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Aktualisiert 11. Aug 2021

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 or later versions on your computer. Previous versions of Matlab are not compatible.

2) 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)
• 2a) For Mac users, install xcode.
• 2b) For PC users, install one of the supported compilers (lcc-win64 or MinGW 5.3 C/C++ or Microsoft Visual C++)

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

4) 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) Open Matlab
2) install gQSPSim.mltbx
3) Run gQSPSim from the APPS toolbar

Updates in v1.1

* compatibility with R2018a-2020b
* updated case studies
* improvements to parallel cohort generation and simulation
* improved cross-platform compatibility of sessions
* limit configurable number of traces to show when rendering plots
* improvements to selection of rules/reactions to inactivate for tasks
* improved support for long file names on Windows
* bundle graphics library dependencies
* various bug fixes

Zitieren als

Iraj Hosseini (2024). gQSPsim-release (https://github.com/gQSPSim/gQSPsim-release/releases/tag/v1.0), GitHub. Abgerufen .

Kompatibilität der MATLAB-Version
Erstellt mit R2018a
Kompatibel mit R2018a und späteren Versionen
Plattform-Kompatibilität
Windows macOS Linux
Communitys
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app

app/+QSP

app/+QSP/+abstract

app/+QSP/@CohortGeneration

app/+QSP/@Model

app/+QSP/@Optimization

app/+QSP/@OptimizationData

app/+QSP/@Parameters

app/+QSP/@PlotSettings

app/+QSP/@Profile

app/+QSP/@Session

app/+QSP/@Settings

app/+QSP/@Simulation

app/+QSP/@SpeciesData

app/+QSP/@Task

app/+QSP/@TaskGroup

app/+QSP/@TaskVirtualPopulation

app/+QSP/@VirtualPopulation

app/+QSP/@VirtualPopulationData

app/+QSP/@VirtualPopulationGeneration

app/+QSP/@VirtualPopulationGenerationData

app/+QSPViewer

app/+QSPViewer/@App

app/+QSPViewer/@CohortGeneration

app/+QSPViewer/@Optimization

app/+QSPViewer/@OptimizationData

app/+QSPViewer/@Parameters

app/+QSPViewer/@Session

app/+QSPViewer/@Simulation

app/+QSPViewer/@Task

app/+QSPViewer/@VirtualPopulation

app/+QSPViewer/@VirtualPopulationData

app/+QSPViewer/@VirtualPopulationGeneration

app/+QSPViewer/@VirtualPopulationGenerationData

app/+uix/+abstract

app/+uix/+mixin

app/+uix/+utility

app/+uix/+widget

app/20130227_xlwrite

app/utilities

case studies/CaseStudy_aPCSK9/aPCSK9_v7_MES_blank/Plotting_validation

case studies/CaseStudy_aPCSK9/aPCSK9_v7_MES_blank/UDF

case studies/CaseStudy_aPCSK9/aPCSK9_v7_MES_complete/Plotting_validation

case studies/CaseStudy_aPCSK9/aPCSK9_v7_MES_complete/UDF

utilities

utilities/20130227_xlwrite/20130227_xlwrite

Version Veröffentlicht Versionshinweise
1.0.0.0

See release notes for this release on GitHub: https://github.com/gQSPSim/gQSPsim-release/releases/tag/v1.0

Um Probleme in diesem GitHub Add-On anzuzeigen oder zu melden, besuchen Sie das GitHub Repository.
Um Probleme in diesem GitHub Add-On anzuzeigen oder zu melden, besuchen Sie das GitHub Repository.