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Helix Studio Tour (v1)

Fast path to “wow” with the current Studio + CLI stack.

Launch & welcome

  • Start Helix Studio; the welcome dialog offers: Open demo, Open .helix, or start empty.
  • Demo is the fastest tour: pick it to pre-load guides/runs.

Guide Inspector

  • Left pane: guides with Score, rank, cut%, frameshift%, top outcome, E_pred.
  • Filters: text, frameshift threshold, E_pred threshold; Export all (HTML) and Compare selected.
  • Selecting a guide drives Outcome Explorer + Helix view; rank chip shows position within the filtered list.

Outcome Explorer

  • Summary chips: Cut / No-cut / Frameshift / Frameshift|cut / physics backend / rank.
  • Metadata chips: Project, Sample, Author (from RunModel.metadata).
  • Heat strip + category bars; click to inspect an outcome.
  • Detail card: Δbp, frameshift, position range, physics, diff, “View on helix”, “Design PCR assay”.
  • Export menu: chart PNG, outcomes CSV, report HTML (includes engine/backend + metadata).

Compare guides

  • Select two guides in Inspector → Compare: two full Outcome Explorers side by side, each with rank + backend chips.

PCR CTA

  • From an outcome, click “Design PCR assay”; PCR panel opens with ±150 bp window prefilled around the cut/outcome.

Reports

  • Studio: Export report (HTML) from Outcome Explorer or batch via Inspector; metadata and engine/backend included.
  • CLI: after saving a session .helix, run:
    • helix-cli report --session my_session.helix --outdir reports/
    • helix-cli report --session my_session.helix --run-id demo_crispr_g2 --outdir reports/
  • Reports bundle guide info, physics + backend, outcomes JSON + CSV, and run metadata.
  • Ready-to-use demo: docs/demo/demo_session.helix (load in Studio or run helix-cli report --session docs/demo/demo_session.helix --outdir reports_demo/).

Headless simulation + reports

  1. Simulate from a JSON config into a session:
    • helix-cli simulate guides.json batch.helix
    • append to an existing session: helix-cli simulate more_guides.json batch.helix --append
    • config schema: see docs/cli_config_schema.md (supports CRISPR and PRIME via prime.pbs_sequence, prime.rt_sequence, etc.)
  2. Generate reports headlessly:
    • helix-cli report --session batch.helix --outdir reports/
    • or filter: helix-cli report --session batch.helix --run-id demo_crispr_g2 --outdir reports/
  3. Open batch.helix in Studio for interactive inspection at any time.

Suggested demo flow

  1. Open demo session.
  2. Use Inspector filters to pick a high-scoring guide; note rank/backend chips.
  3. In Outcome Explorer, click the top outcome; hit “View on helix”.
  4. Click “Design PCR assay” to see the prefilled window.
  5. Export HTML report; open it to see the same chips + metadata.
  6. Save session as .helix; run helix-cli report to generate the same report headlessly.

That’s the full loop: design → simulate → inspect → helix highlight → PCR CTA → report → headless batch.