@mutagent/helix 0.1.0-alpha.14

package/LICENSE

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package/NOTICE

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+@mutagent/helix
+Copyright 2026 MutagenT
+
+This product is licensed under the Apache License, Version 2.0 (the "License");
+you may not use this product except in compliance with the License. You may
+obtain a copy of the License in the accompanying LICENSE file or at:
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software distributed
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+CONDITIONS OF ANY KIND, either express or implied. See the License for the
+specific language governing permissions and limitations under the License.
+
+----------------------------------------------------------------------------
+
+@mutagent/helix is the ADL bundle: it ships the Helix orchestrator (the
+Agentic Development Lifecycle conductor) together with the lifecycle-stage
+skills it sequences — @mutagent/agentspec (SPEC), @mutagent/diagnostics
+(DIAGNOSE), and @mutagent/evaluator (EVALUATE). Each of those skills is also
+published independently under its own name; the copies bundled here carry the
+same Apache-2.0 License.

package/README.md

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+# 🧬 @mutagent/helix
+
+> **The MutagenT Agentic Development Lifecycle (ADL) bundle.** One install gives you **Helix** — a
+> natural-language conductor — plus the lifecycle-stage skills it sequences: **spec → build →
+> evaluate → diagnose → improve**. **Standalone** — the bundle carries its own context.
+
+---
+
+## Install
+
+The whole system ships as one npm package — **`@mutagent/helix`** — the ADL bundle (the Helix
+orchestrator + the lifecycle-stage skills it conducts):
+
+```bash
+pnpx @mutagent/helix init        # installs Helix + agentspec · builder · diagnostics · evaluator
+                                 #   into <your project>/.claude, links CLAUDE.md / AGENTS.md
+pnpx @mutagent/helix init --global   # ... or into ~/.claude
+pnpx @mutagent/helix doctor      # report what's installed
+```
+
+Then open your coding agent and boot the conductor:
+
+```
+claude   →   *mutagent      (or  /mutagent-helix )
+```
+
+Each lifecycle skill is **also** designed to publish independently if you want just one stage:
+`@mutagent/diagnostics` (live on npm) · `@mutagent/evaluator` (publish wired, not yet released) ·
+`@mutagent/agentspec` and `@mutagent/builder` (publish paths not yet wired). Release mechanics:
+`RELEASING.md`.
+
+---
+
+## ① What the system is
+
+MutagenT covers the **entire** lifecycle of an AI agent as **one flexible DAG** — you can enter at any
+stage, and the conductor routes onward from there. Each stage is owned by a self-contained skill that
+ships and runs independently; **Helix** is the natural-language router that sequences them and
+adjudicates the gates between stages.
+
+| Stage | Owner | What happens |
+|---|---|---|
+| **① SPEC** | operator | Define the agent: its responsibilities, tools, integrations, and where it lives. |
+| **② BUILD** | **Builder** | Implement a validated `agentspec.yaml` into the chosen framework/harness; resync drift with `*sync-spec`. |
+| **③ EVALUATE** ★ | **Evaluator** | Decide success/failure from real traces; emit a gated verdict. *The v1 focus.* |
+| **④ DIAGNOSE** | **Diagnostics** | Root-cause the failures on real evidence; rank the remedies. |
+| **⑤ IMPROVE** | gated apply ↻ | Apply approved remedies, then loop back to BUILD to re-validate. |
+
+Two principles hold the loop together:
+
+- **Judge, never fix.** The Evaluator only decides whether something works — failures it finds are
+  *routed* to Diagnostics, which proposes the fixes that IMPROVE applies. Every change is re-built and
+  re-evaluated before it counts.
+- **Explicit and gated.** No stage auto-advances; every apply (a code change, a platform update) is
+  approval-gated. The operator stays in control.
+
+---
+
+## ② The Evaluator — from real traces to a trustworthy eval suite
+
+The Evaluator turns a subject (a skill or agent **plus its real production traces**) into an eval suite
+you can trust. It flows as a pipeline:
+
+```
+discover ──▶ judge ──▶ validate ──▶ human review ──▶ dataset
+```
+
+1. **Discover** — mine **binary, actionable** evaluation criteria directly from real agent traces
+   (it deep-reads each trace to decide success/failure, even when nothing was marked by a human).
