Arthur Goldsipe
MathWorks
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Restricting output times when calling simfunctions
Yes, if you use tStop = [], then only results at tOutput will be reported.
4 días ago | 0
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Diagnosing simfunction acceleration failure
Hi Abed, There is currently no publicly documented way to get additional debugging information. These situations have historica...
7 días ago | 0
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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...
14 días ago | 0
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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...
27 días ago | 0
| accepted
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...
2 meses ago | 1
| accepted
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...
2 meses ago | 0
| accepted
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 ...
2 meses ago | 0
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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...
3 meses ago | 0
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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...
3 meses ago | 1
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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...
3 meses ago | 1
| accepted
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, ...
4 meses ago | 1
| accepted
Volume change in simbiology
As described here, SimBiology conserves amounts when changing compartment volumes. If I were building the model, I would not use...
4 meses ago | 0
| accepted
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...
4 meses ago | 1
| accepted
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. ...
4 meses ago | 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...
4 meses ago | 0
| accepted
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...
4 meses ago | 0
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...
5 meses ago | 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...
5 meses ago | 0
| accepted
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...
6 meses ago | 0
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...
8 meses ago | 0
SimBiology - sundials - ODE solver - CVODE
Hi Mary, You are correct that MaximumNumberOfLogs and MaximumWallClock are SimBiology-specific options. In order to simulate y...
8 meses ago | 0
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...
8 meses ago | 0
| accepted
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...
10 meses ago | 0
| accepted
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...
10 meses ago | 0
"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...
10 meses ago | 0
| accepted
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...
11 meses ago | 0
| accepted
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...
11 meses ago | 1
| accepted
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 ...
alrededor de 1 año ago | 0
| accepted
Do simfunctions support parameterized dosing?
Yes, parameterized doses are supported with SimFunctions. However, you cannot change the type of parameterization after creating...
alrededor de 1 año ago | 0
| accepted
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...
alrededor de 1 año ago | 0
| accepted
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