DiVil

DiVil visualizes structural differences between two versions of biochemical models at the network level to facilitate inspection of model evolution.

Key Features:

• Structural difference visualization: Visualizes structural changes between two model versions at the network level.
• BiVeS integration: Extends BiVeS by using its detected model differences as input for network-level visualization.
• JSON schema: Uses a JSON schema to encode and communicate detected differences between model versions.
• Network representation: Represents biochemical models as standardized networks for structural comparison.
• Automatic layout: Applies an automatic network layout to arrange model components for comparison.
• D3.js rendering: Employs D3.js to render dynamic network visualizations.
• Export formats: Exports network representations to images and markup language formats.

Scientific Applications:

• Model evolution tracking: Track and visualize the evolution of biochemical models developed across multiple branches and collaborators.
• Version inspection and diff analysis: Inspect and analyze structural differences between model versions for curation, extensions, and adaptations.
• Collaborative model reconciliation: Support alignment and discussion among collaborators by clarifying network-level changes.
• Figure and markup generation: Generate images or markup outputs of network differences for figure preparation or downstream processing.

Methodology:

Consumes differences detected by BiVeS, encodes them via a JSON schema, represents models as standardized networks, applies an automatic layout, renders visualizations with D3.js, and supports export to images and markup language formats.