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Biological Uncertainty Stack is a public HIR/OAM architecture map for genomic uncertainty, GRCh38 reference limits, provenance gates, measurement failure, and hard blocks against hidden positive evidence.

This Space uses the Primordial DNA Layer · GRCh38 First-Pass Architecture Plan v0.1 as its source direction. It treats GRCh38 / GRCh38.p14 as Source Layer 1: an initial baseline reference frame for first-pass feature typing and uncertainty mapping, not a complete model of human diversity and not a final biological authority.

Core invariant:
Unknown biology may preserve possibility space. Untrusted data may invalidate the comparison. Neither may be converted into hidden positive evidence.

Biological unresolvedness does not equal measurement/provenance unresolvedness. These categories must remain separate throughout all schemas, scoring, and downstream layers.

Boundary:
This is a bounded architecture and public review prototype.

It is not clinical advice, diagnosis, treatment guidance, identity proof, family-relation proof, forensic conclusion, ancestry result, genetic counseling, or validated genomic-comparison software.

GRCh38 is used as a reference frame only. All genomic inferences beyond declared evidence limits are explicitly blocked by the HIR rule set.

Structural correspondence, not ontological equivalence.

CHECKSUMS_SHA256.txt

@@ -0,0 +1,5 @@
+dbd0a885d7199f2c14e2238cd5660ffd3b478d3101130aa41ac1d15210bc4819  LICENSE
+417db1c0ce5c4883ae658ed78168d1a0250d4c3a79e1a53c528d69f98d418a2c  MANIFEST.md
+9d28a42ee18543d7fe96a7e99b41d817937595e6033a1246c80126bdc61ac5cd  README.md
+efe394f58a018532803984a3d3663f76a06e1acf5e274a434746538a9cd1c885  SOURCE_REFERENCE.md
+afba95bad509c00a1d49d88ebcfcf016ea7e35939efb9a3840d50732d181d3af  index.html

LICENSE

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+Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
+
+This project may be shared and adapted with attribution for non-commercial purposes.
+
+This Biological Uncertainty Stack packet is a bounded architecture and public review prototype. It is not clinical advice, diagnosis, treatment guidance, identity proof, family-relation proof, forensic conclusion, ancestry result, genetic counseling, or validated genomic-comparison software.
+
+Structural correspondence, not ontological equivalence.

MANIFEST.md

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+# Biological Uncertainty Stack — Hugging Face Fresh Packet
+
+Prepared for Hugging Face Static HTML Space:
+
+```text
+biological-uncertainty-stack
+```
+
+## Upload target
+
+Upload all files in this packet to the root of the Hugging Face Space.
+
+The app file is:
+
+```text
+index.html
+```
+
+## Main source/search target
+
+```text
+Primordial_DNA_GRCh38_First_Pass_Architecture_Plan_v0.1.html
+```
+
+## Source used
+
+```text
+Primordial_DNA_GRCh38_First_Pass_Architecture_Plan_v0.1.html
+```
+
+## Included files
+
+- `index.html`
+- `README.md`
+- `LICENSE`
+- `MANIFEST.md`
+- `CHECKSUMS_SHA256.txt`
+- `SOURCE_REFERENCE.md`
+
+## Boundary
+
+Architecture and public review prototype only. Not clinical advice, diagnosis, treatment guidance, identity proof, family-relation proof, forensic conclusion, ancestry result, genetic counseling, or validated genomic-comparison software.
+
+Structural correspondence, not ontological equivalence.

README.md

@@ -1,12 +1,60 @@
 ---
 title: Biological Uncertainty Stack
-emoji: 📊
-colorFrom: purple
-colorTo: purple
+emoji: 🧬
+colorFrom: blue
+colorTo: indigo
 sdk: static
+app_file: index.html
 pinned: false
 license: cc-by-nc-4.0
 short_description: Genomic uncertainty provenance map
+tags:
+  - genomics
+  - GRCh38
+  - biological-uncertainty
+  - provenance
+  - uncertainty-governance
+  - systems-integrity
+  - HIR
+  - OAM
 ---
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+# Biological Uncertainty Stack
+
+Biological Uncertainty Stack is a public HIR/OAM architecture map for genomic uncertainty, GRCh38 reference limits, provenance gates, measurement failure, and hard blocks against hidden positive evidence.
+
+This Space uses the **Primordial DNA Layer · GRCh38 First-Pass Architecture Plan v0.1** as its source direction. It treats GRCh38 / GRCh38.p14 as Source Layer 1: an initial baseline reference frame for first-pass feature typing and uncertainty mapping, not a complete model of human diversity and not a final biological authority.
+
+## Search target / source file
+
+```text
+Primordial_DNA_GRCh38_First_Pass_Architecture_Plan_v0.1.html
+```
+
+## Non-negotiable invariant
+
+Unknown biology may preserve possibility space. Untrusted data may invalidate the comparison. Neither may be converted into hidden positive evidence.
+
+Biological unresolvedness does not equal measurement/provenance unresolvedness. These categories must remain separate throughout all schemas, scoring, and downstream layers.
+
+## Boundary
+
+This is a bounded architecture and public review prototype.
+
+It is not clinical advice, diagnosis, treatment guidance, identity proof, family-relation proof, forensic conclusion, ancestry result, genetic counseling, or validated genomic-comparison software.
+
+GRCh38 is used as a reference frame only. All genomic inferences beyond declared evidence limits are explicitly blocked by the HIR rule set.
+
+Structural correspondence, not ontological equivalence.
+
+## Ecosystem position
+
+This Space is part of the broader Primordial Code Ecosystem.
+
+Parent hub:
+https://huggingface.co/spaces/HirModel/primordial-code-ecosystem
+
+Collection:
+https://huggingface.co/collections/HirModel/primordial-code-ecosystem
+
+This module is the biological-uncertainty and genomic provenance branch of the HIR/OAM life-first systems-integrity architecture.

