mully: An R Package to Create, Modify and Visualize Multilayered Graphs.

Area of Science:

• Bioinformatics
• Computational Biology
• Systems Biology

Background:

• Modeling complex biological networks, such as pathways, is crucial for scientific research.
• Investigating network components and integrating diverse biomedical knowledge presents significant challenges.
• Existing tools often lack the flexibility to handle multiple pathway types and knowledge sources cohesively.

Purpose of the Study:

• To provide a generic modeling framework for integrating multiple pathway types and related knowledge sources.
• To develop a multi-layered model enabling automatic network transformations and documentation.
• To facilitate data integration, enhance reproducibility, and increase interoperability in pathway research.

Main Methods:

• Development of the 'mully' R package.
• Implementation of features specifically designed for handling multi-layered graphs.
• Creation of a multi-layered modeling framework for biological networks.

Main Results:

• The 'mully' R package allows users to create, modify, and visualize multi-layered graphs.
• The framework supports the integration of diverse pathway types and external knowledge.
• The tool simplifies network transformations and documentation processes.

Conclusions:

• The 'mully' R package offers a robust solution for modeling and analyzing complex biological networks.
• This approach significantly improves data integration, reproducibility, and interoperability in pathway research.
• The multi-layered modeling framework advances the field of systems biology by providing a unified approach to network analysis.