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Arthur Goldsipe

Last seen: 1 dag ago Active since 2011

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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...

4 dagen 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 dagen 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...

16 dagen 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 ...

17 dagen 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...

18 dagen 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...

18 dagen 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...

25 dagen 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....

26 dagen 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...

27 dagen 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...

ongeveer een maand 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 ...

ongeveer een maand 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...

2 maanden 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 ...

3 maanden 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 ...

3 maanden 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...

3 maanden 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...

4 maanden ago | 1

| accepted

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...

4 maanden 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...

4 maanden 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...

5 maanden 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 ...

5 maanden 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.

5 maanden 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...

6 maanden 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...

6 maanden 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 ...

6 maanden 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...

6 maanden 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...

7 maanden 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...

8 maanden ago | 0

Answered
make a data plot
This looks to me like a horizontally oriented box plot. You can easily create such plots using boxchart or boxplot. Since you wa...

8 maanden ago | 1

Answered
How do I use global solver to estimate parameters in SimBiology R2021A
I would not read too much into this message. It simply explains why the optimization stopped when it did. In and of itself that ...

8 maanden ago | 1

| accepted

Answered
Work with ODE model system in Simbiology
Not silly at all. That's a pretty common question. The easiest and most direct way to convert such a model over to SimBiology is...

9 maanden ago | 1

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