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Arthur Goldsipe


MathWorks

253 total contributions since 2011

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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...

8일 ago | 0

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Answered
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...

2달 ago | 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...

2달 ago | 0

Answered
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...

3달 ago | 0

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Answered
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...

4달 ago | 0

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Answered
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...

4달 ago | 0

Answered
"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...

5달 ago | 0

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Answered
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...

5달 ago | 0

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Answered
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...

5달 ago | 1

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Answered
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 ...

7달 ago | 0

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

7달 ago | 0

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Answered
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...

8달 ago | 0

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Answered
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...

8달 ago | 0

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Answered
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:...

8달 ago | 0

Answered
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...

8달 ago | 0

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Answered
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...

8달 ago | 1

| accepted

Answered
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...

8달 ago | 0

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Answered
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...

9달 ago | 0

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Answered
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...

9달 ago | 0

Answered
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...

10달 ago | 0

Answered
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...

10달 ago | 0

Answered
'MassAction' versus 'unknown' kinetic law (SimBiology)
Hi Maciej, This is a good question. We do document what SimBiology does <https://www.mathworks.com/help/simbio/ug/libraries.h...

10달 ago | 0

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Answered
Could Simbiology simulations have a preload function?
Hi Jim, You're not overlooking any functionality. I agree that these would be useful enhancements. I work primarily from func...

10달 ago | 0

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How can I parameter estimate many unknown parameters in a system of nonlinear ODE?
I see that you mentioned SimBiology in a comment on the previous answer. I'm a developer on that product, so I wanted to share t...

10달 ago | 0

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Simbiology Unit testing and Version control
The SimBiology GUI does not have any specific functionality for version control or unit testing. However, you can use the genera...

11달 ago | 0

Answered
Surface Area Calculations in Simbiology
Hi, In SimBiology, compartments can also represent 2-dimensional areas, such as the surface of a cell. I believe the error yo...

11달 ago | 0

Answered
Simbiology - limits in fitting
If you are using the function |sbiofit| from the command line, you can specify bounds using the |estimatedInfo| input argument a...

12달 ago | 0

Answered
how to find growth rate constants?
Are you referring to this example? <https://www.mathworks.com/products/demos/simbiology/anti-cancer-model/anti-cancer-model.html...

12달 ago | 0

Answered
SimBiology Desktop Fitting using Concentration and response time profiles
The SimBiology documentation includes <https://www.mathworks.com/help/search.html?qdoc=sbiofit+type%3Aex several examples> that ...

12달 ago | 0

Answered
a training program on PKPD and PBPK
You can find SimBiology PKPD and PBPK resources <https://www.mathworks.com/discovery/pharmacokinetic.html here>.

12달 ago | 0

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