MOVE: a multi-level ontology-based visualization and exploration framework for genomic networks

Area of Science:

• Bioinformatics
• Systems Biology
• Genomics

Background:

• Systems biology aims to understand dynamic cellular interactions across genomic, transcriptomic, proteomic, and metabolomic levels.
• These interactions form complex, interconnected biological networks.
• Current bioinformatics tools are specialized and lack consistency for diverse network analyses.

Purpose of the Study:

• To conceptually develop an open-source, extensible software framework.
• To support visualization and exploration of complex genomic networks (e.g., metabolic, gene regulatory).
• To address the shortcomings of existing network visualization systems.

Main Methods:

• Analysis of requirements for network visualization.
• Review of the state-of-the-art in network visualization systems and their limitations.
• Conceptual design and initial module implementation of a new software framework.

Main Results:

• The proposed framework is designed to be open-source and extensible.
• Initial modules were implemented and applied to a biological test case.
• Demonstrated the relevance and feasibility of the framework for bacterial gene regulation analysis.

Conclusions:

• The developed framework offers a consistent approach for analyzing diverse biological networks.
• It addresses the limitations of existing specialized bioinformatics tools.
• The approach is relevant and feasible for advancing systems biology research.