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Arthur Goldsipe


MathWorks

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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...

12日 前 | 1

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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, ...

24日 前 | 1

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

24日 前 | 0

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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...

26日 前 | 1

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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. ...

27日 前 | 1

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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...

27日 前 | 0

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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...

約1ヶ月 前 | 0

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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...

2ヶ月 前 | 0

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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...

2ヶ月 前 | 0

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Getting the following error repeatedly for different error setting other than exponential error in population PK PD modelling in Simbiology.
As a general rule, you will need to address anything that causes an error, while a warning indicates something that may or may n...

3ヶ月 前 | 0

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SimBiology - sundials - ODE solver - CVODE
Hi Mary, It is technically possible to use arbitrary MATLAB functions with SimBiology. So you could in theory create a SimBiolo...

5ヶ月 前 | 0

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SimBiology - sundials - ODE solver - CVODE
Hi Mary, You are correct that MaximumNumberOfLogs and MaximumWallClock are SimBiology-specific options. In order to simulate y...

5ヶ月 前 | 0

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ODE Events In SimBiology toolbox
Currently (as of R2019a), SimBiology events cannot directly stop a simulation. I usually handle this sort of situation by post-p...

6ヶ月 前 | 0

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Simbiology Sensitivity analysis on dummy variable assigned through a repeatedAssignment Rule
One approach is to analytically differentiate the repeated assignment rule, and figure out how to calculate the desired sensitiv...

7ヶ月 前 | 0

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Tgspcread function error (line 323)
I think this is a bug in how the function tries to find out the size of the SPC file. You will see this error if the file is loc...

7ヶ月 前 | 0

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"Too many input arguments" error while running clustergram (Bioinformatics toolbox)
I suspect there is a function in your installation that is "shadowing" some other MATLAB function used by clustergram. I would t...

8ヶ月 前 | 0

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Debugging NaN/Inf right-hand-side values in SimBIology
Hi Abed, There's not currently any documented way to do this sort of debugging. We know that's a pain, so we're working on a de...

8ヶ月 前 | 0

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I Want a one line FASTA!
The fastawrite has a hard-coded limit of 70 characters per line. This follows NCBI recommendations. If you want to incease the m...

8ヶ月 前 | 1

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nlme fitting error for covariate in popPK model
Hi Jim, Here are the answers to your question: 1) SimBiology's covariate model expressions are quite constrained. The problem ...

10ヶ月 前 | 0

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Do simfunctions support parameterized dosing?
Yes, parameterized doses are supported with SimFunctions. However, you cannot change the type of parameterization after creating...

10ヶ月 前 | 0

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Simbiology: using a dummy species to fit data to a sum of real species with sbiofit
I think your idea is reasonable. I believe the problem is with the rule you added. As written, |addrule| adds an initial assignm...

11ヶ月 前 | 0

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Help with code to convert Simbiology sbproj file into gPKPDSim session file in .mat format
Ah, I finally figured out what's going on. The function "which" can only be used to locate files that are in the current working...

11ヶ月 前 | 0

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Help with code to convert Simbiology sbproj file into gPKPDSim session file in .mat format
See if your problem is fixed by using two slashes when you define |PathName|. That is, change the line of code to the following:...

11ヶ月 前 | 0

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how do I assign values to parameters in simbiology model from a .m file?
I'm guessing that some of your parameters are scoped to reactions. First, some background: In SimBiology, <https://www.mathwo...

11ヶ月 前 | 0

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I get a mavolcanoplot error and am not sure what it means
I looked at the code for this function. It looks like you are are getting the wrong error message due to a bug in the Bioinforma...

11ヶ月 前 | 1

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How does SimBiology calculate the "lambda" in NCA?
Hi, Currently (as of R2018b), SimBiology's NCA uses linear regression with all of the points weighted equally. I'm guessing t...

11ヶ月 前 | 0

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Can I create a variant that captures all current parameter, species and compartment values?
You're not overlooking anything. We just need to make variants easier to use. Right now, I would probably do this by making a he...

12ヶ月 前 | 0

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IS there a simple way to suppress the pop-up figure which is created automatically when calling clustergram()?
Since |clustergram| was designed to visualize data, there is not currently a documented way to keep a figure from appearing. How...

12ヶ月 前 | 0

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Better understanding of variants sought (also project files)
Hi Jim, Variants (and doses) are handled differently than the objects you see listed in the display for a model. As you disco...

約1年 前 | 0

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Not finding info on arrays of variant objects
Hi Jim, Sorry this wasn't clear from the documentation. I think [var1 var2] should have worked. Here are some equivalent ways...

約1年 前 | 0

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