+2. **Judge** — score both the **whole trajectory** and **each criterion**, producing a severity-gated
+   GATE verdict.
+3. **Validate** — measure the **judge's own accuracy** against human labels (true-positive /
+   true-negative rates, bias-corrected) — because a consistent judge can be consistently wrong.
+4. **Human review** — capture human labels in the loop, grounding the judge.
+5. **Dataset** — **synthesize** coverage cases and **distill** a held-out regression set, kept disjoint
+   from what was mined, so quality holds over time.
+
+**Dispatch pattern — mass-parallel, host-runtime.** The Evaluator runs a `PREP → DISPATCH → AGGREGATE`
+fan-out: the parent prepares the work, then dispatches **many independent subagents at once** — one
+judge per criterion *and* one per whole trajectory, plus dataset generators — and aggregates their
+results into a single gated verdict. Every subagent **reasons on the host runtime (no external provider
+key)**, pinned to one model at **temperature 0** so verdicts are deterministic and reproducible. Judges
+never see each other's answers; the parent is the only place results combine.
+
+> The Evaluator is a **judge only** — it never edits the subject. Failures route to Diagnostics.
+
+---
+
+## ③ Diagnostics — failures to an evidence-grounded fix spec
+
+```
+ingest traces ──▶ analyze (RCA) ──▶ evidence-grounded findings ──▶ handover spec
+```
+
+Diagnostics ingests production agent traces, runs parallel root-cause analysis with causal-chain
+breakdowns, and produces **ranked, evidence-grounded findings** — every claim tied to actual trace
+evidence. The output is a handover spec whose remedies are applied through the gated **IMPROVE** stage.
+
+**Dispatch pattern — parallel analyzers.** Diagnostics fans **root-cause analyzers out in parallel**
+over slices of the trace set; each grounds its findings in actual evidence and returns independently,
+and the parent aggregates and ranks them into one handover spec. Same host-runtime dispatch model as
+the Evaluator — concurrent subagents, no external provider key, results combined only at the parent.
+
+---
+
+## ④ The Evaluator ↔ Diagnostics boundary
+
+The sharpest line in the system is between **deciding** and **fixing** — and it is deliberate.
+The Evaluator decides; Diagnostics remediates; nothing crosses except a verdict and its evidence.
+
+```
+   EVALUATOR  ·  judge, never fix          │  handoff  │       DIAGNOSTICS  ·  diagnose & propose
+   ─────────────────────────────────       │  ───────▶ │       ──────────────────────────────────
+   discover → judge → validate              │  verdict  │       ingest → RCA (causal chains)
+   → human review → datasets                │  + failing│       → ranked, evidence-grounded remedies
+   decides PASS/FAIL · gated verdict        │  criteria │       → handover spec
+   NEVER edits the subject                  │  + cited  │       gated IMPROVE APPLIES → loop to BUILD
+                                            │  evidence │       → re-evaluate
+```
+
+- **Evaluator owns the verdict.** It decides pass/fail and emits a severity-gated verdict — and stops
+  there. It never touches the subject's code.
+- **The boundary is the handoff.** Failures are not fixed where they are found; the **verdict + the
+  failing criteria + the cited trace evidence** are *routed* across to Diagnostics.
+- **Diagnostics owns remediation.** It root-causes the routed failures, ranks evidence-grounded
+  remedies, and writes a handover spec; the **gated IMPROVE** stage applies them, then the loop returns
+  to BUILD and re-evaluates.
+- **Why the split.** A judge that also fixes can rationalize its own verdicts. Keeping decision
+  independent of remediation is what makes the verdict trustworthy.
+
+---
+
+## ⑤ Parts & commands
+
+The system is five parts: a conductor and four standalone skills, each owning a lifecycle stage.
+You drive everything in natural language — the conductor maps it to the `*command` surface below.
