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emjey


Last seen: 10 days ago |  Active since 2018

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I am working on the development of models and software in biotech industry

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Question


Encoding conditional assignments in SimBiology
Is it possible to define conditional assignments in SimBiology, i.e. if a > 0 param1 = a + b else param1 = a + c e...

4 months ago | 2 answers | 0

2

answers

Answered
Plotting experimental data and predictions in one plot in SimBiology Model Analyzer
I have the solution. One has to simply click a dataset from the browser and drag on the prediciton plot one wants overplot.

10 months ago | 0

Question


Plotting experimental data and predictions in one plot in SimBiology Model Analyzer
Basically what the tiitle says, how can I overplot experimental data and the predictions in one plot in SimBiology Model Analyze...

10 months ago | 1 answer | 0

1

answer

Answered
simbiology reaction name display
Go to APPEARNACE/TEXT/Location in the Property Editor and select the place you wish the reaction name to be displayed - see scre...

1 year ago | 1

| accepted

Question


Modeling dissociation using Hill function provides misleading results
I stumbled upon a simple dissociation model using Hill function. The process in question is [A:B] -> A + 2 B A, B, [A:B] sp...

1 year ago | 1 answer | 0

1

answer

Answered
initial assignment and repeated assignment problem
The initial assignments are used to assign initial values of a species, e.g. tumour size, inital concentrations of the species i...

1 year ago | 1

| accepted

Question


readtable disfigures the CSV file header
I need to remove the units within brackets from my CSV file, attached. ID par1 (mol) par2 (meter^3) par3 (kg/L) 1 4 5 11 2 3 ...

1 year ago | 2 answers | 0

2

answers

Answered
Change the zeros to ones and the ones to zeros.
you can do it in one line like this >> V = [ 1, 1, 1, 1, 0, 1, 0, 1]; >> abs(V-1) ans = 0 0 0 0 1 0...

2 years ago | 0

Question


Is it possible to display initial assignments and/or parameters in SimBiology diagram?
Essentially, what the title says. I remember all assignments used to be displayed by default. Now, with R2022a only repeated ass...

2 years ago | 1 answer | 0

1

answer

Question


Is it possible to deactivate all reactions within a compartment in SimBiology?
I would like to test a selected submodule of my model, which amounts to switching off other unwanted compartments which contain ...

2 years ago | 1 answer | 0

1

answer

Question


how to re-assign parameter value assigned in an active variant in SimBiology?
Hi, I cannot re-assign a value to a parameter, kdeg, defined in the active variant, variant1. The following code shows the step...

2 years ago | 1 answer | 0

1

answer

Question


selecting and re-assignment of non-existing parameters in SimBiology does not trigger any warning?
Selection by name and re-assignment of model parameters can be done like this tempVar = sbioselect(modelObj1,'Name','p1'); set(...

2 years ago | 2 answers | 0

2

answers

Question


Suggetsed improvements list in SimBiology
hi SimBiology team, here a list of things I recenlty found in SimBiology not working or worth improving - roughly in the order o...

2 years ago | 1 answer | 0

1

answer

Question


SimBiology parameter estimation for a series of single dose-response data
I would like to estimate set of parameters from a series of experiments with different doses and single measurement points. I.e....

2 years ago | 1 answer | 0

1

answer

Question


Build-in unit conversion in SimBiology
I wonder if you can provide resource with proper definition of units. What one gets with sbiowhos -builtin -unit does not make s...

2 years ago | 1 answer | 0

1

answer

Question


Is specifying objective fuction for multiple variables in SimBiology possible?
I have a question about specification of objective function for multiple variables simultanously in SimBiology. Is it possible a...

2 years ago | 1 answer | 0

1

answer

Question


Incorrect units in simple reaction in SimBiology?
I wonder why SimBiology does not detect any issues in the following model. A cell, Cell, is producing signaling molecule, Sig,...

2 years ago | 1 answer | 0

1

answer

Question


Issues with doses/variants in parfor loop in SimBiology
I have a question about runing the sbproj models in parfor loop 1. I load project and set up the solver: sbioloadproject('mode...

4 years ago | 1 answer | 0

1

answer

Question


using MaximumWallClock in a loop
I run many simulations in a loop (global sensitivity analysis) and would like to terminate stuck simulations by setting 'Maxim...

4 years ago | 2 answers | 0

2

answers

Question


how to plot non-standard contour plots
I would like to plot following contour plots representing two dimensional cumulative distributon functions (CDF) given the data ...

5 years ago | 0 answers | 0

0

answers

Answered
How to run sbproj using sbiosimulate with a selected dose in SimBiology?
OK, I found it out, I was missing the dose object modelName = 'AntibacterialPKPD.sbproj'; sbioloadproject(modelName,'m1') d1 ...

5 years ago | 1

Question


How to run sbproj using sbiosimulate with a selected dose in SimBiology?
Consider the predefiend doses '250 mg bid', '250 mg tid', etc. in the model AntibacterialPKPD.sbproj, see screenshot I am una...

5 years ago | 1 answer | 0

1

answer

Answered
Fail to start parpool
See this discussion below, it should answer your problem: https://uk.mathworks.com/matlabcentral/answers/196549-failed-to-start...

5 years ago | 0

Question


How to handle warnings in SimBiology within series of simulations?
To perform a sensitivity analysis I am running *.sbproj coded models using 'biosimulate' in a for-loop and see for some paramete...

5 years ago | 1 answer | 0

1

answer

Answered
what is the reason for this error ?
Check the following out, this should help: https://uk.mathworks.com/matlabcentral/answers/130609-matlab-coder-build-error-compi...

5 years ago | 0

| accepted

Answered
Problem regarding reading excel file in a loop
It seems your issue was answered here https://uk.mathworks.com/matlabcentral/answers/349109-read-in-excel-sheets-with-a-loop

5 years ago | 0

| accepted

Question


parfor error for global SA Morris method using SimBiology
hi, I am trying to use parallel toolbox to speed up my global SA with Morris method. Basically it averages elementary effects fo...

5 years ago | 1 answer | 0

1

answer

Answered
Issue with SimBiology - parameters from valid .sbproj not loading
OK, problem solved. This is to me a bug in the display of parameters - only those parameters which are visible on the diagram ...

5 years ago | 0

Question


Issue with SimBiology - parameters from valid .sbproj not loading
Hi, I am having an issue pertaining to some *.sbproj models. See for example the attached simple Lotka model version. While the...

5 years ago | 2 answers | 0

2

answers

Question


Issue with parameter array sorting in SimBiology after loading using sbioloadproject
When I load a .sbproj the parameters are often in seemingly random order. Consider the example model 'AntibacterialPKPD.sbproj' ...

5 years ago | 1 answer | 0

1

answer

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