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
引用
Iraj Hosseini (2024). gQSPsim-release (https://github.com/gQSPSim/gQSPsim-release/releases/tag/v1.0), GitHub. に取得済み.
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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
バージョン | 公開済み | リリース ノート | |
---|---|---|---|
1.0.0.0 | See release notes for this release on GitHub: https://github.com/gQSPSim/gQSPsim-release/releases/tag/v1.0 |