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Helix Studio: Core GUI Features Checklist

This is the “Genome IDE” surface area Helix Studio should expose as first-class UX.

Must-have (core IDE)

  • Project/workspace

    • Open/save project (.helix_project.json)
    • Recent projects + recent sessions
    • Deterministic “demo” path (always works offline)

  • Authoring

    • CRISPR / Prime / PCR authoring UI (Sim Builder)
    • Backend selection + capability status (CPU/GPU, deterministic, versions)
    • Presets (load/save)

  • Simulation + artifacts

    • Run execution + run history
    • Snapshot/EVS persistence (so results are reproducible + shareable)

  • Visualization

    • Realtime 3D viewport (rails/helix) + outcome highlighting
    • 2.5D workflow visualization (timeline/bars/heat) + outcome context
    • Edit DAG graph visualization (nodes/edges, probability mass, stages)

  • Analysis

    • Outcome Explorer (ranking, filters, overlays/baseline compare)
    • Guide ranking + guide-level comparison
    • Run-level comparison (baseline vs candidate) + overlay into explorer

  • Export

    • HTML report export
    • Evidence export (schema’d JSON)
    • Resolve clip export (zip: clip.gif + metadata.json; optional clip.mp4 when an encoder is available; optional spec.json via toggle)
    • Snapshot bundle export for support/debugging

“Nice to have” (next tier)

  • Interactive DAG inspection

    • Click node → show genome diff, metadata, parent/child navigation
    • Filter by probability / depth / stage
    • Compare two DAGs visually (A/B overlay)

  • 3D/2.5D capture

    • One-click resolve clip export (zip) that’s shareable evidence
    • Save viewport frames as PNG for reports (camera + time locked)
    • Deterministic camera presets for reproducible screenshots / docs

  • Workflow ↔ DAG ↔ outcomes linkage

    • Selecting an outcome highlights corresponding DAG path + workflow bars
    • Selecting a DAG leaf opens its outcome in Outcome Explorer

  • Plugin spine

    • Commands + panels (including Layer 2 web panels) (see docs/studio/plugins.md)

Continuity (stateful center tabs)

Helix Studio should feel continuous across restarts. Persist and restore:

  • Last active center tab
  • Realtime (3D) camera + toggles (when ModernGL is available)
  • 2.5D Workflow camera (when ModernGL is available)
  • Edit DAG layout + selected node id

Persisted view-state blobs should be versioned so camera/layout schema changes remain backwards compatible.

Center tab contracts (minimal interfaces)

Treat center tabs as first-class artifacts with explicit, stable contracts:

  • Accepts run context: run id + EVS/snapshot payload
  • Accepts DAG: edit DAG payload (from runtime)
  • Emits selection: outcome selection / DAG node selection / run selection

Avoid reaching into private widget fields from main_window.py; prefer a small adapter interface per tab.