NDExEdit

NDExEdit enables visualization and editing of biological networks to support interpretation and manipulation of network-encoded biological data.

Key Features:

• Data-dependent visualization: Adjusts visual mappings such as edge thickness and node/edge styles based on underlying data attributes, including interaction strength.
• Local data storage: Stores network data locally in the client environment to keep network state and edits isolated from remote repositories.
• Cytoscape Exchange (CX) format compatibility: Conforms to the CX data model, enabling import from NDEx and export of modified networks as CX files or standard image formats (PNG, JPEG).
• Support for collaborative workflows: Enables in-place edits that reduce repeated visualization steps and minimize transfer of full network datasets between collaborators.

Scientific Applications:

• Molecular network interpretation: Visualization of associations among biological entities such as proteins, genes, and metabolites to aid interpretation of interactions and processes.
• Integration with NDEx/Cytoscape workflows: Exchange of network data with NDEx and Cytoscape for downstream analysis, visualization sharing, and presentation.

Methodology:

Uses the CX format for data modeling, supports importing networks from NDEx, applies node and edge visual mappings based on data attributes, and exports modified networks as CX files or images.