gQSPSim

The app is used for QSP Modeling and Simulation.

gQSPSim is a GUI-based MATLAB® application that performs key steps in QSP model development and analyses, including:

1) model calibration using global and local optimization methods
2) development of virtual subjects to explore variability and uncertainty in the represented biology
3) simulations of virtual populations for different interventions.

gQSPSim works with SimBiology®-built models, utilizing components such as species, doses, variants, and rules. All functionalities are equipped with an interactive visualization interface and the ability to generate presentation-ready figures. In addition, standardized gQSPSim sessions can be shared or saved for future extension and reuse.

The source code and case studies are included in the referenced github account. The description of gQSPSim and case studies are in the publication titled "gQSPSim: a GUI application based on SimBiology® for standardized QSP model development
and application".

Instructions:

1) Install Matlab 2018a on your computer. Previous versions of Matlab are not compatible and we have not yet tested the app in 2018b or later versions.

2) Install GUI Layout Toolbox (https://www.mathworks.com/matlabcentral/fileexchange/47982-gui-layout-toolbox)

3) See the following link for a list of supported compilers for Mac and PC users (https://www.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/SystemRequirements-Release2018a_SupportedCompilers.pdf)
• 3a) For Mac users, install xcode.
• 3b) For PC users, install one of the supported compilers (lcc-win64 or MinGW 5.3 C/C++ or Microsoft Visual C++)

4) Once the compiler is installed, open Matlab and run the following commands
• mex -setup c
• mex -setup c++

5) To check that the compiler was successfully configured on your computer, run the following commands:
• modelObj = sbmlimport('lotka');
• em = export(modelObj)
• accelerate(em);
• em.isAccelerated

The answer should be 1

Enabling Long file names on Windows

1) Start the registry editor (regedit.exe)
2) Navigate to HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\FileSystem
3) Double click LongPathsEnabled
4) Set to 1 and click OK
5) Reboot

Uncompressing Case Study Zip Files on Windows

1) Download and install 7-zip from https://www.7-zip.org/
2) Use 7-zip to uncompress case study zip files

gQSPSim Installation:

1) Unzip gQSPSim.zip in home directory
2) Open Matlab
3) Go to home directory/gQSPsim/app
4) Run QSPapp