ReactionFlow

ReactionFlow: Visual Analytics for Biochemical Pathway Causality

ReactionFlow analyzes causal relationships in complex biochemical pathways by modeling upstream and downstream connections between proteins and biochemical reactions to support pathway-level reasoning.

Key Features:

• Causality Analysis: Identifies upstream and downstream relationships, visualizes effects of protein perturbation, detects feedback loops, and computes shortest paths between proteins within biochemical networks.
• Network Exploration: Enables filtering, clustering, and selection of pathway components to examine structural and functional relationships across biomolecular interaction networks.
• Activity Flow Representation: Illustrates propagation of biochemical activity through pathways to model dynamic interaction flow.

Scientific Applications:

• Biomolecular Network Analysis: Supports identification of downstream effects, feedback mechanisms, shared pathway components, and causal structures for hypothesis generation, experimental design, and interpretation of molecular and systems biology data.

Methodology:

Implements causality-focused pathway analysis tasks defined through domain expert evaluation, integrating graph-based modeling of protein–reaction networks with dynamic activity flow representation to characterize pathway structure and causal connectivity.