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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.

Iraj Hosseini
Iraj Hosseini
Last activity on 1 Oct 2019

gQSPSim Workshop at ACoP10

ACoP10 Workshop – October 19, 2019

QSP Model Development Using gQSPSim: A GUI-Based Open-Source Platform for SimBiology Models

Organized by Genentech and MathWorks

Andrew Heitman
Andrew Heitman
Last activity on 16 Jun 2020

Add AUC to SimBiology Model

IS there a quick and easy way to calculate AUC in SimBiology without exporting results to an NCA analysis>?

can we directly get the SD of the concentration-time AUC after fitting in Simbiology?

Hi, How do I get a numeric integral from a function that uses Excel file input data? I have been able to import the excel file but am having trouble continuing the code,please guide me, thank you

We have a Systems Biology and Biotechnology Specialization on Coursera which has the following specific courses:

1. Introduction to Systems Biology

2. Experimental Methods in Systems Biology

3. Network Analysis in Systems Biology

4. Dynamical Modeling Methods for Systems

5. Integrated Analysis in Systems Biology

6. Systems Biology and Biotechnology Capstone

For "Systems Biology and Biotechnology Capstone", "Dynamical Modeling Methods for Systems", and ":Integrated Analysis in Systems Biology", MATLAB is used for mathematical models and bioinformatics analyses. All assignments with dynamical models are also presented as MATLAB codes and SimBiology Models. The Systems Biology Specialization covers the concepts and methodologies used in systems-level analysis of biomedical systems. Successful participants will learn how to use experimental, computational and mathematical methods in systems biology and how to design practical systems-level frameworks to address questions in a variety of biomedical fields. In the final Capstone Project, students will apply the methods they learned in five courses of specialization to work on a research project.

Here is the link to all of these courses:

https://www.coursera.org/specializations/systems-biology

If you have any question about these courses please let me know.

Iman Tavassoly MD, PhD Icahn School of Medicine at Mount Sinai

Hi, I am intrigued by the idea of using the simbiology stochastic solvers for a project that I have so far coded in the idnlgrey framawork.

Some of the ODE right hand sides (ionic fluxes) in my model are given via fitobjects.

My question is: can I use a fit object in simbiology? Or should I figure out an analytical form and use it as a custom reaction rate?

Thanks, Francesco

On using Simbiology, I am realizing how wonderful it is! It is equivalent and infact better than much commercial software available in the market for hefty prices (not to name anyone in purpose). Moreover, the product is backed up by the world leaders in software engineering - MATLAB (which gives more confidence to the product). It would be very helpful if someone can share the list or some of the PubMed indexed publication on population pharmacokinetics in which Simbiology is utilized for modeling and computation.

Identification of model (one compartment, two compartments or three compartments) which a drug follows is an important step before population pharmacokinetic modeling. I am aware that the graph between the concentration vs time, gives an idea of the number of compartment a drug follows.

But is there a standard way to explore and determine the number of compartment a drug follows in a more objective manner. This would also be helpful to determine the model in which the data needs to be fit. In addition, a note on determining the order of reaction is also welcomed and would make the discussion complete.

Jeremy Huard
Jeremy Huard
Last activity on 7 Jun 2019

SimBiology at PAGE 2019

Fulden and I will have a booth at PAGE next week. Come and chat with us to learn the latest with MATLAB and SimBiology for PK/PD, PBPK, and QSP modeling.

I use Simbiology for population PK-PD model development. During the model fitting of data, I understand that the model diagnostics play a major decisive role in selecting the suitable model. Hence would like to make it clear regarding the interpretation of the model diagnostics.

If for example, I have two models. First model: DFE= 411, LogLikelihood = - 807.6 (minus 807.6), AIC = 1633.2 , BIC = 1647.2 and RMSE = 1.92 Second model: DFE= 410, LogLikelihood = - 888.8 (minus 888.8), AIC = 1797.6 , BIC = 1813.2 and RMSE = 0.34 Which among the model is better and why? What are the individual interpretation of DFE, LogLikelihood, AIC, BIC and RMSE?

In PK-PD research paper generally, they take Objective Function value as decisive model diagnostics. What is the Objective Function Value in Simbiology? I did some literature search and found that Objective Function Value is -2 times LogLikelihood value? So should I multiply the LogLikelihood value given in Simbiology by - 2 to obtain Objective Function Value? Moreover, if the LogLikelihood value is multiplied with -2 then the entire interpretation will be changing (as minus will reverse the direction). So please guide in this regard and give your valuable inputs.

Anas Saadeddin
Anas Saadeddin
Last activity on 5 Jun 2019

PK/PD courses

Hi I would like to improve my skills in PK/PD modelling using Simbiology. Are you going to organize any courses in the near future? Many thanks Anas

On Wednesday, April 17, 12-1 PM EDT, Dr. Ing. Markus Rehberg, QSP Scientist at Sanofi in Frankfurt (Germany) will show how Sanofi and Rosa & Co created a QSP model for Rheumatoid Arthritis, using SimBiology, that transformed the way Sanofi uses and implements data in drug research and early development.

I invite you to register for the webinar, and afterward let me know what you think: https://register.gotowebinar.com/register/325575685872200717

What is it?

SimFunction allows you to perform multiple simulations in a single line of code by providing an interface to execute SimBiology® models like a regular MATLAB function.

Consider the following similarity: If you want to calculate the value of the sine function at multiple times defined in the variable t, you use the following syntax:

 >> y = sin(t)

If mymodel represents a SimFunction, you can simulate your model with multiple parameter sets using the following syntax:

 >> simulationData = mymodel(parameterValues, stopTime, dose)

.

What is it good for?

Multiple simulations

Because it allows you to perform multiple simulations in a single line of code by providing a matrix of parameter values or variants or a cell array of dosing tables, it is particularly suited for

  • parameter and dose scans
  • Monte Carlo simulations
  • customized analyses that require multiple model simulations such as a customized optimization

Performance

SimFunctions are optimized for performance as they are automatically accelerated at the first function execution, which converts the model into compiled C code. Those simulations can be distributed to multiple cores or to a cluster and run in parallel if Parallel Computing Toolbox™ is available thanks to its built-in parallelization or within a parfor loop.

Simulation deployment

Since SimFunction objects cannot be changed once created, they can be shared with others without the risk of altering the model inadvertently.

Also, you can use SimFunctions to integrate a SimBiology model into a customized MATLAB App and compile it as standalone application to share with anyone without the need of a MATLAB license.

.

How does it work?

Create a SimFunction object using the createSimFunction method by choosing:

  1. which parameters it should take as inputs
  2. which targets will be dosed
  3. which model quantities it should return
  4. which sensitivities it should return if any

Have a look at the following example from the SimBiology documentation for an executable script to help you get started: Perform a Parameter Scan.