Resultados de

Tetiana Slavnikova
Tetiana Slavnikova
Última actividad el 12 de Nov. de 2022

Repeated assignment with measured variable

Dear community,
I would like to develop a fermentation model with 4 ODEs, one of which contains variable y. A "repeated assignment", e. g. y=5x+5, contains variable x that has been measured each second. These data (columns with time and corresponding value x in each row) are recorded in the Excel file.
Does anyone have any suggestion how to implement this in symbiology?
Thank you very much in advance,
Tetiana
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
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

Antonello Zito
Antonello Zito
Última actividad el 13 de En. de 2025

Mathworks: it's time for a dark theme.

This is not a question, but a point of discussion for the entire community. I am aware that every 1/2 months this theme comes out, but until this is not fixed it is totally necessary that this comes, indeed, out. And I said "fix" because Mathworks has to understand that a dark theme is not only a visual/aesthetic matter, it is a substantial part of the game. Most of the OS, GUIs, programs are actually in dark mode, and a vast majority of the users makes indeed use of a global dark mode. How much one does like it is personal, but the benefits to power savings and eye health is instead a fact. Mathworks being ignoring this for years is nothing but ridiculous. Of course it is not an easy task, but every minute of committment for it is worthy. And nope, Schemer is not helpful because it does not provide a real fix to this question.
I feel free to suggest something similar to the Spyder's dark theme, which came out like 2 years ago if I remember correctly.
Of course, my point is not being disrespectful (I am instead very respectful to the huge efforts of Mathworks for making this wonderful program run). But, form a user's point of view, the fact that not a single word has so far come out from Mathworks about a dark theme (meaning that for sure we will not see it in a timing of months) requires us to put a strong pressure on this.
Mathworks, please: it's time for a dark theme.
Stephen23
Stephen23
Última actividad el 12 de Abr. de 2024

TUTORIAL: Comma-Separated Lists and How to Use Them

Introduction
Comma-separated lists are really very simple. You use them all the time. Here is one:
a,b,c,d
That is a comma-separated list containing four variables, the variables a, b, c, and d. Every time you write a list separated by commas then you are writing a comma-separated list. Most commonly you would write a comma-separated list as inputs when calling a function:
fun(a,b,c,d)
or as arguments to the concatenation operator or cell construction operator:
[a,b,c,d]
{a,b,c,d}
or as function outputs:
[a,b,c,d] = fun();
It is very important to understand that in general a comma-separated list is NOT one variable (but it could be). However, sometimes it is useful to create a comma-separated list from one variable (or define one variable from a comma-separated list), and MATLAB has several ways of doing this from various container array types:
1) from a field of a structure array using dot-indexing:
struct_array.field % all elements
struct_array(idx).field % selected elements
2) from a cell array using curly-braces:
cell_array{:} % all elements
cell_array{idx} % selected elements
3) from a string array using curly-braces:
string_array{:} % all elements
string_array{idx} % selected elements
Note that in all cases, the comma-separated list consists of the content of the container array, not subsets (or "slices") of the container array itself (use parentheses to "slice" any array). In other words, they will be equivalent to writing this comma-separated list of the container array content:
content1, content2, content3, .. , contentN
and will return as many content arrays as the original container array has elements (or that you select using indexing, in the requested order). A comma-separated list of one element is just one array, but in general there can be any number of separate arrays in the comma-separated list (zero, one, two, three, four, or more). Here is an example showing that a comma-separated list generated from the content of a cell array is the same as a comma-separated list written explicitly:
>> C = {1,0,Inf};
>> C{:}
ans =
1
ans =
0
ans =
Inf
>> 1,0,Inf
ans =
1
ans =
0
ans =
Inf
How to Use Comma-Separated Lists
Function Inputs: Remember that every time you call a function with multiple input arguments you are using a comma-separated list:
fun(a,b,c,d)
and this is exactly why they are useful: because you can specify the arguments for a function or operator without knowing anything about the arguments (even how many there are). Using the example cell array from above:
>> vertcat(C{:})
ans =
1
0
Inf
which, as we should know by now, is exactly equivalent to writing the same comma-separated list directly into the function call:
>> vertcat(1,0,Inf)
ans =
1
0
Inf
How can we use this? Commonly these are used to generate vectors of values from a structure or cell array, e.g. to concatenate the filenames which are in the output structure of dir:
S = dir(..);
F = {S.name}
which is simply equivalent to
F = {S(1).name, S(2).name, S(3).name, .. , S(end).name}
Or, consider a function with multiple optional input arguments:
opt = {'HeaderLines',2, 'Delimiter',',', 'CollectOutputs',true);
fid = fopen(..);
C = textscan(fid,'%f%f',opt{:});
fclose(fid);
Note how we can pass the optional arguments as a comma-separated list. Remember how a comma-separated list is equivalent to writing var1,var2,var3,..., then the above example is really just this:
C = textscan(fid,'%f%f', 'HeaderLines',2, 'Delimiter',',', 'CollectOutputs',true)
with the added advantage that we can specify all of the optional arguments elsewhere and handle them as one cell array (e.g. as a function input, or at the top of the file). Or we could select which options we want simply by using indexing on that cell array. Note that varargin and varargout can also be useful here.
Function Outputs: In much the same way that the input arguments can be specified, so can an arbitrary number of output arguments. This is commonly used for functions which return a variable number of output arguments, specifically ind2sub and gradient and ndgrid. For example we can easily get all outputs of ndgrid, for any number of inputs (in this example three inputs and three outputs, determined by the number of elements in the cell array):
C = {1:3,4:7,8:9};
[C{:}] = ndgrid(C{:});
which is thus equivalent to:
[C{1},C{2},C{3}] = ndgrid(C{1},C{2},C{3});
Further Topics:
MATLAB documentation:
https://www.mathworks.com/help/matlab/matlab_prog/comma-separated-lists.html
https://www.mathworks.com/help/matlab/matlab_prog/access-multiple-elements-of-a-nonscalar-struct-array.html
https://www.mathworks.com/company/newsletters/articles/matlab-tips-and-tricks-exploiting-the-comma-separated-list-vectorizing-cell-array-and-structure-references.html
Click on these links to jump to relevant comments below:
Dynamic Indexing (indexing into arrays with arbitrary numbers of dimensions)
Nested Structures (why you get an error trying to index into a comma-separated list)
Summary
Just remember that in general a comma-separated list is not one variable (although they can be), and that they are exactly what they say: a list (of arrays) separated with commas. You use them all the time without even realizing it, every time you write this:
fun(a,b,c,d)
Andrew Janke
Andrew Janke
Última actividad el 16 de Ag. de 2025

