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Arthur Goldsipe


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283 total contributions since 2011

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Answered
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...

25 days ago | 0

Answered
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...

1 month ago | 0

| accepted

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...

1 month ago | 0

Answered
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...

2 months ago | 0

Answered
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...

2 months ago | 0

Answered
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...

3 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...

3 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...

3 months ago | 0

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Answered
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...

3 months ago | 0

| accepted

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...

3 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/...

3 months ago | 0

Answered
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 ...

3 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.

4 months ago | 0

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Answered
Diagnosing simfunction acceleration failure
Hi Abed, There is currently no publicly documented way to get additional debugging information. These situations have historica...

4 months ago | 0

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Answered
Stopping simulation early on event
Hi Abed, Interesting question. The only way an event can stop a simulation early is if the event errors. sbiofit would handle s...

4 months ago | 0

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Answered
Constant parameter setting throws error, or... if I don't set a parameter to constant, but don't change it, does it stay constant?
Great feedback as always, Jim. As for your immediate questions: "If I leave the parameter variable all the time, but nothing i...

5 months ago | 0

| accepted

Answered
deleting or removing variant using variant array handle gives unexpected results.
I know it's confusing, and I'll try to explain what's going on. But let me start by saying that the behavior you're seeing is wh...

6 months ago | 1

| accepted

Answered
Error model with curve-fitting
SimBiology's error models are only available when fitting data to SimBiology models using functions like sbiofit. If you are dir...

6 months ago | 0

| accepted

Answered
Mass balance issues with PBPK model in Simbiology
One way to confirm that that your model structure is correct is to use SimBiology sbioconsmoiety function to identify conserved ...

6 months ago | 0

| accepted

Answered
Add multiple doses in ODEsolver
Because doses introduce discontinuities in the solution, you basically need to stop the ODE simulation every time a dose is appl...

7 months ago | 0

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Answered
Can I force Matlab to wait 'til it finishes one command to run another?
Hi Jim, The previous responses are correct: The simbiology command returns before the desktop completely loads the project, bec...

7 months ago | 1

| accepted

Answered
How to handle warnings in SimBiology within series of simulations?
Hi, It's difficult to say for sure whether you can trust the simulation results when you see this warning. I would definitely e...

7 months ago | 1

| accepted

Answered
Issue with SimBiology - parameters from valid .sbproj not loading
As described here, parameters can be scoped to either the model or to a reaction. The display counts both scopes of parameters, ...

8 months ago | 1

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Answered
Volume change in simbiology
As described here, SimBiology conserves amounts when changing compartment volumes. If I were building the model, I would not use...

8 months ago | 0

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Answered
Issue with parameter array sorting in SimBiology after loading using sbioloadproject
Hi, By default, the parameters appear in this list in the order in which they were added to the model. However, you can reorder...

8 months ago | 1

| accepted

Answered
Error using SimBiology model over command line
Hi, I would expect the setting you see for AbsoluteToleranceStepSize in the GUI to be the same as you see in the command line. ...

8 months ago | 1

| accepted

Answered
SimBiology | simulation tolerance fails at beginning if time increased
My guess is that you are encountering the problem described in the tip on the AbsoluteToleranceStepSize reference page. The sugg...

8 months ago | 0

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Answered
GETGEODATA problems, any suggests?
I believe the problem is that the records for these samples do not contain any actual data tables. For example, if you look at G...

8 months ago | 0

Answered
Fitting multiple dependent variables with time less than zero
Right now, SimBiology simulations always have to start at zero. So for your problem, you'd have to adjust the data with an offse...

9 months ago | 0

| accepted

Answered
Can more than one model be used for " fit data" in Simbiology
No, SimBiology’s built-in fitting capabilities only support fitting one model to one dataset. If I needed to do this, I would ch...

9 months ago | 0

| accepted

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