SOURCE_REFERENCE.md

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+# Source Reference
+
+Primary search/download target:
+
+```text
+Primordial_DNA_GRCh38_First_Pass_Architecture_Plan_v0.1.html
+```
+
+Local source used for `index.html`:
+
+```text
+Primordial_DNA_GRCh38_First_Pass_Architecture_Plan_v0.1.html
+```
+
+Architecture title:
+
+```text
+Primordial DNA Layer · GRCh38 First-Pass Genomic Uncertainty Engine
+```
+
+Core invariant:
+
+```text
+Unknown biology may preserve possibility space.
+Untrusted data may invalidate the comparison.
+Neither may be converted into hidden positive evidence.
+
+Biological unresolvedness ≠ measurement/provenance unresolvedness.
+```
+
+This Hugging Face packet is a public-facing Static HTML front door for the biological uncertainty / genomic provenance branch.

index.html

@@ -1,19 +1,178 @@
 <!doctype html>
-<html>
-	<head>
-		<meta charset="utf-8" />
-		<meta name="viewport" content="width=device-width" />
-		<title>My static Space</title>
-		<link rel="stylesheet" href="style.css" />
-	</head>
-	<body>
-		<div class="card">
-			<h1>Welcome to your static Space!</h1>
-			<p>You can modify this app directly by editing <i>index.html</i> in the Files and versions tab.</p>
-			<p>
-				Also don't forget to check the
-				<a href="https://huggingface.co/docs/hub/spaces" target="_blank">Spaces documentation</a>.
-			</p>
-		</div>
-	</body>
+<html lang="en">
+<head>
+  <meta charset="utf-8"/>
+  <meta name="viewport" content="width=device-width, initial-scale=1"/>
+  <title>Biological Uncertainty Stack</title>
+  <meta name="description" content="GRCh38 genomic uncertainty and provenance map."/>
+  <style>
+    :root{
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+        linear-gradient(135deg,var(--bg),var(--bg2) 56%,#050611);
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+    .gridbg,.helix,.stars{position:fixed;inset:0;pointer-events:none}
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+    .wrap{width:min(1160px,calc(100% - 34px));margin:0 auto;position:relative}
+    header{padding:76px 0 38px}
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+    .btn.secondary{background:rgba(255,255,255,.055);color:var(--muted)}
+    nav{position:sticky;top:0;z-index:20;background:rgba(6,8,18,.72);border-bottom:1px solid rgba(255,255,255,.12);backdrop-filter:blur(16px)}
+    nav .wrap{display:flex;gap:8px;overflow:auto;padding:11px 0}
+    nav a{white-space:nowrap;text-decoration:none;color:var(--muted);border:1px solid rgba(255,255,255,.13);background:rgba(255,255,255,.045);padding:8px 11px;border-radius:999px;font-size:13px}
+    section{padding:52px 0}
+    h2{font-size:clamp(28px,4vw,44px);line-height:1.05;letter-spacing:-.045em;margin:0 0 10px}
+    .lead{color:var(--muted);max-width:900px;font-size:17px;margin:0 0 22px}
+    .grid{display:grid;grid-template-columns:repeat(3,1fr);gap:16px}
+    @media(max-width:920px){.grid{grid-template-columns:repeat(2,1fr)}}
+    @media(max-width:650px){.grid{grid-template-columns:1fr}}
+    .card,.panel{border:1px solid var(--line);background:linear-gradient(180deg,rgba(255,255,255,.088),rgba(255,255,255,.038));border-radius:var(--radius);box-shadow:var(--shadow);padding:22px;position:relative;overflow:hidden}
+    .card:before,.panel:before{content:"";position:absolute;inset:0 0 auto;height:3px;background:linear-gradient(90deg,transparent,var(--accent,var(--cyan)),transparent);opacity:.8}
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+    .top{display:flex;align-items:center;justify-content:space-between;gap:12px;margin-bottom:14px}
+    .pill{font-size:11px;text-transform:uppercase;letter-spacing:.1em;font-weight:900;border:1px solid rgba(255,255,255,.16);border-radius:999px;padding:5px 8px;color:var(--dim);background:rgba(0,0,0,.18)}
+    .pill.ok{color:var(--green);border-color:rgba(125,255,173,.35)}
+    .pill.stop{color:var(--red);border-color:rgba(255,107,138,.35)}
+    h3{font-size:21px;line-height:1.14;margin:0 0 8px;letter-spacing:-.02em}
+    p{color:var(--muted)}