+
+| Part | Stage | Commands | What it does |
+|---|---|---|---|
+| **Helix** · `mutagent-orchestrator` | conductor | `*sync` · `*status` · `*onboard` · `*help` | The NL router. Indexes the system, tracks where you are in the loop, sequences the stages, and adjudicates the gates between them. |
+| **AgentSpec** · `mutagent-agentspec` | SPEC | `*spec` · `*validate-spec` · `*sync-spec` | Guided requirements interview → a portable, validated `agentspec.yaml` (the agent's Definition). `*sync-spec` reconciles the spec against a target (cold construct or warm drift), delegating the code-read to builder's `ai-architect`. |
+| **Builder** · `mutagent-builder` | BUILD | `*build` | Implement the spec into the chosen target, run TDD + coverage. Provides the `ai-architect #sync-spec` reader that AgentSpec's `*sync-spec` delegates to (and that `*build` reuses on drift). |
+| **Evaluator** · `mutagent-evaluator` ★ | EVALUATE / AUDIT | `*discover` · `*evaluate` · `*audit` · `*validate` · `*review` · `*build-dataset` · `*derive-dataset` | The eval-development engine: mine criteria from real traces → judge → measure the judge's accuracy → capture human labels → synthesize & distill datasets. **Judge only — never fixes.** |
+| **Diagnostics** · `mutagent-diagnostics` | DIAGNOSE / IMPROVE | `*diagnose` | Root-cause routed failures on real evidence → ranked remedies → the gated IMPROVE apply. |
+
+Boot the conductor from this directory (`*mutagent`); it renders the dashboard and waits for a
+`*command`. The deeper map of stages, decisions, and status lives in
+`.memory/features/adl-v3/adl-prd-final.md`.
+
+---
+
+## ⑥ How it runs — the dispatch DAG
+
+The lifecycle is a directed graph: work flows forward, failures route *sideways* to Diagnostics, and
+the loop returns to BUILD. The dotted edges are the **mass-parallel dispatch** — both the Evaluator and
+Diagnostics fan work out across many subagents at once, all reasoning on the host runtime (no external
+provider key, pinned model at temperature 0), aggregated only at the parent.
+
+```mermaid
+flowchart LR
+  SPEC(["SPEC"]) --> BUILD(["BUILD"]) --> EVAL{{"EVALUATE"}}
+  EVAL -->|"pass · gated verdict"| SHIP(["ship ✓"])
+  EVAL -->|"fail · verdict + evidence"| DIAG(["DIAGNOSE"])
+  DIAG --> IMPROVE(["IMPROVE · gated"]) --> BUILD
+  EVAL -. dispatch .-> EJ1["judge / criterion"]
+  EVAL -. dispatch .-> EJ2["judge / trajectory"]
+  EVAL -. dispatch .-> EDS["dataset gen"]
+  DIAG -. dispatch .-> DA1["RCA analyzer"]
+  DIAG -. dispatch .-> DA2["RCA analyzer"]
+```
+
+---
+
+## Status — tested & verified (current)
+
+The system has been put through a **goal-driven verification loop**: every Evaluator command was run
+end-to-end by **real subagents** against a **live production agent's traces**, and — separately — the
+**quality of what each command produced** was checked by an **independent reviewer** (reviewer ≠
+executor), fed the raw artifacts plus the source trace.
+
+**Two axes, both green:**
+
+1. **Workflow** — does each command run end-to-end and produce its artifact? → **9 / 9 verified.**
+2. **Output quality** — is what it produced correct, grounded, and useful? → **independently validated.**
+
+**Verified, command by command:**
+
+| Command | Produces | Verified |
+|---|---|---|
+| `*discover` | binary, actionable criteria mined from a real trace | every criterion grounded in the trace — strings & counts checked verbatim; **zero fabricated** |
+| `*evaluate` | per-criterion verdicts + a severity-gated GATE | all verdicts correct; whole-trace counts matched exactly; gate logic sound |
+| `*build-evals` | per-criterion judge verdicts | well-formed prompts · critique-before-verdict · honest caveats · calibrated confidence |
+| `*validate` | judge accuracy (TPR / TNR, bias-corrected) | math hand-verified; Rogan-Gladen correction exact; confidence interval present |
+| `*review` | human-in-the-loop label UI | full annotation toolkit — pass/fail/defer · notes · autosave · export |
+| `*build-dataset` | curated coverage cases | all honor the operator-curated focus; diverse + idiomatic |
+| `*derive-dataset` | distilled held-out regression set | correct schema + provenance; label→outcome mapping correct |
+| `*audit` | data-flow / leak / context audit | runs end-to-end |
+
+**Output-quality headline.** Across the eval-engine outputs, the independent reviewer found
+**zero ungrounded criteria and zero false verdicts** — the verdicts are not merely consistent, they are
+demonstrably *right*. The loop even surfaced and confirmed a real production defect along the way.
