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Arthur Goldsipe


MathWorks

252 2011 年以降の合計貢献数

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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...

3日 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...

3日 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...

17日 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...

約2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...

2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...

3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...

3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...

3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 ...

5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...

5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...

6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...

6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:...

6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...

6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...

6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...

6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...

7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...

7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...

8ヶ月 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...

8ヶ月 前 | 0

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'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...

8ヶ月 前 | 0

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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...

8ヶ月 前 | 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...

8ヶ月 前 | 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...

9ヶ月 前 | 0

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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...

9ヶ月 前 | 0

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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...

10ヶ月 前 | 0

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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...

10ヶ月 前 | 0

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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 ...

10ヶ月 前 | 0

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

10ヶ月 前 | 0

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How can we use bayesian information in simbiology?
If you want to custom your objective function, you probably cannot use |sbiofit|. Instead, you must write the complete objective...

11ヶ月 前 | 0

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