ST-Analyzer: A Packaged Web and Command-Line Interface for Simulation Trajectory Analysis

Area of Science:

• Computational chemistry and molecular dynamics simulations.
• Bioinformatics and computational biology.

Background:

• High-performance computing generates large simulation datasets, posing challenges for reproducible analysis.
• Diverse and rapidly evolving software ecosystems complicate data analysis and hinder reproducibility.
• Extracting scientific insights requires expertise in computational methods beyond the molecular system itself.

Purpose of the Study:

• To present ST-Analyzer, an open-source software suite for simulation trajectory analysis.
• To provide both command-line (CLI) and graphical (GUI) user interfaces for accessibility.
• To facilitate reproducible scientific insights from molecular dynamics simulations.

Main Methods:

• Developed ST-Analyzer as a free, open-source conda-forge package.
• Implemented both CLI and GUI for user interaction.
• Ensured cross-platform compatibility (macOS, Linux, Windows via WSL2).
• GUI provides users with the exact CLI commands for tasks.

Main Results:

• ST-Analyzer successfully reproduces results from published studies on biomembranes and viral protein-antibody interactions.
• Demonstrated the tool's utility for common analysis tasks.
• Validated the GUI's ability to guide users towards CLI command execution.

Conclusions:

• ST-Analyzer enhances the accessibility and reproducibility of simulation trajectory analysis.
• The tool serves both expert users needing efficient task setup and non-experts seeking guided learning.
• Open-source availability and cross-platform support promote wider adoption in computational research.