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Automating Parameter Identifiability Analysis in SimBiology
Is it possible to develop a MATLAB Live Script that automates a series of SimBiology model fits to obtain likelihood profiles? The goal is to fit a kinetic model to experimental data while systematically fixing the value of one kinetic constant (e.g., k1) and leaving the others unrestricted.
The script would perform the following:
Use a pre-configured SimBiology project where the best fit to the experimental data has already been established (including dependent/independent variables, covariates, the error model, and optimization settings).
Iterate over a defined sequence of fixed values for a chosen parameter.
For each fixed value, run the estimation to optimize the remaining parameters.
Record the resulting Sum of Squared Errors (SSE) for each run.
The final output would be a likelihood profile—a plot of SSE versus the fixed parameter value (e.g., k1)—to assess the practical identifiability of each model parameter.
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For some time now, this has been bugging me - so I thought to gather some more feedback/information/opinions on this.
What would you classify Recursion? As a loop or as a vectorized section of code?
For context, this query occured to me while creating Cody problems involving strict (so to speak) vectorization - (Everyone is more than welcome to check my recent Cody questions).
To make problems interesting and/or difficult, I (and other posters) ban functions and functionalities - such as for loops, while loops, if-else statements, arrayfun() and the rest of the fun() family functions. However, some of the solutions including the reference solution I came up with for my latest problem, contained recursion.
I am rather divided on how to categorize it. What do you think?
Hey cody fellows :-) !
I recently created two problem groups, but as you can see I struggle to set their cover images :
What is weird given :
- I already did it successfully twice in the past for my previous groups ;
- If you take one problem specifically, Problem 60984. Mesh the icosahedron for instance, you can normally see the icon of the cover image in the top right hand corner, can't you ?
- I always manage to set cover images to my contributions (mostly in the filexchange).
I already tried several image formats, included .png 4/3 ratio, but still the cover images don't set.
Could you please help me to correctly set my cover images ?
Thank you.
Nicolas
I want to observe the time (Tmax) to reach maximum drug concentration (Cmax) in my model. I have set up the OBSERVABLES as follows (figure1): Cmax = max(Blood.lL15); Tmax_LT = time(Conc_lL15_LT_nm == max(Conc_lL15_LT_nm)); Tmax_Tm = time(Conc_lL15_Tumor_nm == max(Conc_lL15_Tumor_nm)); After running the Sobol indices program for global sensitivity analysis, with inputs being some parameters and their ranges, the output for Cmax works, but there are some prompts, as shown in figure2. Additionally, when outputting Tmax, the program does not run successfully and reports some errors, as shown in figure2. How can I resolve the errors when outputting Tmax?
I like this problem by James and have solved it in several ways. A solution by Natalie impressed me and introduced me to a new function conv2. However, it occured to me that the numerous test for the problem only cover cases of square matrices. My original solutions, and Natalie's, did niot work on rectangular matrices. I have now produced a solution which works on rectangular matrices. Thanks for this thought provoking problem James.
I have written, tested, and prepared a function with four subsunctions on my computer for solving one of the problems in the list of Cody problems in MathWorks in three days. Today, when I wanted to upload or copy paste the codes of the function and its subfunctions to the specified place of the problem of Cody page, I do not see a place to upload it, and the ability to copy past the codes. The total of the entire codes and their documentations is about 600 lines, which means that I cannot and it is not worth it to retype all of them in the relevent Cody environment after spending a few days. I would appreciate your guidance on how to enter the prepared codes to the desired environment in Cody.
I've been trying this problem a lot of time and i don't understand why my solution doesnt't work.