+
+**Current focus** — `*discover` → **eval & dataset quality verification**: mining high-quality criteria
+and held-out datasets from real production traces and *proving their quality*, so every verdict built on
+them can be believed.
+
+---
+
+<sub>🧬 Built by the MutagenT Team · internal · standalone ADL system</sub>

package/assets/adl-loop.svg

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+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"
+     viewBox="0 0 920 600" width="920" height="600" role="img"
+     aria-label="The Agentic Development Lifecycle: spec, build, evaluate, diagnose, improve — a loop that routes back to build.">
+  <title>The Agentic Development Lifecycle (ADL)</title>
+  <desc>A five-stage cycle — SPEC, BUILD, EVALUATE, DIAGNOSE, IMPROVE — sequenced by the Helix orchestrator. A pulse of work flows clockwise around the loop; IMPROVE iterates straight back to BUILD.</desc>
+
+  <defs>
+    <!-- adapted from the agent-lifecycle deck: cyan (build-side) -> violet (learn-side) -->
+    <radialGradient id="bg" cx="50%" cy="42%" r="75%">
+      <stop offset="0%" stop-color="#101a30"/>
+      <stop offset="60%" stop-color="#0b1224"/>
+      <stop offset="100%" stop-color="#070b16"/>
+    </radialGradient>
+    <linearGradient id="ring" x1="0" y1="0" x2="1" y2="1">
+      <stop offset="0%"  stop-color="#22d3ee"/>
+      <stop offset="45%" stop-color="#06b6d4"/>
+      <stop offset="75%" stop-color="#7E47D7"/>
+      <stop offset="100%" stop-color="#a78bfa"/>
+    </linearGradient>
+    <radialGradient id="comet" cx="50%" cy="50%" r="50%">
+      <stop offset="0%" stop-color="#f5f3ff"/>
+      <stop offset="55%" stop-color="#c4b5fd"/>
+      <stop offset="100%" stop-color="#7E47D7" stop-opacity="0"/>
+    </radialGradient>
+    <radialGradient id="hubFill" cx="50%" cy="40%" r="70%">
+      <stop offset="0%" stop-color="#1c2740"/>
+      <stop offset="100%" stop-color="#0d1426"/>
+    </radialGradient>
+    <filter id="soft" x="-80%" y="-80%" width="260%" height="260%">
+      <feGaussianBlur stdDeviation="5"/>
+    </filter>
+    <marker id="arrow" viewBox="0 0 10 10" refX="8" refY="5" markerWidth="7" markerHeight="7" orient="auto-start-reverse">
+      <path d="M0,0 L10,5 L0,10 z" fill="#a78bfa"/>
+    </marker>
+    <marker id="arrowC" viewBox="0 0 10 10" refX="8" refY="5" markerWidth="6.5" markerHeight="6.5" orient="auto-start-reverse">
+      <path d="M0,0 L10,5 L0,10 z" fill="#06b6d4"/>
+    </marker>
+
+    <style>
+      .stagename{font:700 17px 'Helvetica Neue',Arial,sans-serif;letter-spacing:.5px}
+      .owner{font:500 10.5px 'Helvetica Neue',Arial,sans-serif;fill:#94a3b8}
+      .cmd{font:600 10px 'SFMono-Regular',Consolas,monospace}
+      .card{fill:#0e1730;stroke-width:1.6;rx:12}
+      /* breathing halo behind each stage, staged to chase the comet (~9s loop) */
+      .halo{opacity:.12;transform-box:fill-box;transform-origin:center}
+      @keyframes pulse{
+        0%,100%{opacity:.10;transform:scale(.92)}
+        12%{opacity:.55;transform:scale(1.06)}
+        30%{opacity:.10;transform:scale(.92)}
+      }
+      .h0{animation:pulse 9s ease-in-out infinite}
+      .h1{animation:pulse 9s ease-in-out infinite 1.8s}
