Helix Features Catalog (CLI + GUI)

A concise, single-page map of every shipped surface. Commands are helix ... unless noted; artifacts are reproducible and schema-tagged.

CLI surfaces

• Sessions & reports
  • helix-cli simulate|run <config.json> <session.helix> [--append --backend gpu|native-cpu|cpu-reference] → .helix session with RunModels stamped with scoring/backend metadata.
  • helix-cli report --session … [--run-id …] --outdir … and helix-cli export --session … --run-id … --outdir … → per-run HTML + PNG + JSON.
• CRISPR / Prime / PCR artifacts
  • crispr dag → helix.crispr.edit_dag.v1.1 JSON, optional frames; prime dag → helix.prime.edit_dag.v1.1; pcr dag → helix.pcr.amplicon_dag.v1.
  • crispr genome-sim cut events JSON; crispr find-guides|offtargets|score|simulate stubs for guide discovery, hits, scoring, outcome sim + viz-spec.
  • prime simulate → prime edit sim JSON + viz-spec.
  • edit-dag viz → PNG + .viz.json + provenance; edit-dag generate-dataset → JSONL dataset rows.
• Visualization helpers
  • viz subcommands: crispr-track, triage, alignment-ribbon, hydropathy, minimizers, seed-chain, rna-dotplot, distance-heatmap, motif-logo; every save emits PNG + viz-spec + provenance sidecar.
  • viz schema prints sample viz schema payloads; schema manifest|diff exports/diffs viz schema manifest (spec versioned).
• DNA/RNA/protein/triage utilities
  • dna GC/k-mer windows; spectrum leaderboard; rna mfe|ensemble dot-bracket/ensemble JSON; triage ORF/k-mer/GC summary + optional viz triage.
• Engine + performance
  • bench quick seeded CRISPR/Prime perf; caches summary to ~/.helix/benchmarks.json.
  • engine benchmark --backends … --crispr-shapes … --prime-workloads … --json … (structured result), engine info prints resolved backend availability.
• Reproducibility & artifacts
  • run --out … --backends all|… → reproducibility bundles; verify --kind repro|auto --manifest … checks parity.
  • artifacts build --config … --outdir … [--backend … --zip --with-support-bundle] → manifest + reports (+zip); artifacts manifest pretty-prints manifest.
  • support bundle emits redacted diagnostics; evidence --snapshot … --out … [--include-sequence] produces VeriBiota evidence JSON.
• Partner/demo
  • partner run generates three deterministic design-partner bundles + optional support bundle + JSON summary.
  • demo run builds CRISPR/Prime demo bundles; demo viz writes canned viz assets.
• HelixSpec toolchain
  • compile → canonical IR/manifest; diff → manifest diff; helixspec-run → compile+execute spec with optional policy; verify --kind helixspec|auto validates manifests.
• Live runtime (LiveGraph)
  • Commands described in docs/cli/live.md: helix live run|viz|inspect|plan|dev|demo for multirate HGX models, realtime delta streaming, GLFW+moderngl viewer, bundle export (snapshots.json, deltas.json, events.json, meta.json). Note: console entrypoint not yet wired in pyproject; requires realtime extra.
• Plugins (packaging)
  • plugins keygen|hash|pack|sign|verify create signed deterministic .helixplugin packages with HASHES.json + Ed25519 signatures. Trust/registry enforced in Studio via HELIX_STUDIO_PLUGIN_* envs.

GUI (Helix Studio) surfaces

• Project/session UX: open/save .helix_project.json, recent projects/sessions, offline demo path, load .helix from CLI.
• Authoring spine: CRISPR/Prime/PCR Sim Builder with presets, backend chooser (CPU/native/GPU) + status hints, deterministic seeds, batch parallelism knob.
• Run execution/history: launch runs, clone runs with lineage, persist snapshots/EVS for replay; Outcome Explorer for ranking/filters/overlays; guide-level ranking and baseline-vs-candidate compare overlays.
• Visualization: realtime 3D viewport (rails/helix) + outcome highlighting; 2.5D workflow/timeline; edit DAG graph with node/edge probabilities and stage filters; selection linking to outcomes.
• Exports/evidence: HTML reports, evidence JSON, resolve clip export (GIF/MP4 + metadata), snapshot bundle export, Lightcone audit pack export/verify when extra installed.
• Plugin manager: install/update/rollback signed .helixplugin packages, registry URL + trust store; namespaced commands/dock panels; optional user plugin roots via env.
• State continuity: restores last center tab, cameras/layouts for 3D/2.5D/DAG views; per-view versioned state blobs.

Notable gaps to document further

• Wire helix live console entrypoint (currently only documented).
• Public doc page for HelixSpec CLI (compile/run/diff/verify) and policy injection.
• Evidence/export knobs (--include-sequence, support bundle toggles) and artifact bundle layout examples.

Validation suggestions

• Smoke the CLI matrix: tools/test.sh -q tests/test_cli_smoke.py (covers stubs/dispatch).
• Add a docs check to ensure this file stays in sync: simple grep in CI comparing pyproject scripts against the catalog headings.
• Manual: run helix-cli --help to confirm no unlabeled subcommands after future additions.