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| <html lang="en"> | |
| <head> | |
| <meta charset="utf-8"> | |
| <meta name="viewport" content="width=device-width,initial-scale=1"> | |
| <title>BIO-SEMANTICS — Gene-Expression Semantic Modeling Pipeline</title> | |
| <style> | |
| @import url('https://fonts.googleapis.com/css2?family=JetBrains+Mono:wght@300;400;500&family=Inter:wght@300;400;600&display=swap'); | |
| :root { | |
| --bg: #0a0e14; --surface: #111820; --border: #1e2a38; | |
| --text: #c5d0dc; --dim: #5a6a7a; --bright: #e8edf2; | |
| --cyan: #00e5ff; --blue: #448aff; --violet: #b388ff; | |
| --green: #69f0ae; --amber: #ffd740; --red: #ff5252; | |
| --bio: #00c853; --glow-cyan: 0 0 20px rgba(0,229,255,.15); | |
| --glow-violet: 0 0 20px rgba(179,136,255,.15); | |
| --mono: 'JetBrains Mono', monospace; --sans: 'Inter', system-ui, sans-serif; | |
| --radius: 8px; | |
| } | |
| *, *::before, *::after { box-sizing: border-box; margin: 0; padding: 0; } | |
| body { font: 14px/1.6 var(--sans); color: var(--text); background: var(--bg); min-height: 100vh; } | |
| h1, h2, h3 { font-weight: 600; color: var(--bright); } | |
| /* HEADER */ | |
| .header { | |
| text-align: center; padding: 32px 24px 24px; | |
| background: linear-gradient(180deg, rgba(0,229,255,.04) 0%, transparent 100%); | |
| border-bottom: 1px solid var(--border); | |
| } | |
| .header h1 { font: 600 2.2rem var(--mono); letter-spacing: .15em; color: var(--cyan); text-shadow: var(--glow-cyan); } | |
| .header .subtitle { font: 300 1rem var(--sans); color: var(--dim); margin-top: 4px; } | |
| .header .authors { font: 400 .85rem var(--mono); color: var(--violet); margin-top: 12px; letter-spacing: .05em; } | |
| .header .protocol { font: 500 .75rem var(--mono); color: var(--dim); margin-top: 8px; letter-spacing: .2em; text-transform: uppercase; } | |
| /* NAV */ | |
| nav { | |
| display: flex; gap: 2px; justify-content: center; padding: 12px 24px; | |
| background: var(--surface); border-bottom: 1px solid var(--border); flex-wrap: wrap; | |
| } | |
| nav button { | |
| font: 500 .7rem var(--mono); color: var(--dim); background: transparent; | |
| border: 1px solid transparent; padding: 6px 14px; border-radius: 4px; | |
| cursor: pointer; letter-spacing: .1em; text-transform: uppercase; transition: all .2s; | |
| } | |
| nav button:hover, nav button.active { color: var(--cyan); border-color: var(--border); background: rgba(0,229,255,.04); } | |
| /* GRID */ | |
| .main { display: grid; grid-template-columns: 1fr 1.4fr 1fr; gap: 16px; padding: 20px; max-width: 1600px; margin: 0 auto; } | |
| @media (max-width: 1200px) { .main { grid-template-columns: 1fr; } } | |
| /* PANELS */ | |
| .panel { | |
| background: var(--surface); border: 1px solid var(--border); border-radius: var(--radius); | |
| padding: 16px; position: relative; overflow: hidden; | |
| } | |
| .panel::before { | |
| content: ''; position: absolute; top: 0; left: 0; right: 0; height: 2px; | |
| background: linear-gradient(90deg, transparent, var(--cyan), transparent); opacity: .3; | |
| } | |
| .panel h2 { | |
| font: 600 .8rem var(--mono); color: var(--cyan); letter-spacing: .12em; | |
| text-transform: uppercase; margin-bottom: 12px; padding-bottom: 8px; | |
| border-bottom: 1px solid var(--border); | |
| } | |
| .panel h3 { font: 500 .7rem var(--mono); color: var(--violet); letter-spacing: .1em; text-transform: uppercase; margin: 12px 0 6px; } | |
| /* TAGS */ | |
| .tag { | |
| display: inline-block; font: 500 .65rem var(--mono); padding: 2px 8px; | |