+    .card p{font-size:14.5px;margin:0}
+    .tags{display:flex;gap:7px;flex-wrap:wrap;margin-top:14px}
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+    .invariant{border:1px solid rgba(255,210,122,.30);border-left:5px solid var(--gold);background:rgba(255,210,122,.09);border-radius:0 24px 24px 0;padding:22px}
+    .danger{border:1px solid rgba(255,107,138,.32);border-left:5px solid var(--red);background:rgba(255,107,138,.09);border-radius:0 24px 24px 0;padding:22px}
+    .equation{font-family:ui-monospace,SFMono-Regular,Menlo,Consolas,monospace;border:1px solid rgba(112,232,255,.22);background:rgba(0,0,0,.26);border-left:4px solid var(--cyan);border-radius:18px;padding:16px;color:#eaffff;overflow:auto;margin:12px 0;white-space:pre-wrap}
+    .split{display:grid;grid-template-columns:1fr 1fr;gap:16px}
+    @media(max-width:820px){.split{grid-template-columns:1fr}}
+    .links{display:flex;gap:8px;flex-wrap:wrap;margin-top:12px}
+    .links a{color:var(--ink);text-decoration:none;font-size:13px;font-weight:850;border:1px solid rgba(255,255,255,.14);padding:8px 10px;border-radius:12px;background:rgba(255,255,255,.06)}
+    footer{padding:34px 0 70px;color:var(--dim);border-top:1px solid rgba(255,255,255,.14);margin-top:30px}
+    footer a{color:var(--cyan)}
+  </style>
+</head>
+<body>
+<div class="gridbg"></div><div class="helix"></div><div class="stars"></div>
+
+<header class="wrap">
+  <div class="kicker"><span class="dot"></span> Biological Uncertainty · GRCh38 Source Layer 1</div>
+  <h1>Unknown biology is not bad evidence. <span>Untrusted evidence is not biology.</span></h1>
+  <p class="sub">A public HIR/OAM map for genomic uncertainty, GRCh38 reference limits, provenance gates, measurement failure, and hard blocks against hidden positive evidence.</p>
+  <div class="actions">
+    <a class="btn" href="#invariant">Read invariant</a>
+    <a class="btn secondary" href="#map">Explore source model</a>
+    <a class="btn secondary" href="https://huggingface.co/spaces/HirModel/primordial-code-ecosystem" target="_blank" rel="noopener">Parent hub</a>
+  </div>
+</header>
+
+<nav>
+  <div class="wrap">
+    <a href="#invariant">Invariant</a>
+    <a href="#map">GRCh38 layer</a>
+    <a href="#rules">HIR rules</a>
+    <a href="#roadmap">Staged ingest</a>
+    <a href="#boundary">Boundary</a>
+  </div>
+</nav>
+
+<main>
+  <section class="wrap" id="invariant">
+    <h2>Non-negotiable invariant</h2>
+    <div class="invariant">
+      <p><strong>Unknown biology may preserve possibility space. Untrusted data may invalidate the comparison. Neither may be converted into hidden positive evidence.</strong></p>
+      <p><strong>Biological unresolvedness ≠ measurement/provenance unresolvedness.</strong> These categories must remain separate throughout all schemas, scoring, and downstream layers.</p>
+    </div>
+  </section>
+
+  <section class="wrap" id="map">
+    <h2>GRCh38 first-pass source model</h2>
+    <p class="lead">GRCh38 is treated as Source Layer 1: an initial baseline reference frame, not a complete model of human diversity and not a final biological authority.</p>
+    <div class="grid">
+      <article class="card" style="--accent:#70e8ff"><div class="top"><div class="icon">🧬</div><span class="pill ok">Layer 1</span></div><h3>Reference frame</h3><p>GRCh38 / GRCh38.p14 anchors first-pass coordinates and feature typing while carrying explicit reference limitations.</p><div class="tags"><span class="tag">GRCh38</span><span class="tag">reference</span></div></article>
+      <article class="card" style="--accent:#ffd27a"><div class="top"><div class="icon">⚠️</div><span class="pill stop">Limits</span></div><h3>Known gaps</h3><p>Gap-adjacent, centromeric, telomeric, repeat-dense, and segmentally duplicated regions must carry reference confidence limits.</p><div class="tags"><span class="tag">gaps</span><span class="tag">confidence</span></div></article>
