PkDE Unified Mission Control & Interactive Scientific Dashboard (pkde-dashboard)

Use this skill whenever you need to build, update, or serve the unified Multi-Agent + PkDE Interactive Scientific Dashboard (dashboard.html) or start the non-blocking background HTTP/SSE server (0.0.0.0:8765).

What the Dashboard Renders

1. Pane 1 -- Multi-Agent Operations (Split & Agents Views):
   • Interactive SVG Agent Lineage Forest: Hierarchical layout (NODE_W=180, NODE_H=76) with vertical/horizontal orientation transpose (t), zoom/pan, fit-to-screen (f), bezier state edges, and pulse animations on active agents.
   • Agent & Work-Order Inspector Drawer: Clicking any agent node displays its Work Order metadata (WO-NNN-rM, stage, cycle, attempt counter), Injected Skills pills (from templates/<role>/agent.yaml), Recent Agent Communications, and the 10-Check Mechanical Validation Matrix (deliverables_exist, report_headings, paths_resolve, provenance_valid, analysis_citations, relay_coverage, version_policy, findings_integrity, source_tags_resolve, unrecognized_json).
   • Resource Leases & Inter-Agent Event Stream: Live tracker for .pkde/control/leases/*.json (af3, hypex-supervisor) and filterable .pkde/control/events.ndjson message log.
2. Pane 2 -- PkDE Scientific Output & Embedded Interactive Viewers (Split & Discovery Views):
   • Overview, Session Prompt Charter, Stage Gates & Mandatory Relays: Active Session Prompt Charter (.pkde/program.yaml), Stage 0-4 Triage Scorecard, Liability Tracker table, and Mandatory Relays audit matrix.
   • Specialist Findings & Dossier Reader (Layer 1): Discipline-grouped Markdown/KaTeX reports with interactive {source: ...} verification badges and **Relay: ...** callouts.
   • Interactive Scientific Viewers Studio (Layer 0 + Analysis):
     • 3Dmol.js 3D Structure (.cif/.pdb colored by AlphaFold pLDDT bands), Pocket Druggability (.pockets.json), 3D Molecule SDF (.3d.sdf), and Docking Poses (.receptor.pdbqt + .poses.pdbqt).
     • Plotly.js 5-Axis ADMET Radar (.predict.json), pLDDT Confidence Line Plot (.afdb.json), 2D PAE Heatmap (.pae.json), gnomAD Constraint Gauges (.gnomad-constraint.json), and GTEx Tissue Expression Bars (.tissue.json).
     • BRICS Fragment & SAR Studio (.brics.json), Docking Pose Score Comparison (.docking_result.json), Contact Map (.contacts.json), Hypothesis ELO Tournament Studio (.tournament.json / .hypex.json), and the 3-File Provenance Inspector (Layer 0 + .meta.json + .analysis.json).
3. Live Telemetry Console (#telemetry-drawer + 4th Telemetry Full-Screen View):
   • Persistent Collapsible Bottom Console (#telemetry-drawer): Anchored across Split, Agents, and Discovery views with Ticker (38px), Console (205px), and Full View toggles, category filter pills, text search, and hover/scroll auto-pause.
   • 4th Full-Screen Telemetry View (#telemetry-view): Dedicated two-column Mission Telemetry Terminal + Live Active Agents & Recent Discovery Additions status board.
   • One-Click Deep Navigation: Clicking any telemetry one-liner automatically opens the corresponding pane and selects the exact Agent node, Layer 1 Finding, Layer 0 Scientific Studio viewer, or Mandatory Relay table.
   • Non-Blocking Differential DOM Updates: Per-section signatures and requestAnimationFrame coalescing ensure active 3Dmol.js WebGL cameras, Plotly.js charts, Findings reader scroll positions, and SVG pan/zoom states never reset while live telemetry streams in.

Usage

1. Start Non-Blocking Background Server from Prompt (0.0.0.0:8765)

./bin/pkde dashboard start --prompt "<user prompt>" --host 0.0.0.0 --port 8765 --json
./bin/pkde dashboard status --json
./bin/pkde dashboard stop --json

2. Build Self-Contained Standalone Snapshot (dashboard.html)

python3 skills/pkde-dashboard/scripts/render_dashboard.py
# Or directly via the pkde CLI:
./bin/pkde dashboard build --standalone --json

3. Serve Foreground Auto-Refreshing Dashboard (SSE /api/stream)

./bin/pkde dashboard serve --host 0.0.0.0 --port 8765