| border-radius: 3px; letter-spacing: .08em; text-transform: uppercase; | |
| } | |
| .tag-observed { color: var(--green); border: 1px solid rgba(105,240,174,.3); background: rgba(105,240,174,.06); } | |
| .tag-inferred { color: var(--violet); border: 1px solid rgba(179,136,255,.3); background: rgba(179,136,255,.06); } | |
| .tag-derived { color: var(--blue); border: 1px solid rgba(68,138,255,.3); background: rgba(68,138,255,.06); } | |
| .tag-predicted { color: var(--amber); border: 1px solid rgba(255,215,64,.3); background: rgba(255,215,64,.06); } | |
| .tag-constrained { color: var(--cyan); border: 1px solid rgba(0,229,255,.3); background: rgba(0,229,255,.06); } | |
| .tag-encoded { color: #ff80ab; border: 1px solid rgba(255,128,171,.3); background: rgba(255,128,171,.06); } | |
| .tag-executed { color: #ea80fc; border: 1px solid rgba(234,128,252,.3); background: rgba(234,128,252,.06); } | |
| /* TABLES */ | |
| table { width: 100%; border-collapse: collapse; font: 400 .75rem var(--mono); } | |
| th { text-align: left; color: var(--dim); font-weight: 500; padding: 4px 8px; border-bottom: 1px solid var(--border); letter-spacing: .05em; } | |
| td { padding: 4px 8px; border-bottom: 1px solid rgba(30,42,56,.5); color: var(--text); } | |
| tr:hover td { background: rgba(0,229,255,.02); } | |
| /* FLOW */ | |
| .flow { display: flex; flex-direction: column; align-items: center; gap: 2px; } | |
| .flow-node { | |
| font: 500 .7rem var(--mono); color: var(--bright); background: rgba(0,229,255,.06); | |
| border: 1px solid rgba(0,229,255,.2); padding: 6px 16px; border-radius: 4px; | |
| text-align: center; letter-spacing: .08em; text-transform: uppercase; width: 100%; max-width: 260px; | |
| cursor: pointer; transition: all .2s; | |
| } | |
| .flow-node:hover { border-color: var(--cyan); box-shadow: var(--glow-cyan); } | |
| .flow-arrow { color: var(--dim); font-size: .6rem; } | |
| /* HELIX */ | |
| .helix-container { position: relative; height: 600px; display: flex; align-items: center; justify-content: center; } | |
| .helix-svg { width: 200px; height: 100%; } | |
| .helix-labels { | |
| position: absolute; top: 0; left: 50%; transform: translateX(-50%); | |
| height: 100%; display: flex; flex-direction: column; justify-content: space-between; | |
| padding: 20px 0; | |
| } | |
| .helix-label { | |
| font: 400 .65rem var(--mono); color: var(--dim); text-align: center; | |
| padding: 2px 12px; border-radius: 3px; letter-spacing: .06em; | |
| transition: all .3s; | |
| } | |
| .helix-label:hover { color: var(--cyan); background: rgba(0,229,255,.06); } | |
| /* VALIDATOR */ | |
| .rule-grid { display: grid; grid-template-columns: auto 1fr auto; gap: 2px 8px; align-items: center; } | |
| .rule-num { font: 500 .65rem var(--mono); color: var(--dim); } | |
| .rule-text { font: 400 .72rem var(--sans); color: var(--text); } | |
| .rule-status { width: 8px; height: 8px; border-radius: 50%; } | |
| .rule-status.pass { background: var(--green); box-shadow: 0 0 6px rgba(105,240,174,.4); } | |
| .rule-status.pending { background: var(--amber); box-shadow: 0 0 6px rgba(255,215,64,.3); } | |
| /* PTM */ | |
| .tape { display: flex; gap: 1px; margin: 8px 0; } | |
| .tape-cell { | |
| width: 28px; height: 28px; display: flex; align-items: center; justify-content: center; | |
| font: 500 .8rem var(--mono); border: 1px solid var(--border); border-radius: 3px; | |
| color: var(--bright); background: var(--bg); transition: all .3s; | |
| } | |
| .tape-cell.head { border-color: var(--cyan); color: var(--cyan); box-shadow: var(--glow-cyan); background: rgba(0,229,255,.08); } | |