+      <article class="card" style="--accent:#a05cff"><div class="top"><div class="icon">🧾</div><span class="pill ok">Provenance</span></div><h3>Evidence chain</h3><p>Contamination, mixed sample, broken chain of custody, and undocumented provenance invalidate or suspend comparison authority.</p><div class="tags"><span class="tag">provenance</span><span class="tag">chain</span></div></article>
+      <article class="card" style="--accent:#7dffad"><div class="top"><div class="icon">🔬</div><span class="pill ok">Feature</span></div><h3>Typed features</h3><p>SNPs, indels, structural placeholders, gap regions, regulatory placeholders, and unknown unresolved features require explicit status.</p><div class="tags"><span class="tag">schema</span><span class="tag">feature classes</span></div></article>
+      <article class="card" style="--accent:#ff6b8a"><div class="top"><div class="icon">⛔</div><span class="pill stop">Hard stop</span></div><h3>No hidden positives</h3><p>Unknown biological or measurement/provenance classes may not be promoted into positive similarity, identity, or continuity evidence.</p><div class="tags"><span class="tag">blocked</span><span class="tag">HIR</span></div></article>
+      <article class="card" style="--accent:#70e8ff"><div class="top"><div class="icon">🧭</div><span class="pill ok">Next</span></div><h3>Staged layers</h3><p>Layer expansion should proceed through T2T-CHM13, pangenome references, and functional annotation only after schema validation.</p><div class="tags"><span class="tag">T2T</span><span class="tag">pangenome</span></div></article>
+    </div>
+  </section>
+
+  <section class="wrap" id="rules">
+    <h2>HIR rule layer</h2>
+    <div class="split">
+      <div class="panel">
+        <h3>Honesty</h3>
+        <p>Every feature record must carry explicit status, uncertainty class, reference confidence, and coverage confidence.</p>
+        <div class="equation">Unknown must be labeled unknown.
+No field may be implicitly clean.
+Not assessed cannot default to high confidence.</div>
+      </div>
+      <div class="panel">
+        <h3>Integrity + Respect</h3>
+        <p>Biological unresolvedness and measurement/provenance unresolvedness remain separate; identity and family-relation claims are blocked beyond declared evidence limits.</p>
+        <div class="equation">Category A ≠ Category B.
+Biological unknown ≠ sample failure.
+Sample failure ≠ biology.
+No identity/family/continuity inference.</div>
+      </div>
+    </div>
+  </section>
+
+  <section class="wrap" id="roadmap">
+    <h2>Staged ingest discipline</h2>
+    <p class="lead">Do not ingest raw genome files or perform scoring until schema, uncertainty classes, and provenance rules are validated with sample records.</p>
+    <div class="panel">
+      <div class="equation">1. GRCh38 / GRCh38.p14 — active Source Layer 1
+2. Machine-readable HIR rule table
+3. Structured GRCh38 gap-region catalog
+4. Sample feature records in JSONL
+5. T2T-CHM13 source model
+6. Liftover / coordinate alignment spec
+7. Pangenome graph-coordinate extension before HPRC Layer 3</div>
+    </div>
+  </section>
+
+  <section class="wrap" id="boundary">
+    <h2>Boundary</h2>
+    <div class="danger">
+      <p><strong>This is not a genomic analysis pipeline or medical/forensic authority.</strong></p>
+      <p>This Space is a bounded architecture and public review prototype. It is not clinical advice, diagnosis, treatment guidance, identity proof, family-relation proof, forensic conclusion, ancestry result, genetic counseling, or validated genomic-comparison software.</p>
+      <p>GRCh38 is used as a reference frame only. All genomic inferences beyond declared evidence limits are explicitly blocked by the HIR rule set.</p>
+      <p><strong>Structural correspondence, not ontological equivalence.</strong></p>
+    </div>
+  </section>
+</main>
+
+<footer class="wrap">
+  <strong>Biological Uncertainty Stack</strong><br/>
+  Created and developed by Collin D. Weber · HIR/OAM genomic uncertainty architecture.<br/>
+  Source search target: <code>Primordial_DNA_GRCh38_First_Pass_Architecture_Plan_v0.1.html</code>
+</footer>
+</body>
 </html>