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Fernando Ortega
Fernando Ortega
Última actividad el 8 de Nov. de 2022

PK model: absorption

Hi,
I want to develop a PK model based on some PK data. The PK data seems to display 2 peaks when one initial dose is given.
I would like to give one dose. A fraction of this dose (fr) is absorbed following the linear relationship - ka*Drug the other fraction (1-fr) is absorbed following a linear absorption (ka1*Drug) with a Tlag (it maybe a zero order). The fraction fr is unknown so it must be estimate.
Does anyone have can provide any suggestion to implement this in symbiology or provide a link where I can look?
Thank you very much in advance,
Ferran
I have a species which is absorbed in a zero-order manner. I want to model the reaction rate as "UptakeRate*ActiveState". So I can give value of 1 or 0 to ActivateState to control the active state of this process. The species itself is under control multiple processes, so I want to use Event to automatically change the active state of absorption.
However, when I use these two events:
Event 1，trigger: species > 0, Function: ActiveState =1; Event 2, trigger: species <=0, Function: ActiveState=0
The simulation seems to be stuck without stop.
Is there any way to solve this ? Thanks
Just in case, I have my license of MATLAB. I just have this question and I didn't find any information. I wouldn't like to create another account, for this reason I prefer to ask here.
Hi,
Im a new user of simbiology, can any one tell me How to fix a parameters to a known constant when estimating models.
Rutwij Dave
Rutwij Dave
Última actividad el 28 de Jul. de 2022

2021b - reactions

Hello,
In the previous versions, we were able to change the reaction line properties to Reactant, Product, or Reactant and Product. This option is not available in 2021b. How do we change the proerpties if we reaction line is both Reactant and Product?
Thanks
Rutwij Dave
Rutwij Dave
Última actividad el 27 de Abr. de 2022

Exporting simulations to MATLAB workspace

Simulations and model results do not get exported to the MATLAB workspace automatically. 2021b. Under Model Analyzer preferences, I checked "export results when model run is complete", but to no effect. I have to manually expert simulations after each run. Please advise. Thanks RD

Suraj Kumar
Suraj Kumar
Última actividad el 5 de En. de 2023

Matlab cody problem submission is removed. Why?

I have submitted a problem in cody some days back. Now it is not showing in my profile. Initially it was accepted and some people submitted the solutions also, however It has been removed after that, are there some guidelines which I am not following?
Hi everyone
I am a new of this community and I very interested in this forum and Matlab.I am trying to submit a soultion but as tiltle my code has a built-in function so the test systerm dont reconisie it.It run completely ok on my computer.
This is problem
https://www.mathworks.com/matlabcentral/cody/problems/45196-determine-whether-a-given-point-is-inside-or-outside-a-polygon/solutions/new
This is my solution
function [boOut] = BoIfPointInPoly(PolyMatrix,p_test)
%Summary of this function goes here
%{
if we draw a line from test point to a central point of a side of The polygon
then we extend that line to the furthest point of the polygon ensure that
line go through all side of Polygon in 1 direction.I call that line is line_test
Next find number of intersert of line test and all sides w polyxpoly
function
num interset point is odd mean p_test inside
num interset point is even mean p_test outside
this solution go from the concept that if a line go in from a side it has go out
from other side.So if it go in but not go out that mean it start from
inside.
%}
% Detailed explanation goes here
%line from p test throuh central of a side to furthest point of polygon
%find vector
V = ((PolyMatrix(1,:) + PolyMatrix(2,:)) /2) - p_test ;
%draw that vector to furtest point
pend = p_test + V * max(PolyMatrix(:));
%with multi of V and biggest element I assume that line will go all out the
%polygon which ensure out logic will right
line_test = [p_test ; pend];
disp('Our line test\n');
disp(line_test);
%find interst point
p_inter = polyxpoly(PolyMatrix(:,1),PolyMatrix(:,2),line_test(:,1),line_test(:,2));
%find number of interset (row)
[numIntere,trash] = size(p_inter);
disp('Number of interest point:');
disp(numIntere);
%determine in or out
if (rem(numIntere,2) == 0)
boOut = 0;
else
boOut = 1;
end
end
Can anyone has solution.
I'm trying to solve one problem in Cody, but a function 'fmincon' is not recognized by the online compiler. Is there any way to use functions in optimization toolbox in Cody?
Mariola Camacho Lie
Mariola Camacho Lie
Última actividad el 23 de Oct. de 2021

Problemas in Cody Area

I already solved some problems in Cody, why does he not increase my points or allow me to earn badges?
Rahul Gulia
Rahul Gulia
Última actividad el 26 de Sept. de 2021

Creating a Problem Group in MATLAB cody.