In 4 tests i get the error Assertion failed but when i run the code myself i get the diag and antidiag correctly.
function [diag_elements, antidg_elements] = your_fcn_name(x)
[m, n] = size(x);
% Inicializar los vectores de la diagonal y la anti-diagonal
diag_elements = zeros(1, min(m, n));
antidg_elements = zeros(1, min(m, n));
% Extraer los elementos de la diagonal
for i = 1:min(m, n)
diag_elements(i) = x(i, i);
end
% Extraer los elementos de la anti-diagonal
for i = 1:min(m, n)
antidg_elements(i) = x(m-i+1, i);
end
end
My following code works running Matlab 2024b for all test cases. However, 3 of 7 tests fail (#1, #4, & #5) the QWERTY Shift Encoder problem. Any ideas what I am missing?
Thanks in advance.
keyboardMap1 = {'qwertyuiop[;'; 'asdfghjkl;'; 'zxcvbnm,'};
keyboardMap2 = {'QWERTYUIOP{'; 'ASDFGHJKL:'; 'ZXCVBNM<'};
if length(s) == 0
se = s;
end
for i = 1:length(s)
if double(s(i)) >= 65 && s(i) <= 90
row = 1;
col = 1;
while ~strcmp(s(i), keyboardMap2{row}(col))
if col < length(keyboardMap2{row})
col = col + 1;
else
row = row + 1;
col = 1;
end
end
se(i) = keyboardMap2{row}(col + 1);
elseif double(s(i)) >= 97 && s(i) <= 122
row = 1;
col = 1;
while ~strcmp(s(i), keyboardMap1{row}(col))
if col < length(keyboardMap1{row})
col = col + 1;
else
row = row + 1;
col = 1;
end
end
se(i) = keyboardMap1{row}(col + 1);
else
se(i) = s(i);
end
% if ~(s(i) = 65 && s(i) <= 90) && ~(s(i) >= 97 && s(i) <= 122)
% se(i) = s(i);
% end
end
We are thrilled to announce the grand prize winners of our MATLAB Shorts Mini Hack contest! This year, we invited the MATLAB Graphics and Charting team, the authors of the MATLAB functions used in every entry, to be our judges. After careful consideration, they have selected the top three winners:
Judge comments: Realism & detailed comments; wowed us with Manta Ray
2nd place – Jenny Bosten
Judge comments: Topical hacks : Auroras & Wind turbine; beautiful landscapes & nightscapes
3rd place - Vasilis Bellos
Judge comments: Nice algorithms & extra comments; can’t go wrong with Pumpkins
Judge comments: Impressive spring & cubes!
In addition, after validating the votes, we are pleased to announce the top 10 participants on the leaderboard:
Congratulations to all! Your creativity and skills have inspired many of us to explore and learn new skills, and make this contest a big success!
Dear MATLAB contest enthusiasts,
Welcome to the third installment of our interview series with top contest participants! This time we had the pleasure of talking to our all-time rock star – @Jenny Bosten. Every one of her entries is a masterpiece, demonstrating a deep understanding of the relationship between mathematics and aesthetics. Even Cleve Moler, the original author of MATLAB, is impressed and wrote in his blog: "Her code for Time Lapse of Lake View to the West shows she is also a wizard of coordinate systems and color maps."
you to read it to learn more about Jenny’s journey, her creative process, and her favorite entries.
Question: Who would you like to see featured in our next interview? Let us know your thoughts in the comments!
Over the past 4 weeks, 250+ creative short movies have been crafted. We had a lot of fun and, more importantly, learned new skills from each other! Now it’s time to announce week 4 winners.
Nature:
3D:
Seamless loop:
Holiday:
Fractal:
Congratulations! Each of you won your choice of a T-shirt, a hat, or a coffee mug. We will contact you after the contest ends.
Weekly Special Prizes
Thank you for sharing your tips & tricks with the community. These great technical articles will benefit community users for many years. You won a limited-edition pair of MATLAB Shorts!
In week 5, let’s take a moment to sit back, explore all of the interesting entries, and cast your votes. Reflect what you have learned or which entries you like most. Share anything in our Discussions area! There is still time to win our limited-edition MATLAB Shorts.
