Notations
In NAViFluX, the metabolic network is represented as a bipartite graph consisting of two distinct node types:
- Reaction nodes (representing biochemical reactions)
- Metabolite nodes (representing chemical compounds)
Edges (arrows) in the graph denote the directionality of reactions based on model constraints. This section explains the visual notations used for nodes and edges in the application.
Node Notations
🔹 Reaction Nodes
Reaction nodes are displayed as rectangles. Their appearance is determined by two properties:
1. Normalized Weights (Color Encoding)
- Each reaction node is assigned a normalized weight in the range [0, 1].
- Colors transition from light blue → dark blue as the weight increases.
- Higher weights correspond to darker shades, making it easier to visually identify high-influence reactions.
2. Size
- Reaction nodes have a fixed size, kept constant for readability.
![ReactionNode-Image]
🔸 Metabolite Nodes
Metabolite nodes are represented as orange circles. They maintain:
- Fixed size
- Fixed color
![Metabolite-Image]
Edge Notations
Edges describe the directionality of reactions in the bipartite network.
Priority Rule: Bounds > Flux
- If lower bound (
lb) and upper bound (ub) are defined, directionality is determined from the bounds. - If bounds are missing, the flux value is used to determine directionality.
Direction Cases
| Case | Conditions | Direction Meaning | Arrow Notation |
|---|---|---|---|
| 1 | lb = -1000, ub = 1000 |
Fully reversible | ←→ |
| 2 | lb = -1000, ub = 0 |
Irreversible (reverse only) | ← |
| 3 | lb = 0, ub = 1000 |
Irreversible (forward only) | → |
| 4 | lb = -250, ub = -150 |
Only negative flux allowed (reverse) | ← |
| 5 | lb = 150, ub = 450 |
Only positive flux allowed (forward) | → |
| 6 | lb = -350, ub = 250 |
Reversible (asymmetric range) | ←→ |
| 7 | No bounds, flux > 0 |
Flux-based forward direction | → |
| 8 | No bounds, flux = 0 |
Inactive / no net flux | — |
| 9 | No bounds, flux < 0 |
Flux-based reverse direction | ← |