+      .h2{animation:pulse 9s ease-in-out infinite 3.6s}
+      .h3{animation:pulse 9s ease-in-out infinite 5.4s}
+      .h4{animation:pulse 9s ease-in-out infinite 7.2s}
+      /* marching-ants on the iterate-back arc */
+      @keyframes march{to{stroke-dashoffset:-44}}
+      .iterate{stroke-dasharray:8 6;animation:march 1.1s linear infinite}
+      /* faint hub spokes shimmer */
+      @keyframes spoke{0%,100%{opacity:.10}50%{opacity:.30}}
+      .spoke{stroke:#475569;stroke-width:1;animation:spoke 4.5s ease-in-out infinite}
+      .ring-flow{stroke-dasharray:3 9;animation:march 2.4s linear infinite reverse}
+    </style>
+  </defs>
+
+  <rect width="920" height="600" fill="url(#bg)"/>
+
+  <!-- ===== the loop (faint guide ring through the 5 stages, clockwise) ===== -->
+  <path id="loop" d="M460,100 L635.9,227.8 L568.7,434.7 L351.3,434.7 L284.1,227.8 Z"
+        fill="none" stroke="url(#ring)" stroke-width="2.4" opacity="0.5" stroke-linejoin="round"/>
+  <path d="M460,100 L635.9,227.8 L568.7,434.7 L351.3,434.7 L284.1,227.8 Z"
+        fill="none" stroke="#a78bfa" stroke-width="2.4" opacity="0.6" stroke-linejoin="round" class="ring-flow"/>
+
+  <!-- ===== Helix hub: the NL orchestrator that routes between stages ===== -->
+  <g>
+    <line class="spoke" x1="460" y1="285" x2="460"   y2="100"/>
+    <line class="spoke" x1="460" y1="285" x2="635.9" y2="227.8"/>
+    <line class="spoke" x1="460" y1="285" x2="568.7" y2="434.7"/>
+    <line class="spoke" x1="460" y1="285" x2="351.3" y2="434.7"/>
+    <line class="spoke" x1="460" y1="285" x2="284.1" y2="227.8"/>
+    <circle cx="460" cy="285" r="47" fill="url(#hubFill)" stroke="#334155" stroke-width="1.4"/>
+    <text x="460" y="281" text-anchor="middle" class="stagename" fill="#e2e8f0">HELIX</text>
+    <text x="460" y="298" text-anchor="middle" class="owner">NL router</text>
+  </g>
+
+  <!-- ===== iterate ↻ : IMPROVE loops straight back to BUILD ===== -->
+  <path class="iterate" d="M312,212 Q460,150 608,212"
+        fill="none" stroke="#a78bfa" stroke-width="2.2" marker-end="url(#arrow)"/>
+  <text x="460" y="162" text-anchor="middle" class="cmd" fill="#a78bfa">iterate &#8635; loop back to build</text>
+
+  <!-- ===== flowing pulse of work (clockwise around the loop) ===== -->
+  <circle r="13" fill="url(#comet)" filter="url(#soft)">
+    <animateMotion dur="9s" repeatCount="indefinite" rotate="auto">
+      <mpath xlink:href="#loop"/>
+    </animateMotion>
+  </circle>
+  <circle r="5" fill="#f5f3ff">
+    <animateMotion dur="9s" repeatCount="indefinite" rotate="auto">
+      <mpath xlink:href="#loop"/>
+    </animateMotion>
+  </circle>
+  <circle r="9" fill="url(#comet)" filter="url(#soft)" opacity="0.6">
+    <animateMotion dur="9s" begin="-3s" repeatCount="indefinite" rotate="auto">
+      <mpath xlink:href="#loop"/>
+    </animateMotion>
+  </circle>
+  <circle r="9" fill="url(#comet)" filter="url(#soft)" opacity="0.6">
+    <animateMotion dur="9s" begin="-6s" repeatCount="indefinite" rotate="auto">
+      <mpath xlink:href="#loop"/>
+    </animateMotion>
+  </circle>
+
+  <!-- ===== stage cards ===== -->
+  <!-- SPEC -->
+  <g>
