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Helix Studio Strategy Playbook

0. Positioning

Helix Studio is the Visual Studio of bioinformatics: a multi-process, snapshot-driven IDE that designs, simulates, compares, and reports on CRISPR/Prime, PCR, signaling, and cell dynamics—with a headless CLI and GPU backend (OGN) built for real pipelines.

1. Strategic Arc (Wedge → Platform → Ecosystem)

  • Wedge (Months 0–6): Dominate CRISPR/Prime design loops with an end-to-end workflow (design helpers → run → compare → report) and stand up PCR as proof of the multi-process architecture.
  • Platform (Months 6–12): Integrate OGN for remote GPU runs + batch sweeps, ship a headless CLI with Nextflow/Cromwell modules, and publish a versioned snapshot specification.
  • Ecosystem (Months 9–18): Deliver a plugin API + scripting surface, a marketplace for metrics/panels/run kinds, and importers for wet-lab outputs (CRISPResso, AMP-seq, BAM/VCF) so real labs can unify wet + dry results.

2. North-Star & KPIs

  • North-Star: Successful design loops per week (create design → run → compare → report).
  • Supporting KPIs:
    • Time-to-first-verdict ≤ 10 minutes from new project.
    • Snapshot share rate ≥ 30% of sessions export a report.
    • Compare usage ≥ 60% of runs get compared.
    • Headless adoption ≥ 50% of runs via CLI/OGN by Month 9.
    • Engineering reliability: job success ≥ 99%, p95 run metadata ingest < 5 seconds.
  • Instrument each metric from day one.

3. 12-Month Milestone Plan (Branches)

Q1 (Months 0–3) – Nail the Wedge

  • v1.0 (stabilize): CRISPR/Prime IDE spine, snapshots, compare, reports (release/v1.0).
  • v1.1: Design helpers + verdicts + report v1.1 + snapshot migrations (feature/studio-v1-1-design-helpers → release/v1.1).
  • Go-to-market: LOIs with 5 design-partner labs, weekly design reviews.

Q2 (Months 3–6) – Prove Multi-Process

  • v2.0: PCR engine + metrics + compare + reports (feature/studio-pcr → release/v2.0).
  • Importers α: CRISPResso/AMP-seq summary importer to align sims ↔ wet-lab (feature/studio-importers-alpha).
  • Docs: Public snapshot spec v1 + CLI alpha.

Q3 (Months 6–9) – Become a Platform

  • v5.0 (pulled forward): OGN integration (remote jobs, perf overlay, batch sweeps, remote snapshot ingest) via feature/studio-ogn-gpu → release/v5.0.
  • Headless: CLI 1.0 + Nextflow/Cromwell modules (feature/studio-cli-headless).
  • Telemetry: Privacy-safe metrics + opt-in crash reports + reliability SLOs.

Q4 (Months 9–12) – Open the Ecosystem

  • v6.0: Plugin API + scripting console + notebooks (feature/studio-plugins → release/v6.0).
  • Marketplace β: Signed plugins, verified authors, revenue share.
  • Case studies: Prime campaign, PCR assay, OGN batch with figure-quality reports.

Parallel Track (Optional)

  • v3.0: Signaling/expression to round out cell-logic story (feature/studio-signaling).

4. Technical Moats

  • Snapshot as Contract: schema-versioned, content-addressed, deterministic rehydration—Terraform for biology.
  • Compare/Verdict UX: one-click “Improved/Worse/Tradeoff” with transparent diffs across run kinds.
  • OGN Flight Deck: GPU job control with perf HUD + batch sweep grid.
  • Plugin safety + determinism: isolated workers, time-boxed calls, reproducible notebooks referencing snapshot IDs.
  • Real-data calibration loop: import wet-lab results next to sims, compute calibration error, bake into reports.

5. Headless & Pipeline Integration

CLI (v1 syntax)

helix run \
  --snapshot session.hxs \
  --kind Prime \
  --params params.json \
  --engine local \
  --out out/

helix compare --run A123 --run B456 --out compare.json

helix report --run B456 --format md --out report.md

helix run \
  --snapshot session.hxs \
  --kind CRISPR \
  --engine ogn --queue gpu-a100 \
  --out s3://my-bucket/helix/A123/

Snapshot Bundle (.hxs)

Zipped JSON manifest + referenced assets (refs, primers, pathway graphs) with a content-address map for reproducibility.

Nextflow Module

process HELIX_PRIME {
  container 'helixstudio/cli:1.0'
  input:
    path snapshot
    path params_json
  output:
    path "out/**"
    path "report.md"
  script:
  """
  helix run \
    --snapshot ${snapshot} \
    --kind Prime \
    --params ${params_json} \
    --engine ogn \
    --out out/
  helix report --run $(cat out/run_id.txt) --format md --out report.md
  """
}

Cromwell/WDL Snippet

task HelixCRISPR {
  input {
    File snapshot
    File params_json
  }
  command <<<
    helix run --snapshot ~{snapshot} --kind CRISPR --engine ogn --out out/
    helix report --run `cat out/run_id.txt` --format json --out report.json
  >>>
  output {
    File report = "report.json"
    Directory artifacts = "out"
  }
}

