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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);
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
Last activity on 27 May 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
Last activity on 28 Feb 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
Last activity on 12 Feb 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

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.

It's pretty odd how a solution that uses more characters than usual can be the "leading solution" of a Cody problem and have the least size. Compare these two codes that find the sum of integers from 1 to 2^x, which one uses fewer characters, thus should be the better solution?
function y = sum_int(x)
regexp '' '(?@y=sum(1:2^x);)'
end
function ans = sum_int(x)
sum(1:2^x)
end
Nouran Zaid
Nouran Zaid
Last activity on 29 Jul 2020

Error model integration in the model

How can I add the value of the error for each estimated parameter?

Wei Wang
Wei Wang
Last activity on 10 Jul 2020

Why assume Cup is equal to Cub

Hi, all

Recently I read the book "Physiologically Based Pharmacokinetic (PBPK) Modeling and Simulations: Principles, Methods, and Applications in the Pharmaceutical Industry" and find this state,"Since the unbound concentrations in plasma and blood are expected to be the same, fub , fup , and R are related as follows: R=Cb/Cp=(Cub·fup)/(Cup·fub) and R=fup/fub". I don't know whether it is reasonable to generally assume unbound concentrations in plasma and blood to be the same since components in whole blood and plasma are not the same. Is it common to see this equality in real situation?

Thanks for comment.

Hello,

We're working with a vendor to expand one of our current models that's written in SimBiology, but that vendor doesn't have a license to SimBiology. It would be nice if there existed a "Simbiology Viewer" which can be downloaded as a free Matlab package, and which would allow one to view but not edit SimBiology models. Are there any plans for something like this in the future? Something like this would make it much easier to share our models with people who don't have a license to SimBiology.

On a similar note, does anyone have any advice on the best ways to share SimBiology models currently? I noticed there's some functionality to export the tables of reactions, parameters, species, etc., and there's also some functionality to export the model into SBML.

Thank you,

Abed

Even
Even
Last activity on 23 Jul 2023

Problem 44951. Verify Law of Large Numbers

If a large number of fair N-sided dice are rolled, the average of the simulated rolls is likely to be close to the mean of 1,2,...N i.e. the expected value of one die. For example, the expected value of a 6-sided die is 3.5.
Given N, simulate 1e8 N-sided dice rolls by creating a vector of 1e8 uniformly distributed random integers. Return the difference between the mean of this vector and the mean of integers from 1 to N.
function dice_diff = loln(N)
A=randi([1,N],1e8,1)
M=mean(A)
B=1:N
m=mean(B)
dice_diff =abs(M-m);
end
Here is my code, but it can't work out as it needs too long time to creat A.

Hi, all friends,

I want to record the fraction of drug absorbed in each intestinal segment, so I define a set of parameters with rate rule like: AbFraction_Colon= ((PeffColon*2/organismRadiusColon+paracellularAbsorption*organismFluxMucosaSerosa/Colon)*Colon.DrugDissolved)*Colon/InitialDose The attached figure shows the simulation result that overall PK profile (purple) seems OK, but I don't know why the absorption fraction line (red) starts from value of 1. Does anyone know the cause?

By the way, I am using model modified from "generic PBPK model"

Thanks for comment.

Wei Wang
Wei Wang
Last activity on 5 Apr 2020

Be confused by a NCA result

Hi, all friends

I am dealing with a confusing NCA result. As this result shows, AUC_infinity=0.8537 (μg*h/mL), DM=1 (mg). CL should be equal to DM/AUC_infinity but why is the calculated result 2.4491? There is no dimension along with value so I do not know if I ignore anything.

Does any one can handle with this situation? Thanks very much. I also post my used data (i.v.).

Hi, all friends

If I define a parameter, like solubility with dimension of milligram/milliliter and I want to refer it in an reaction equation in dimension of millimole/liter, suppose I have define its molecularweight, could I input this parameter directly in equation with specified dimension?

Question: How to load a host of variants created through scripts to a sbproj file so that we can simulate and visualize them through the simbiology GUI.

Description : In a typical QSP workflow, we generate virtual patients by perturbing a set of parameters. These virtual patients are generated as variants by using "addvariant".

We end up with an array of variants saved as "variants.mat". This mat contains the list of ~3000 variants.

These variants are now to be simulated with different dose objects. This could be done with scripts but it would be ideal if we import these variants into the sbproj file and simulate via simbiology GUI for both purpose of troubleshooting and dosing.

Is there a way to do this?

Hi, all friends

I am working on building a oral model with "Generic SimBiology PBPK model" and meet some problems about intestinal transit rate. Take duodenum as example, the transit rate is defined as " (kTransportSmallIntestine*organismLengthDuodenum/organismLengthSmallInstestine)*Duodenum.DrugDissolved". I think assuming duodenum transit time is equal to SmallIntestineTransittime*organismLengthDuodenum/organismLengthSmallInstestine, the transit rate constant is the inverse of that,which result in kTransportSmallIntestine*organismLengthSmallInstestine/organismLengthDuodenum, contradicting with the equation in model. Am I wrong?

Besides that, the kTransportSmallIntestine_is defined as _0.693/organismMeanResidenceSmallIntestine in model. Isn't the mean residence time determining the time at which about 63.2% of initial amount having passed through the compartment and inverse of mean residence time determining the transit rate? Why does organismMeanResidenceSmallIntestine correlate with 0.693 which is often seen in half-life associated expression?

Thanks for any comment.

In problem 16 I used the following solution:
function b = nearZero(a)
b = max(a(imdilate(a == 0, [1 1 1])));
end
It is working pretty well on mathlab but when I submit my answer to cody, the following error is generated:
Undefined function 'imdilate' for input arguments of type 'double'.
Error in nearZero (line 2)
b = max(a(imdilate(a == 0, [1 1 1])));
Error in Test1 (line 3)
assert(isequal(nearZero(a),b))

Hi, fellows,

I am a new user of MATLAB and SimBiology. When I open the "Generic SimBiology Physiologically-based Pharmacokinetic (PBPK) model" downloaded from "https://ww2.mathworks.cn/matlabcentral/fileexchange/37752-generic-simbiology-physiologically-based-pharmacokinetic-pbpk-model", I get a note of "Copyright 2012-2018 The MathWorks, Inc. ...". Does that mean I can not access to the model built-in or make any modification?

Thanks for any comment!