Arthur Goldsipe
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Feeds
Jump species quantity then stay constant
I don't yet understand what your goal is. Can you provide more details on what behavior you want? A concrete example illustratin...
8 days ago | 1
how to understand and set the constant and boundarycondition properties.
If the Constant property of a species is true, then the value of that species cannot change at simulation times > 0. At time = 0...
23 days ago | 0
Unit conversion in Simbiology model
Hi, I'm a developer on the SimBiology team. I'm not sure I fully understand your question, but I'll try to answer based on my cu...
2 months ago | 0
| accepted
How to find the sensitivity of the model output if it is a variable for repeated assignment?
The solution I generally recommend is to calculate the sensitivities yourself by manualy differentiating the repeated assignment...
2 months ago | 0
how to handle the error 'Levenberg-Marquardt algorithm the Jacobian at BETA0 is ill-conditioned'?
It's difficult to say exactly what's going on without seeing your model and data. One explanation is that your model is not appr...
2 months ago | 0
How to write code for repetitive process?
If I understand your question, you're asking how to create an event that fires repeatedly. I'm not sure exactly what kind of rep...
2 months ago | 0
Investigating the effect of two covariates to an estimated parameter
Yes, you can specify multiple covariates. An example covariate expresssion would be exp(theta_fixed + theta1*covariate1 + theta2...
2 months ago | 0
| accepted
Why are population estimated parameters values the same as individual estimated parameters values?
Without the actual project, it's difficult to say what's going on. So let me offer some potential explanations for what you're s...
2 months ago | 0
How to simulate a drug concentration-time curve with confidence intervals?
Where did this plot come from? Without more information, we won't be able to say exactly how it was created. However, it looks ...
2 months ago | 0
| accepted
Oral Dose Not Exhibiting Absorption/Bioavailability in Simulation
Copying the answer from the comments: "Just wanted to update that I figured out a solution to the problem! I ended up creating a...
4 months ago | 0
Simbiology Previous Initial Parameters
The results of a fit only contain the outputs of the fit itself (for example, parameter estimates). If you want to reproduce tho...
4 months ago | 0
Transfer parameter estimates to model
For item #1, the SimBiologyModelAnalyzer app allows you to create a variant of the parameter estimates (see here for more detail...
4 months ago | 2
| accepted
Encoding conditional assignments in SimBiology
Hi emjey, I see this problem solved in one of two ways: 1) Take advantage of true/false getting converted to 1/0 in mathematic...
5 months ago | 1
How do I fit multiple curves at once, sharing some fitting parameters and floating others?
Are the 6 different analyte concentrations something you want to specify or estimate? Both of these these are possible in SimBio...
5 months ago | 1
| accepted
Different dilution effect on the kinetics of a time course
Hi Luis, Because you don't use units in your model, SimBiology interprets the reaction rates to have dimensions of amount/time....
5 months ago | 0
| accepted
Question re/ matlab.codetools.requiredFilesAndProducts function.
I'd first check the "Certain" field of the pList output to see if these products have been marked as definitely or just possibly...
6 months ago | 0
changes the the simulated mass with changing the absolute and relative tolerance
First, a disclaimer. I'm a SimBiology developer, not a modeler. So I'm most knowledgable about what is technically possible with...
6 months ago | 0
different event functions for the same species
The problem is that you have two conflicting mathematical definitions of Fw. You are trying to set it with both a repeated assig...
7 months ago | 0
| accepted
How do I fix a duplicate name error ?
It's hard to know exactly what's going on without more details. Can you share more details? Ideally, can you share the project a...
7 months ago | 0
| accepted
A variable is specified by more than one assignment rule
It sounds like you have an ill-defined problem with an algebraic loop. Specifically, A_Total is a function of a, but a is a func...
8 months ago | 0
Data fit to observables
Hi Justine, I just tried this in R2023b, and I was able to select an observable in the mapping for the response. I'm attaching ...
8 months ago | 0
| accepted
Fitting model on a Debian machine
If you want to fit a SimBiology model using a command-line function, you can directly call sbiofit (or sbiofitmixed). This is ex...
8 months ago | 0
Modeling Mitochondria Voltage depending on the Sodium/Potassium Pumps results in Algebraic loops Error.
Can you share your model? That would allow me to offer more specific advice. (If you're not comfortable posting it publicly, ple...
8 months ago | 0
| accepted
How can I add stoichiometry value in simbiology model builder 2023b ?
I believe your question is similar to this one. Please see the accepted answer there.
8 months ago | 0
| accepted
Dimensional analysis issue because of the function 'log' in the rule
Since your expression is dimensionally correct, you can safely ignore this warning. Note that is an informational warning (as o...
8 months ago | 0
| accepted
Using simFunction Object in Simbiology when my stoichiometry depends on a model parameter
The error you report is intended to communicate that SimBiology does not allow the following the following combination of condit...
8 months ago | 0
| accepted
Sensitivity analysis in Simbiology
SimBiology does not currently support local sensitivity analysis on models with active events. One potential workaround is to pe...
11 months ago | 0
Apply fmincon nonlinear parameter inequality constraints into SimBiology for parameterization
The estimation program in the SimBiology Model Analyzer app uses the command-line function sbiofit. Unfortunately, this function...
12 months ago | 0
| accepted
Parameter unit setting problem
Hi Bohao, SimBiology's units functionality does not support embedding numeric multipliers like 10^15. And even after you addres...
12 months ago | 0
| accepted
Categorical covariates in parameter estimation
Do you want to do nonlinear regression or nonlinear mixed effects (NLME)? The feature Joe mentions in his comment only applies t...
1 year ago | 0
| accepted
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