I need to put a number of problems on MATLAB cody under same Problem group, as many other people have done.
Can anyone please help me on this.
Aaron S
Aaron S
Última actividad el 8 de Mzo. de 2023

Rectangular pulse for input species

Hello

I would like to pulse an input species. I read in the forums that repeated assignments can be used for this, but I am not exactly sure how to implement this. This is the MATLAB code that resembles what I would like the input pattern to be:

t = 0:1/1e3:60;
d = [10:2:30]';
x = @rectpuls;
y = pulstran(t,d,x);

plot(t,y)
hold off
xlabel('Time (s)')
ylabel('Waveform')

Thanks for any help! Aaron

George Bittar
George Bittar
Última actividad el 30 de Dic. de 2022

How do I call the reference solution in Cody?

I created a problem in Cody that approximates e. To test the user's solution, I compare their solution to e. What I want to do instead is compare the user's solution to my reference solution. The question is how do I call the reference solution in the test suite?
This is currently my test suite.
sol=exp(1);
y_correct = playgame();
assessVariableEqual('y_correct',sol);
Anirban Pal
Anirban Pal
Última actividad el 8 de Jun. de 2021

My Cody problems are getting deleted by the server

I created several problems recently in CODY. Some of them got removed automatically. I was curious as to why.
It is possible that the problems used latex in their description, so I am not sure if that was the reason they got rejected by the cody server.
Muhtasim Haque Nahian
Muhtasim Haque Nahian
Última actividad el 27 de Mayo de 2021

My problems are vanished

I created some problems last night and created a group too. All those are now missing.
Also my ranking progress, activites, badges earned last night are missing too.
Tungky Subroto
Tungky Subroto
Última actividad el 28 de Feb. de 2021

Cody challenges for Simulink ?

Hi all,
I hope everyone is doing well and keeping safe. I was wondering, are there any Cody challenges for Simulink these days?
I saw a post from 2015 (https://blogs.mathworks.com/simulink/2015/08/07/modeling-and-simulation-challenge-in-cody/) and it seems there was a Simulink or "Modeling and Simulation Challenge" problem group, but I couldn't find this group anymore. Perhaps I missing something?
Thank you beforehand.
Tungky
Abed Alnaif
Abed Alnaif
Última actividad el 12 de Feb. de 2021

Creating standalone app from model

Hello, We would like to share one of our QSP models with non-modeler colleagues for them to play with. Is there a simple way to generate a standalone app from a SimBiology model, with sliders allowing the user to change various parameter values?

Thank you,

Abed

Abed Alnaif
Abed Alnaif
Última actividad el 4 de Dic. de 2020

Handling "Below Limit of Quantification" (BLoQ) data

Hello, Does the 'sbiofit' function have functionality implemented for likelihood=based handling of BLoQ censored data, similar to functionality in NONMEM and other softwares? If not, are there plans to implement this?

Thanks,

Abed

I see this solution on the Cody solutions list. Solution 1949216
I am puzzled as to how this could possibly be rated as correct (size 48)
(BTW - I am pretty sure I saw this, or similar, before.)
function ans = fileread(varargin)
' ';
a=1;
b=3;
a=1;
b=3;a=1;
b=3;a=1;
b=3;a=1;
b=3; end

Hello,

I recently downloaded the GlobalSensitivityAnalysisApp. I am trying to perform a GSA using a simbiology model. I try running the App, but I get the error "No Sobol Indices Available to Plot. Configure the Sobol section and click the Compute button." I'm not sure if there is a step I'm overlooking. I'm following the instructional video for this app on the Matlab website, and I'm not sure what Configure the Sobol section is referring to. Any guidance would be greatly appreciated.