Arthur Goldsipe

Last seen: 1 day ago

MathWorks

313 total contributions since 2011

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Answered
lsqnonlin multiple dataset optimisation
You can use lsqnonlin with or without SimBiology. If you want to do this without SimBiology, you need to write a function that t...

1 day ago | 0

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Events during the fitting in Simbiology
Yes, all active events will be used during simulations, including simulations performed while doing NLME estimation.

15 days ago | 0

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SImbiology: access "Initial Conditions" (not InitialValues)
As you discovered, getequations is intended as a textual report and is not well suited for programmatic access to initial values...

16 days ago | 0

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In Online Matlab under App menu, Signal Analyzer not working?
The Signal Analyzer App is not supported with MATLAB Online. You will need to use the desktop version of MATLAB if you need acce...

18 days ago | 2

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Error in data fitting in simbiology
When you perform a fit in SimBiology, one of the first things that happens is the model is simulated using the initial parameter...

19 days ago | 0

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When will sbmlimport support sbml level 3?
SimBiology already supports SBML level 3 version 1. That was introduced in R2016a. You can read more about what is supported her...

1 month ago | 0

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Installing Supported Compliers on Ubuntu 20.01
You can use "apt" to install these compilers. Try googling "install gcc ubuntu" and "install jdk ubuntu" if you need more detail...

1 month ago | 0

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Creating a cell growth model using SimBiology.
Hi, The capacity of a compartment can vary during the course of a simulation. To do this, you must set the Constant property to...

3 months ago | 1

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Fit data with weight in Simbiology
You can use NaN to indicate a missing value in your data. Such points will be ignored during fitting. If you are getting an erro...

3 months ago | 1

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Will Matlab work on ARM based MacBook stated to launch in the fall of 2020?
Please see this MATLAB Answers post for the latest news on running MATLAB on Apple Silicon: https://www.mathworks.com/matlabcent...

4 months ago | 2

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Will Matlab support future Apple computers based on their in house ARM silicon?
Please see this MATLAB Answers post for the latest news on running MATLAB on Apple Silicon: https://www.mathworks.com/matlabcent...

4 months ago | 1

Solved

Eliminate Polysyllabics: Long live short words!
Given a string s1, return s2 in which all the words with more than one syllable have been removed. To make things simple, we ...

4 months ago

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Which module is best for modeling large cell populations?
As stated, your question is too general to answer with specific recommendations. SimBiology is certainly useful for certain kind...

4 months ago | 0

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Simbiology with matlab background
It's very hard to say what's going on without having reproduction steps. Can you share your model and the steps you used to simu...

8 months ago | 0

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Answered
Invalid Reaction Value error for SBML transfer from COPASI to Matlab
Hi Darke, This is a bug in how SimBiology imports reaction modifiers. The model is imported incorrectly if either the name of a...

8 months ago | 1

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Answered
AUC for Pharmacokinetic Study
The simplest way to calculate AUC in MATLAB using the trapezoidal rule is probably to use the function trapz. Within SimBiology,...

8 months ago | 1

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Answered
Simultaneous Fit of IV and PO data using SimBiology
Yes, it is possible to fit two model outputs at the same time. Do you want to do this using sbiofit or a fit program in the SimB...

8 months ago | 0

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fastawrite error with string array as input datatype
You generally should be able to cell arrays of character vectors and string vectors interchangeably, and a character vector inte...

8 months ago | 0

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Simutaneous parameter estimation for multiple compartments and multiple dataset
Hi, Depending on the details of the estimation, you might be able to use sbiofit for this sort of problem by merging the 3 data...

8 months ago | 0

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Semicolons in SimBiology species names: just characters, or functionally active?
Hi Jim, You can name your species almost anything. The naming restrictions are documented here. However, if the name is not a v...

9 months ago | 0

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Answered
using a nested for loop to edit a structure
As mentioned in the comments, if you want to compare one atom at a time, the proper way to index is Atom(i3).AtomSerNo. But if y...

9 months ago | 0

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FRET data analysis with simulation
Hi Parul, This sounds like a fitting problem that can be solved using sbiofit from the command line or using a fit program with...

9 months ago | 0

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In Simbiology, Is there a way to set a slider with an integer scaling?
It is not currently possible to constrain the value of a slider to an integer. It's a great suggestion for a future enhancement,...

9 months ago | 0

Answered
What is the difference between BoundaryCondition and ConstantAmount?
Constant=true means that the value of a species cannot change during the course of a simulation. It can only be modified at time...

9 months ago | 0

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implement quasi zeroth order kinetic in Simbio
Hi, Whenever you have a discontinuous step change like this in your model, you should include either doses or events at the dis...

9 months ago | 0

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Any simulation speed differences between models loaded with SimBiology() vs sbioloadproject?
I don't expect you to see any noticeable performance impact when simulating a model from the command line, while the same model ...

10 months ago | 0

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Answered
simbiology problem PK PD modeling
Hi, The problem is that the two variables "time" and "drug" in your data were imported as text instead of numbers. I'm not sure...

10 months ago | 0

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How can I find 4 constants values from and indirect fitting value?
I see that the SimBiology product is tagged for this post, but the attached files are not using SimBiology. I'm one of the devel...

10 months ago | 0

Answered
Why does my .sbproj file can't open on other's computer?
This is expected. Please see the following discussion: https://www.mathworks.com/matlabcentral/answers/500762-loading-simbiolog...

10 months ago | 0

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Answered
How to correctly compile a function containing variables with dimension and call it in SimBiology
Hi, The issue you are seeing is addressed in the "Tip" on the documentation for UnitConversion. The problem is that you are ha...

10 months ago | 1