PluMA

PluMA enables construction of modular bioinformatics pipelines by dynamically loading plugins to integrate algorithms implemented in compiled and scripting languages for sequence-based microbiome analyses.

Key Features:

• Dynamic plugin loading: Dynamically loads plugins at runtime to extend backend functionality.
• Language-agnostic plugin support: Accepts plugins developed in compiled or scripting languages.
• Decoupled pipeline stages: Decouples pipeline stages from specific source languages and file formats to enable interoperability and extensibility.
• Algorithm integration: Allows integration of existing algorithms into new pipelines without requiring knowledge of their underlying implementations.
• Modular composition and testing: Supports composing pipelines that combine novel algorithms with established stages for evaluation and experimentation.

Scientific Applications:

• Microbiome research: Supports analysis of complex microbiome datasets and sequence-based studies to investigate microbial community structure and function.
• P-M16S example pipeline: Demonstrates integration of plugins written in different languages and formats to reproduce an obesity study involving gut microbiome samples from mice.

Methodology:

Constructs lightweight, adaptable pipelines with a backend extendable through dynamically loaded plugins, enabling modular workflows without language or file-format constraints.