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How to set boundary conditions for a reaction to occur in SimBiology?
Hi, Take a look at this answer I shared. It's from several years ago, but the information is still accurate. Some additional ti...

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Invalid assignment syntax or parse error for event function (Simbiology)
Hi, Events can only assign a value to a component, not to an expression. So your assignment ((syn_CT.PD1_PDL1+syn_CT.PD1_PDL2)/...

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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...

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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...

mehr als 2 Jahre vor | 0

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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...

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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...

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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...

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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 ...

mehr als 2 Jahre vor | 0

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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...

mehr als 2 Jahre vor | 0

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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...

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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...

mehr als 2 Jahre vor | 0

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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...

fast 3 Jahre vor | 0

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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...

fast 3 Jahre vor | 0

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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...

fast 3 Jahre vor | 2

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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...

fast 3 Jahre vor | 1

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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 ...

fast 3 Jahre vor | 1

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Steady State in insulindemo
Hi Pierre, Apologies for the long response, but answering your question acurately requires discussing a lot of details, at leas...

fast 3 Jahre vor | 0

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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...

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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...

etwa 3 Jahre vor | 0

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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...

etwa 3 Jahre vor | 1

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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". ...

etwa 3 Jahre vor | 0

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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...

etwa 3 Jahre vor | 0

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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 ...

etwa 3 Jahre vor | 0

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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...

etwa 3 Jahre vor | 0

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Events during the fitting in Simbiology
Yes, all active events will be used during simulations, including simulations performed while doing NLME estimation.

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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...

etwa 3 Jahre vor | 0

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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...

etwa 3 Jahre vor | 2

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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...

etwa 3 Jahre vor | 0

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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...

etwa 3 Jahre vor | 0

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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...

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