Results for

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!

In number 5, its written that the correct answer is c = 1 but the secomnd person has more change than the first person, therefor the correct answer should be 2.Likewise in number 6.

New Features

R2019b introduces the new SimBiology Model Analyzer which replaces Task Editor enabling you to do a lot more within the app.

For a detailed look into enhancements with Model Analyzer, we created a few short videos. Below is a list of the new features together with videos describing each feature.

Compatibility considerations with earlier versions of SimBiology

There are a few things that one needs to be aware of if planning to use R2019b with a SimBiology project created in older versions. If you load a project created pre-R2019b, the existing tasks are converted to equivalent programs. However, keep in mind the following for the current version of SimBiology Model Analyzer:

  • Live Plots functionality of the Task Editor is not supported. If Live Plots in the Task Editor is turned on and shows a time plot of simulation results, then an equivalent time plot is added on import to the SimBiology Model Analyzer app with the main difference being that the time plot is updated and displayed after the program finishes (not while it is running).
  • Previously available Calculate Conserved Cycles, Search Model(s), and Generate Report tasks are not supported.
  • Any Group Simulation task is converted to a Scan program.
  • Fit Data program does not support nlinfit as the estimation method. However, the command-line function sbiofit still supports nlinfit.
  • To help with the transition to R2019b, when you open an existing project created in R2019a or earlier, the app creates a backup of the original file. The backup file has the release information suffixed to its name, filename_release.sbproj. For example, if you open an R2019a project named foo.sbproj in the app, the app creates a backup file called foo_R2019a.sbproj.
  • Also, when you open and save a project, the app creates a backup file of the version prior to the saved version of the project. The backup file has the .bak extension (for example, foo.sbproj.bak).

See the complete list of general behavior change, compatibility considerations, and new features in the release notes.

Hi, I'm trying to solve this problem but I'm getting an error so far.
Problem:
Given a vector a, find the number(s) that is/are repeated consecutively most often. For example, if you have
a = [1 2 2 2 1 3 2 1 4 5 1]
The answer would be 2, because it shows up three consecutive times
What I've written so far (not done):
a = [1 2 2 2 1 3 2 1 4 5 1];
[x,y] = size(a);
counter = zeros(1,10);
if x == 1
for i=1:1:y
if a(i) == a(i+1)
counter(a(i)) = counter(a(i))+1
end
end
else
for i=1:1:x
if a(i) == a(i+1)
counter(a(i)) = counter(a(i))+1
end
end
end
But it says "error" in the line of "if a(i) == a(i+1)". I noticed that it creates a variable called "i" which value is 11, but it should create a vector from 1 to 11. What's wrong here?
I know my solution might not be in the right direction or something, but please don't tell me anything!
Thanks in advance

I am fitting a generic TMDD model to date. Model fits look reasonable. Once I create a variant and simulate data for various doses to create observed vs predicted concentrations vs time profile, then simulated concentrations do not match fitted profiles. Simulated concentrations are either significantly higher or lower than the model fits. Not sure what is wrong. Fits look fine but simulated profiles using fitted parameters are all over the place.

Hello all,

I have created an arbitrary model for microtubule behavior. More or less just trying to familiarize with the software. I have created plots for multiple types of reactions that may occur and am looking to now plot the instantaneous derivative of each reaction. Would anyone have any suggestions as to how I could do this? I am familiar with how to do it with a clearly defined function with x,y,z,etc. values. However the 'sbiomodel' command doesn't seem to show me a function so I'm really lost on this.

Thanks for any and all help/suggestions.

Hello,

I have a suggestion for a feature which I think would be nice to add in SimBiology: a "date modified" field for all of the objects (species, parameters, rules, etc). It would be nice for this to be visible in the tables in the GUI, as well as being available through code, and to be able to sort on this field in the GUI. The reason I thought about this is because I just got a model with some updates from a colleague, and this would help me to identify what they updated.

Thank you,

Abed

There will be an introductory hand-on SimBiology workshop following ACoP on Friday, Oct 24 at University of Florida, Orlando Campus, sponsored by Prof. Sihem Bihorel.

To register, please send me a direct message from the community site or e-mail me at fbuyukoz[at]mathworks.com. Please also let your colleagues know who might be interested in attending. Space is limited and will be allocated to those who sign up first.

Agenda

Introduction

  • Overview of MATLAB and SimBiology
  • Navigating the SimBiology desktop environment
  • Working with a SimBiology project

Building and Simulating Mechanistic Models, using a TMDD example

  • Overview of the building blocks and modeling architecture
  • Building models using the SimBiology block diagram editor
  • Configuring simulation-related settings (solvers, tolerances, sampling time, etc.)
  • Exploring model dynamics and sensitivity using parameter sliders and sensitivity analysis
  • Simulating hypothetical scenarios and dosing schedules

Implementing Traditional Compartmental PK/PD Workflows, using a 1 compartment PK model as example

  • Importing, processing and visualizing data
  • Performing non-compartmental analysis (NCA)
  • Estimating parameters using nonlinear regression and population-based methods

Programmatic SimBiology and Integration with MATLAB

  • Writing custom analysis tasks
  • Automating workflows using MATLAB scripts
David
David
Last activity on 2 Oct 2019

Regarding Recent Spam Attacks

Over the past several months our communities have been the target of ongoing spam attacks. Spam is a common issue online and spam prevention is something we include as part of our standard development processes. The most recent attempts appear to be specifically targeting our sites with a combination of manual and automated attacks, probing with a variety of content attempting to bypass our filters. Regrettably, the attacks sometimes make it through our defenses, cluttering your inboxes and the content in our communities.

Rest assured, we are dedicated to continuing to evolve our tools and improve our capabilities to meet the goal of eliminating all spam in our communities. We appreciate your patience and understanding as we work to get there.

Sincerely,

David Wey

MATLAB Communities Development Manager

MathWorks, Inc.