neural-graph-visualizer

Neural Graph Visualizer

Interactive 3D knowledge graph visualization with pathway-aware layouts, molecule viewer, and configurable templates. Built with Three.js — zero dependencies.

Installation

Claude Code Marketplace (recommended)

/plugin marketplace add cdeust/neural-graph-visualizer
/plugin install neural-graph-visualizer

Manual Setup

git clone https://github.com/cdeust/neural-graph-visualizer.git
cd neural-graph-visualizer
./scripts/setup.sh

Restart Claude Code after installation.

Quick Start

From Claude Code

/neural-graph

Or ask Claude to visualize your data:

"Open the neural graph visualization" "Import my research data from data.json"

From CLI

# Launch the example pipeline
node scripts/launch.js research-templates/drug-discovery-generic/data.json

# Launch the blank starter
node scripts/launch.js research-templates/blank/data.json

# Create your own from a template
node scripts/create-research.js --template blank --name "My Study"

Features

Pathway-Aware Layouts

Nodes are positioned by topology, not just physics. The layout engine computes hierarchical ranks from directed edge types.

Strategy	Axis	Best For
cascade	Y (top → bottom)	Signaling pathways, dependency chains
pipeline	X (left → right)	Sequential stages, workflows
radial	Center → out	Target-centric views, interaction networks
force	Physics-based	Generic graphs, exploration
auto	Detected	Picks strategy from edge type distribution

Configure in your data JSON:

"_config": {
  "_layout": { "strategy": "cascade" }
}

Molecule Viewer

Nodes with pdbId or smiles fields get a "View 3D Structure" button in the detail panel.

• Proteins/biologics — PDB viewer with ribbon, ball-and-stick, and surface modes
• Small molecules — SMILES-based 2D/3D rendering

Templates

Template	Nodes	Layout	Description
drug-discovery-generic	11	pipeline	Target → approval pipeline example
blank	3	force	Starter template — replace with your data

Use these as starting points. Copy, edit the JSON, and launch.

Visual Features

• Bloom post-processing — Cinematic glow on all nodes
• Flow particles — Synaptic pulses traveling along edges
• Holographic grid — Animated floor grid
• Ambient dust — 4000 floating particles for depth
• Hex/sphere shapes — Config-driven per node type
• Analytics dashboard — Type distribution, project breakdown

Interaction

• Hover — Tooltip with node name, type, and project
• Click — Detail panel with description, tags, cross-references, and molecule viewer
• Search — Real-time full-text filtering
• Filter — By type, category, status
• Layout toggle — Cycle between Cluster / Timeline / Pathway (keyboard: T)
• Analytics — Toggle dashboard (keyboard: A)

MCP Tools

Available when installed as a Claude Code plugin:

Tool	Description
open_visualization	Launch the 3D graph in browser
get_graph	Return graph data as JSON
get_stats	Summary statistics
search	Full-text search across nodes
import_json	Import graph from JSON file
import_csv	Import from CSV files
reindex_brain	Rebuild the brain index
get_brain_index	Query the brain index
update_brain_entry	Override brain index fields
manage_thread	CRUD for thread groups
add_cross_reference	Add bidirectional cross-reference
remove_cross_reference	Remove cross-reference

Data Format

A graph is a single JSON file with three sections: