gQSPSim

버전 1.1 (40.2 MB) 작성자: Iraj Hosseini
The app is developed for standardized QSP model development

다운로드 수: 255

업데이트 날짜: 2021/3/5

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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

인용 양식

Iraj Hosseini (2022). gQSPSim (https://github.com/gQSPSim/gQSPsim-release/releases/tag/v1.1), GitHub. 검색됨 .

MATLAB 릴리스 호환 정보
개발 환경: R2018a
R2018a 이상 릴리스와 호환
플랫폼 호환성
Windows macOS Linux
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