+    <rect class="halo h0" x="380" y="68" width="160" height="64" rx="14" fill="#38bdf8"/>
+    <rect class="card" x="380" y="68" width="160" height="64" rx="12" stroke="#38bdf8"/>
+    <text x="460" y="94"  text-anchor="middle" class="stagename" fill="#38bdf8">SPEC</text>
+    <text x="460" y="110" text-anchor="middle" class="owner">operator defines + designs</text>
+    <text x="460" y="124" text-anchor="middle" class="cmd"  fill="#7dd3fc">*spec</text>
+  </g>
+  <!-- BUILD -->
+  <g>
+    <rect class="halo h1" x="555.9" y="195.8" width="160" height="64" rx="14" fill="#06b6d4"/>
+    <rect class="card" x="555.9" y="195.8" width="160" height="64" rx="12" stroke="#06b6d4"/>
+    <text x="635.9" y="221.8" text-anchor="middle" class="stagename" fill="#22d3ee">BUILD</text>
+    <text x="635.9" y="237.8" text-anchor="middle" class="owner">mutagent-skill-builder</text>
+    <text x="635.9" y="251.8" text-anchor="middle" class="cmd"  fill="#67e8f9">*build</text>
+  </g>
+  <!-- EVALUATE -->
+  <g>
+    <rect class="halo h2" x="488.7" y="402.7" width="160" height="64" rx="14" fill="#22d3ee"/>
+    <rect class="card" x="488.7" y="402.7" width="160" height="64" rx="12" stroke="#22d3ee"/>
+    <text x="568.7" y="428.7" text-anchor="middle" class="stagename" fill="#67e8f9">EVALUATE</text>
+    <text x="568.7" y="444.7" text-anchor="middle" class="owner">mutagent-evaluator</text>
+    <text x="568.7" y="458.7" text-anchor="middle" class="cmd"  fill="#a5f3fc">*evaluate &#183; *audit</text>
+  </g>
+  <!-- DIAGNOSE -->
+  <g>
+    <rect class="halo h3" x="271.3" y="402.7" width="160" height="64" rx="14" fill="#7E47D7"/>
+    <rect class="card" x="271.3" y="402.7" width="160" height="64" rx="12" stroke="#7E47D7"/>
+    <text x="351.3" y="428.7" text-anchor="middle" class="stagename" fill="#c4b5fd">DIAGNOSE</text>
+    <text x="351.3" y="444.7" text-anchor="middle" class="owner">mutagent-diagnostics</text>
+    <text x="351.3" y="458.7" text-anchor="middle" class="cmd"  fill="#ddd6fe">*diagnose</text>
+  </g>
+  <!-- IMPROVE -->
+  <g>
+    <rect class="halo h4" x="204.1" y="195.8" width="160" height="64" rx="14" fill="#a78bfa"/>
+    <rect class="card" x="204.1" y="195.8" width="160" height="64" rx="12" stroke="#a78bfa"/>
+    <text x="284.1" y="221.8" text-anchor="middle" class="stagename" fill="#c4b5fd">IMPROVE</text>
+    <text x="284.1" y="237.8" text-anchor="middle" class="owner">gated apply &#8635;</text>
+    <text x="284.1" y="251.8" text-anchor="middle" class="cmd"  fill="#ddd6fe">*improve</text>
+  </g>
+
+  <!-- ===== caption ===== -->
+  <text x="460" y="528" text-anchor="middle"
+        style="font:600 15px 'Helvetica Neue',Arial,sans-serif;letter-spacing:2px" fill="#e2e8f0">THE AGENTIC DEVELOPMENT LIFECYCLE</text>
+  <text x="460" y="552" text-anchor="middle"
+        style="font:500 12px 'SFMono-Regular',Consolas,monospace;letter-spacing:1px" fill="#64748b">spec &#9656; build &#9656; evaluate &#9656; diagnose &#9656; improve &#8635;</text>
+  <text x="460" y="574" text-anchor="middle"
+        style="font:500 11px 'Helvetica Neue',Arial,sans-serif" fill="#475569">one flexible DAG &#183; enter at any stage &#183; Helix sequences the rest</text>
+</svg>