| .tape-cell.blank { color: var(--dim); } | |
| .state-badge { | |
| font: 500 .7rem var(--mono); padding: 3px 10px; border-radius: 4px; | |
| display: inline-block; | |
| } | |
| .state-even { color: var(--cyan); border: 1px solid rgba(0,229,255,.3); background: rgba(0,229,255,.06); } | |
| .state-odd { color: var(--violet); border: 1px solid rgba(179,136,255,.3); background: rgba(179,136,255,.06); } | |
| .state-accept { color: var(--green); border: 1px solid rgba(105,240,174,.3); background: rgba(105,240,174,.06); } | |
| /* DISTRIBUTIONS */ | |
| .dist-bar { display: flex; align-items: center; gap: 8px; margin: 4px 0; } | |
| .dist-label { font: 400 .7rem var(--mono); color: var(--dim); width: 80px; text-align: right; } | |
| .dist-track { flex: 1; height: 4px; background: var(--border); border-radius: 2px; position: relative; } | |
| .dist-fill { height: 100%; border-radius: 2px; background: linear-gradient(90deg, var(--violet), var(--cyan)); } | |
| .dist-ci { position: absolute; top: -4px; height: 12px; border-left: 1px solid var(--amber); border-right: 1px solid var(--amber); background: rgba(255,215,64,.08); } | |
| .dist-val { font: 400 .65rem var(--mono); color: var(--bright); width: 50px; } | |
| /* PROVENANCE */ | |
| .hash { font: 400 .65rem var(--mono); color: var(--dim); word-break: break-all; } | |
| .chain-link { display: flex; align-items: center; gap: 8px; padding: 4px 0; border-bottom: 1px solid rgba(30,42,56,.3); } | |
| .chain-dot { width: 6px; height: 6px; border-radius: 50%; background: var(--cyan); flex-shrink: 0; } | |
| .chain-info { flex: 1; } | |
| .chain-id { font: 500 .7rem var(--mono); color: var(--bright); } | |
| .chain-meta { font: 400 .6rem var(--mono); color: var(--dim); } | |
| /* CIRCUIT */ | |
| .circuit { font: 400 .7rem var(--mono); color: var(--text); background: var(--bg); padding: 8px; border-radius: 4px; border: 1px solid var(--border); overflow-x: auto; white-space: pre; } | |
| /* MAINFRAME */ | |
| .mainframe-box { | |
| border: 1px solid var(--border); border-radius: 4px; padding: 8px; | |
| background: repeating-linear-gradient(0deg, transparent, transparent 19px, rgba(30,42,56,.3) 20px); | |
| font: 400 .7rem var(--mono); color: var(--dim); | |
| } | |
| .job-id { color: var(--amber); } | |
| .dsn { color: var(--green); } | |
| /* BOTTOM BAR */ | |
| .bottom-bar { | |
| display: grid; grid-template-columns: repeat(auto-fit, minmax(200px, 1fr)); | |
| gap: 16px; padding: 20px; max-width: 1600px; margin: 0 auto; | |
| } | |
| /* FULL WIDTH SECTIONS */ | |
| .full-width { grid-column: 1 / -1; } | |
| /* FOOTER */ | |
| footer { | |
| text-align: center; padding: 24px; font: 400 .75rem var(--mono); | |
| color: var(--dim); border-top: 1px solid var(--border); | |
| letter-spacing: .1em; | |
| } | |
| </style> | |
| </head> | |
| <body> | |
| <div class="header"> | |
| <h1>BIO-SEMANTICS</h1> | |
| <div class="subtitle">Gene-Expression Semantic Modeling Pipeline</div> | |
| <div class="authors">AHMAD ALI PARR · JESSICA L. WILLIAMS · SNAPKITTYWEST</div> | |
| <div class="protocol">Evidence or Silence · 2026</div> | |
| </div> | |
| <nav> | |
| <button class="active">OBSERVATIONS</button> | |
| <button>SEMANTICS</button> | |
| <button>BAYESIAN</button> | |
| <button>CONSTRAINTS</button> | |
| <button>BINARY</button> | |
| <button>PTM</button> | |
| <button>QUIPPER</button> | |
| <button>PROVENANCE</button> | |
| <button>RPG/JCL</button> | |
| </nav> | |
| <div class="main"> | |
| <!-- LEFT COLUMN --> | |
| <div style="display:flex;flex-direction:column;gap:16px;"> | |
