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Content Feed
How to customize built-in optimization functions in SimBiology without using MATLAB code?
If I understand your question correctly, you are asking how to customie the cost (or objective) function when using a fit progra...
7 days ago | 0
| accepted
why PSI values are diffrent when nlmefit using ode45 solver compared to when it uses analytical solution?
The reason the results from nlmefit differ significantly is because your ODE solution is not equivalent to your analyitical solu...
13 days ago | 0
Scanning Simbiology variants in Matlab for virtual population simulations
There are lots of ways you could do this. And you certainly could use variants. But I personally would do this by creating a Sim...
17 days ago | 0
| accepted
How do I generate a rectangular pulse for an input species in Simbiology?
I would not use rules to implement discontinuous changes in a SimBiology model. The ODE solver should be restarted whenever ther...
18 days ago | 0
| accepted
Error: expected the time data (independent variable) of the data input argument to be finite
This error means that your time data is invalid because it contains non-finite values. Look for infinite or NaN (not a number) v...
1 month ago | 0
| accepted
use simbiology for radiation dosimetry
SimBiology is primarily designed to model reactions of species in compartments. It can be used to model other problems that are ...
1 month ago | 0
Should plasma membrane be its own compartment?
Yes, I think the simplest approach would be to create separate compartments for each location where you need to consider that sp...
1 month ago | 0
Different units in the same Simbiology model
I would recommend against mixing mass-based units and mole-based units for species participating in the same reaction. In such c...
2 months ago | 1
Status 429 with message "Too Many Requests" in response to NCBI URL
As described here, you are seeing the error because NCBI limits the number of queries from a particular IP address to 3 per seco...
2 months ago | 0
eGPU set up for Simbiology calculation
No, SimBiology does not currently have any built-in support for GPU calculations. I suggest profiling to see what code is takin...
2 months ago | 0
| accepted
What toolboxes are useful to run with SimBiology?
I recommend simulating your model within SimBiology (that is, using SimBiology's ODE solvers rather than exporting your equation...
2 months ago | 0
| accepted
Apply Parallel Computing to Simbiology
Hi Jesse, The simplest fix would be to change 'ProgressPlot',true to 'ProgressPlot',false. The issue is that you're trying to c...
2 months ago | 1
| accepted
Command in Script for Data Comparison
Hi, Are you using the functions sbiofit or sbiofitmixed? If so, you will find RMSE, AIC, and BIC as properties on the first out...
3 months ago | 1
| accepted
Need help converting berkeley madonna code to matlab code
If you'd like to convert a Berkeley Madonna model to the equivalent SimBiology model, you can try using this converter from the ...
4 months ago | 1
Steady State in insulindemo
Hi Pierre, Apologies for the long response, but answering your question acurately requires discussing a lot of details, at leas...
5 months ago | 0
Insulindemo_Change of numerical values in some parameters are not reflected in the simulation
Hi Juliana, Yes, you can change these parameters. However, the values on the parameters themselves are replaced by any values s...
5 months ago | 0
| accepted
How to get rid of "Integration Tolerance Not Met"?
If you simulate from the command line, you should see a warning that infinite or NaN (not-a-number) values occur during the simu...
6 months ago | 0
value of Stomach Glu After Dosing_insulindemo
I believe you are referring to the value of 125 in the variant named "Type 2 diabetic", as shown for example on this page. I bel...
6 months ago | 1
| accepted
Cannot parse function hints
When I do something similar in my installation of MATLAB version R2021a, I get a little popup that says "No completions found". ...
6 months ago | 0
Nucleotides import- not from database
Based on the information you've provided, I would import the data directly from Excel as you currently have it formatted. You ca...
6 months ago | 0
| accepted
How to fit an observable in a SimBiology model using sbiofitmixed function?
HI Budhaditya Chatterjee, This looks like a bug that someone else reported to me a few days ago. The bug is triggered whenever ...
7 months ago | 0
| accepted
lsqnonlin multiple dataset optimisation
You can use lsqnonlin with or without SimBiology. If you want to do this without SimBiology, you need to write a function that t...
7 months ago | 0
Events during the fitting in Simbiology
Yes, all active events will be used during simulations, including simulations performed while doing NLME estimation.
7 months ago | 0
| accepted
SImbiology: access "Initial Conditions" (not InitialValues)
As you discovered, getequations is intended as a textual report and is not well suited for programmatic access to initial values...
7 months ago | 0
In Online Matlab under App menu, Signal Analyzer not working?
The Signal Analyzer App is not supported with MATLAB Online. You will need to use the desktop version of MATLAB if you need acce...
7 months ago | 2
Error in data fitting in simbiology
When you perform a fit in SimBiology, one of the first things that happens is the model is simulated using the initial parameter...
7 months ago | 0
| accepted
When will sbmlimport support sbml level 3?
SimBiology already supports SBML level 3 version 1. That was introduced in R2016a. You can read more about what is supported her...
8 months ago | 0
| accepted
Installing Supported Compliers on Ubuntu 20.01
You can use "apt" to install these compilers. Try googling "install gcc ubuntu" and "install jdk ubuntu" if you need more detail...
8 months ago | 0
| accepted
Creating a cell growth model using SimBiology.
Hi, The capacity of a compartment can vary during the course of a simulation. To do this, you must set the Constant property to...
9 months ago | 1
| accepted
Fit data with weight in Simbiology
You can use NaN to indicate a missing value in your data. Such points will be ignored during fitting. If you are getting an erro...
9 months ago | 1
| accepted
