GUIdock

GUIdock encapsulates GUI-based systems biology applications within Docker containers to enable reproducible execution and distribution across Linux, Macintosh, and Windows.

Key Features:

• Reproducibility: Encapsulates software dependencies and the execution environment necessary for reproducing computational results using container technology.
• Containerization with Docker: Packages applications together with their dependencies into Docker containers for consistent distribution and execution.
• Cross-Platform Compatibility: Configures a common X Windows (X11) graphical interface to support GUI-based workflows on Linux, Macintosh, and Windows platforms.
• Integration with Bioinformatics Tools: Provides a Docker package that includes networkBMA (implemented in R and C++) for gene network inference and integrates Cytoscape (Java) for network visualization.

Scientific Applications:

• Systems biology workflows: Enables reproducible execution and distribution of complex GUI-based systems biology workflows across multiple operating systems.
• Gene network inference and visualization: Supports running networkBMA for gene network inference and visualizing results with Cytoscape within the same reproducible container environment.

Methodology:

Applications and their software dependencies are encapsulated within Docker containers; a common X11 graphical interface is configured for cross-platform GUI support; networkBMA (R, C++) and Cytoscape (Java) are packaged within the Docker images.