Arthur Goldsipe

Last seen: 5 days ago

MathWorks

300 total contributions since 2011

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Answered
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...

26 days ago | 0

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...

1 month 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,...

2 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...

2 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...

2 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...

2 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...

2 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...

2 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...

3 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,...

3 months ago | 0

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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...

3 months ago | 0

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Answered
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...

3 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 ...

3 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...

3 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...

3 months ago | 0

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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...

4 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...

4 months ago | 1

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Issues with doses/variants in parfor loop in SimBiology
First, what version of SimBiology are you using? Prior to R2019b, there was a problem that prevented objects from getting sent t...

5 months ago | 0

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It is possible to add a constant input term (without reaction rate) for a specie in the diagram view in SIMBIOLOGY?
If I understand your question correctly, it sounds like you want to use a rate rule. If you want to build a rate rule in the dia...

5 months ago | 0

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Answered
error saying "dimentional analysis failed for reaction."
Yes, nanomole is a unit with dimensions of amount, and nanomolar is a unit with dimensions of concentration. Can you share your...

6 months ago | 0

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SUNDIALS installation in MATLAB
What exactly did you download? Can you provide the website or download link? I'm not sure how we can help you without knowing mo...

6 months ago | 0

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What is smooth curve?
I'm not sure I fully understand your question. If you're asking what the checkbox labeled "Show smooth curve" does, you can see...

7 months ago | 0

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Namespace and other html / xml information in SimBiology Notes
I would recommend either plain text or XHTML 1.0 as your format. sbmlexport will export both of these to SBML as XHTML 1.0, whic...

7 months ago | 1

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Answered
Loading simbiology models created in MATLAB 2019b in previous version of MATLAB
In general, we cannot guarantee this kind of compatibility (which is called "forward compatibility"). In practice, SimBiology mo...

7 months ago | 0

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Answered
How to implement multiple error model?
It depends on whether you are doing nonlinear regression or nonlinear mixed-effects modeling. If you are doing nonlinear regress...

7 months ago | 0

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seqpdist Kimura "method not available for amino acids" even though working with nucleotides
As Geoff points out in the comments, the problem is that several of the default option values don't work for the Kimura distance...

7 months ago | 0

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Solved

Aquiles y la tortuga
Contaba Zenón en su famosa paradoja que un día Aquiles, el guerrero griego más veloz de la Hélade, se enfrentó a una pequeña tor...

7 months ago

Answered
Microarray Analysis Trouble in Analysis
Let me make sure I understand your problem. You are trying to run the following example: https://uk.mathworks.com/help/bioinfo/...

7 months ago | 0

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Simbiology Stochastic solvers non mass action (nonlinear) propensities
Hi, You correctly understand the current constraints of SimBiology's stochastic solver: reactions must use linear, mass action ...

7 months ago | 1

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Answered
Restricting output times when calling simfunctions
Yes, if you use tStop = [], then only results at tOutput will be reported.

8 months ago | 0

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