not currently any shipping functionality to do this. However, this is something we've been thinking about for a future ...

7 months ago | 0

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Specifying a cost function to optimize a simbiology model response to plausible ranges
Fearass and I had a chat about this. I figured out that the cost function is essentially a modification of some of squares of re...

8 months ago | 1

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Answered
Possible ways to test SimBiology model robustness
The closest thing I can think of off the top of my head is cross-validation. Maybe you want to take a look at this page and see ...

9 months ago | 0

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How to add noise in SimBiology analyzer app
Hi, I can't think of a way to add noise using just the SimBiology Model Analyzer app. I think you will need to export the data ...

9 months ago | 0

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