6. Plugin API Shape

Manifest (TypeScript)

export interface HelixPluginManifest {
  name: string; version: string;
  helixApi: { min: "6.0.0"; max: "6.x" };
  capabilities: ("runKind"|"panel"|"metric"|"analysis")[];
  entry: string;
  permissions?: ("fs.read"|"net.fetch"|"gpu.compute")[];
  signature?: string;
}

Activation Example

export default function activate(ctx: HelixContext) {
  ctx.runs.register("AmpliconQC", {
    validateParams: schemaCheck,
    simulate: async (p, state) => shellOut("amplicon-qc", p, state),
    summarize: metricsToVerdict,
    report: renderReport
  });
  ctx.metrics.register("OnTargetDelta", computeOnTargetDelta);
  ctx.panels.register("AmpliconCloud", AmpliconCloudPanel);
}

Security

Plugins run in isolated workers with structured-clone IPC, resource caps, and signed marketplace packages.

7. Market Motion

  • Ideal customers: Methods teams (CRISPR/Prime/PCR) at biotech/pharma, CROs, advanced academic cores.
  • Design partner program (Q1–Q2): 5–8 labs, LOIs, shared roadmap, monthly office hours, co-authored case studies.
  • Pricing & packaging (open-core):
    • Community (free): local engine, CRISPR/Prime, reports, limited importers.
    • Pro ($/seat/mo): PCR, Compare+, advanced reports, local batch sweeps, plugin install.
    • Teams ($/user/mo + org features): shared storage, access control, private plugin registry.
    • Enterprise (site license + support): OGN remote, SSO/SAML, audit logs, cold storage, priority support.
    • Compute: pass-through for OGN GPU hours at transparent rates.
    • Marketplace: 80/20 revenue share for paid plugins.
  • Growth loops: Shareable reports, “Launch in Helix” badges, template gallery, one-click publish to lab wiki.

8. Proof & Credibility

Validation packs, public datasets, golden snapshots, reproducible scripts, calibration curves, preprint on snapshot model, live demos with batch sweeps + OGN perf HUD.

9. Enterprise Checklist

Security (content-addressed artifacts, encryption, SSO/SAML, RBAC), auditability (append-only provenance, signed snapshots), compliance (SOC2 path, HIPAA readiness), data governance (project-scoped storage, customer-managed keys).

10. Team & Resourcing

Lean, senior team: PM, Tech Lead, 2 engine engineers (CRISPR/Prime/PCR), 1 graphics/viz, 1 infra (OGN/CLI/CI), 1 DevRel/Docs, 1 QA/SDET. Scale in Q3 with plugin platform engineer + importers specialist.

11. Risk Register & Mitigations

  • Perception of inaccuracy: Publish calibration packs, display uncertainty, tunable thresholds, pin engine versions per snapshot.
  • GUI misfit for pipelines: Snapshot as contract + CLI + Nextflow/Cromwell.
  • Plugin security: Worker isolation, permission manifest, signed packages, review program.
  • OGN reliability under load: Backpressure, retries, detailed job states, safe resume for partial runs.
  • Domain fragmentation: Keep State/Dynamics/Viz pattern; new domains plug into shared history/compare/reports.

12. Concrete Artifacts (This Week)

  • Snapshot Spec v1 (JSON schema, canonicalization, hashing, worked CRISPR + Prime examples).
  • CLI α (helix run/compare/report wired to local engines).
  • Design Partner Pack (30-min demo script, 3 sample sessions, logging feedback doc).
  • Template Gallery v0 (5 Prime presets, 3 PCR presets).
  • OGN Contracts Draft (EngineJobSpec/Status/SnapshotPayload + mock server).
  • Website README framing (positioning line, design loop GIF, links to snapshot spec + CLI).

13. Branch & Release Hygiene

Long-lived helix-studio. Version branches release/vX.Y, tags vX.Y.Z. Feature branches per epic. CI gates: typecheck, engine tests, golden snapshot diff, report rendering diff, CLI smoke. Every release ships 1 demo session, 1 tutorial, 1 case study outline.

14. Opinionated Yes/No

Yes: snapshot as immutable content-addressed bundle; deterministic engines with fixed seeds + pinned versions; compare/verdict as one button with transparent math. No: adding domains without Metrics/Compare/Report; feature flags that bypass snapshot schema migration; plugins with unbounded FS/network access.

15. User Value (Why They Switch)

Design loops end in verdicts; consolidated view across CRISPR/Prime/PCR/signaling/cell outcomes; single artifact (snapshot) that runs locally or on OGN/Nextflow; publication-grade reports; plugin ecosystem where scripts become first-class citizens.

16. Immediate Next Steps (Execution Checklist)

  • Create repos/docs for Snapshot Spec v1 and CLI α, publish minimal examples.
  • Open feature/studio-v1-1-design-helpers and land guide/peg suggestions + verdict aggregator behind a flag.
  • Start design-partner cadence: weekly sessions, track TTFV/compare usage/report exports.
  • Draft OGN client stubs and local fake for job lifecycle testing.
  • Write Nextflow and Cromwell examples and check them into the repo.
  • Ship v1.1 with magical design helpers + verdicts, then harden headless loops at scale.