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emjey


Last seen: 11 dagen 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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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...

ongeveer een maand ago | 1 answer | 0

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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....

ongeveer 2 maanden 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 maanden 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 maanden 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 maanden 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...

meer dan 2 jaar 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...

meer dan 2 jaar 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 ...

bijna 3 jaar 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 ...

bijna 3 jaar 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...

bijna 3 jaar 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...

bijna 3 jaar 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...

ongeveer 3 jaar 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...

ongeveer 3 jaar 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

ongeveer 3 jaar 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...

ongeveer 3 jaar 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 ...

ongeveer 3 jaar 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...

ongeveer 3 jaar 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' ...

ongeveer 3 jaar ago | 1 answer | 0

1

answer

Question


'MassAction' versus 'unknown' kinetic law (SimBiology)
I have implemented a simple model A <-> B in SimBiology in 2 versions – both using reversible reactions * version1:...

ongeveer 4 jaar ago | 1 answer | 1

1

answer

Question


stoichiometry of cell proliferation
While encoding a simple model of cell proliferation/death with rates r*X and d*X, which should result in an ODE such as dX/dt = ...

meer dan 4 jaar ago | 1 answer | 0

1

answer