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Arthur Goldsipe

MathWorks

Last seen: 1 day ago Active since 2011

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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,...

22 days 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...

1 month 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...

1 month 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...

2 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...

2 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...

2 months ago | 0

Answered
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 ...

2 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...

2 months ago | 0

Answered
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...

2 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...

3 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....

3 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...

3 months ago | 1

Answered
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...

3 months ago | 0

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Answered
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 ...

3 months ago | 0

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Answered
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...

4 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 ...

5 months ago | 0

Answered
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 ...

5 months ago | 0

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Answered
Reaction continues even after the concentration is below zero in Simbiology
I answered a similar question here. As I mention there, there's currently no way to completely prevent negative numbers in all c...

5 months ago | 0

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Answered
Simbiology plot problem when using global solvers
Can you share the project or provide some other way for us to reproduce what you're seeing? That would help us definitely say wh...

5 months ago | 1

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Answered
How to introduce a delay in a simbiology model?
SimBiology does not directly support delays. One approach would be a more mechanistic model of the delay. For exampe, you might...

6 months ago | 0

Answered
How can I estimate PD parameters for two - compartment model?
I looked at the project you attached in the comments. I didn't see any obvious problems. Your parameter estimates are within a f...

6 months ago | 0

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Answered
Creating a 3-D bar graph with parameter sensitivities with respect to all model species
I'm guessing the configset is not configured for sensitivity analysis. You probably need to do something like the following befo...

7 months ago | 0

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Answered
How to plot categorical data to compare with SimBiology simulation result?
If I understand your question, you're primarily asking how to extract the simulation results at a specific time (for example, 5 ...

7 months ago | 0

Answered
Excluding C and N terminus from Isoelectric calculation
I think you want to set the N_term and C_term entries to 7.0 rather than 0.0, since 7.0 is the the "neutral" pK value.

7 months ago | 0

Answered
Can we estimate different variance of the error model for different data set in NLME Simbiology?
I don't completely understand your workflow, but my guess is that this is not possible today with the NLME methods provided in M...

8 months ago | 0

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Answered
SimBio: Running Stochastic SSA Simulation of SBML imported model
First, a little background on why you're seeing this behavior. SBML does not indicate whether a particular reaction follows mass...

8 months ago | 0

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Answered
Any progress on relaxing the constraints on species units?
I'd love to pick your brain about exactly what you need and expect from such functionality! Which is to say that today species ...

8 months ago | 0

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Answered
dose dependence in simbiology model
I think the answer depends on how, mathematically, you want to model dose-dependent absorption. You can easily create various PK...

8 months ago | 0

Answered
Error while validating MEX Setup
Hi, This is a warning, not an error. You can still use SimBiology. But if you install a supported compiler, you should see fitt...

9 months ago | 0

Answered
How to consider steady state concentration of biomarker in Simbiology
The SimBiology app does not currently provide any direct way to automatically fit steady state data. However, if I'm correctly u...

10 months ago | 0

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