What should go in a next-generation MATLAB X?

Let's say MathWorks decides to create a MATLAB X release, which takes a big one-time breaking change that abandons back-compatibility and creates a more modern MATLAB language, ditching the unfortunate stuff that's around for historical reasons. What would you like to see in it?
I'm thinking stuff like syntax and semantics tweaks, changes to function behavior and interfaces in the standard library and Toolboxes, and so on.
(The "X" is for major version 10, like in "OS X". Matlab is still on version 9.x even though we use "R20xxa" release names now.)
What should you post where?
Wishlist threads (#1 #2 #3 #4 #5): bugs and feature requests for Matlab Answers
Frustation threads (#1 #2): frustrations about usage and capabilities of Matlab itself
Missing feature threads (#1 #2): features that you whish Matlab would have had
Next Gen threads (#1): features that would break compatibility with previous versions, but would be nice to have
@anyone posting a new thread when the last one gets too large (about 50 answers seems a reasonable limit per thread), please update this list in all last threads. (if you don't have editing privileges, just post a comment asking someone to do the edit)
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

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

Daniel Dolan
Daniel Dolan
Última actividad el 7 de Ag. de 2024

Is anyone else disappointed with uifigures?

Is anyone else disappointed with uifigures? It seems apparent that these will eventually replace traditional figures, but there is still so much that doesn't quite work. I've tinkered with uifigures since their introduction in release 2016a, but even in 2020a I can't reliably export a uifigure to a graphics file. Sure it works sometimes, but not if a uipanel is present. The exportgraphics command is not as powerful as the print command, leaving some graphic formats (such as *.svg and *.eps) unsupported. How do you generate graphic files of a specific size? You can't even use subplots without overriding the default AutoResizeChildren setting!
Everything with uifigures seems to be slower and less stable than the figure variant. App Designer is much better than GUIDE, but that is not exactly high praise. I would rather generate "apps" programatically across several files instead of dealing with a single-file class definition containing 1000+ lines.
Where is this transition going? MATLAB graphics are moving away from Java in favor of JavaScript, and I'm not sure that we are at all ready for that.
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

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.

Rik
Rik
Última actividad el 7 de Oct. de 2024

What is missing from MATLAB #2 - the next decade edition

Meta threads have a tendency to grow large. This has happened several times before (the wishlist threads #1 #2 #3 #4 #5, and 'What frustrates you about MATLAB?' #1 and #2).
No wonder that a thread from early 2011 has also kept growing. After just under a decade there are (at time of writing) 119 answers, making the page slow to load and navigate (especially on mobile). So after a friendly nudge; here is a new thread for the things that are missing from Matlab.
Same question: are there things you think should be possible in Matlab, but aren't? What things are possible with software packages similar to Matlab that Matlab would benefit from? (note that you can also submit an enhancement request through support, although I suspect they will be monitoring activity on this thread as well)
What should you post where?
Wishlist threads (#1 #2 #3 #4 #5): bugs and feature requests for Matlab Answers
Frustation threads (#1 #2): frustations about usage and capabilities of Matlab itself
Missing feature threads (#1 #2): features that you whish Matlab would have had
Next Gen threads (#1): features that would break compatibility with previous versions, but would be nice to have
@anyone posting a new thread when the last one gets too large (about 50 answers seems a reasonable limit per thread), please update this list in all last threads. (if you don't have editing privileges, just post a comment asking someone to do the edit)
Nouran Zaid
Nouran Zaid
Última actividad el 29 de Jul. de 2020

Error model integration in the model

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

Wei Wang
Wei Wang
Última actividad el 10 de Jul. de 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.

Abed Alnaif
Abed Alnaif
Última actividad el 12 de Mayo de 2020

SimBiology Viewer suggestion for sharing models

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

Wei Wang
Wei Wang
Última actividad el 17 de Abr. de 2020

How to properly record absorbed dose fraction?

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
Última actividad el 5 de Abr. de 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.).