| <!-- cDNA Observations --> | |
| <div class="panel"> | |
| <h2>cDNA Observations</h2> | |
| <span class="tag tag-observed">OBSERVED</span> | |
| <table style="margin-top:8px;"> | |
| <thead><tr><th>GENE</th><th>SAMPLE</th><th>COUNT</th><th>NORM</th></tr></thead> | |
| <tbody> | |
| <tr><td>BRCA1</td><td>S001</td><td>4,892</td><td>8.24</td></tr> | |
| <tr><td>TP53</td><td>S001</td><td>12,340</td><td>11.02</td></tr> | |
| <tr><td>MYC</td><td>S002</td><td>891</td><td>6.15</td></tr> | |
| <tr><td>EGFR</td><td>S002</td><td style="color:var(--amber)">MISSING</td><td style="color:var(--amber)">MISSING</td></tr> | |
| <tr><td>KRAS</td><td>S003</td><td>2,107</td><td>7.89</td></tr> | |
| <tr><td>PTEN</td><td>S003</td><td>6,723</td><td>9.41</td></tr> | |
| </tbody> | |
| </table> | |
| <div style="margin-top:8px;font:.65rem var(--mono);color:var(--dim);">6 observations · 3 samples · 6 genes · 1 missing cell</div> | |
| </div> | |
| <!-- Gene Expression Matrix --> | |
| <div class="panel"> | |
| <h2>Gene Expression Matrix</h2> | |
| <div style="display:grid;grid-template-columns:auto repeat(3,1fr);gap:1px;margin-top:8px;"> | |
| <div style="font:.6rem var(--mono);color:var(--dim);padding:4px;">GENE</div> | |
| <div style="font:.6rem var(--mono);color:var(--dim);padding:4px;text-align:center;">S001</div> | |
| <div style="font:.6rem var(--mono);color:var(--dim);padding:4px;text-align:center;">S002</div> | |
| <div style="font:.6rem var(--mono);color:var(--dim);padding:4px;text-align:center;">S003</div> | |
| <div style="font:.65rem var(--mono);color:var(--text);padding:4px;">BRCA1</div> | |
| <div style="padding:4px;text-align:center;background:rgba(0,229,255,.15);font:.65rem var(--mono);color:var(--cyan);">8.24</div> | |
| <div style="padding:4px;text-align:center;background:rgba(0,229,255,.06);font:.65rem var(--mono);color:var(--text);">5.12</div> | |
| <div style="padding:4px;text-align:center;background:rgba(0,229,255,.10);font:.65rem var(--mono);color:var(--text);">7.01</div> | |
| <div style="font:.65rem var(--mono);color:var(--text);padding:4px;">TP53</div> | |
| <div style="padding:4px;text-align:center;background:rgba(105,240,174,.20);font:.65rem var(--mono);color:var(--green);">11.02</div> | |
| <div style="padding:4px;text-align:center;background:rgba(105,240,174,.12);font:.65rem var(--mono);color:var(--text);">9.88</div> | |
| <div style="padding:4px;text-align:center;background:rgba(105,240,174,.16);font:.65rem var(--mono);color:var(--text);">10.45</div> | |
| <div style="font:.65rem var(--mono);color:var(--text);padding:4px;">MYC</div> | |
| <div style="padding:4px;text-align:center;background:rgba(179,136,255,.06);font:.65rem var(--mono);color:var(--text);">4.21</div> | |
| <div style="padding:4px;text-align:center;background:rgba(179,136,255,.10);font:.65rem var(--mono);color:var(--text);">6.15</div> | |
| <div style="padding:4px;text-align:center;background:rgba(179,136,255,.04);font:.65rem var(--mono);color:var(--dim);">3.89</div> | |
| </div> | |
| </div> | |
| <!-- Validation --> | |
| <div class="panel"> | |
| <h2>Data Validation</h2> | |
| <div style="font:.65rem var(--mono);color:var(--dim);margin-bottom:8px;">semantics.py · 10 VALIDATOR RULES</div> | |
| <div class="rule-grid"> | |
| <span class="rule-num">01</span><span class="rule-text">Version and discriminant check</span><span class="rule-status pass"></span> | |
| <span class="rule-num">02</span><span class="rule-text">Value XOR missing reason</span><span class="rule-status pass"></span> | |
| <span class="rule-num">03</span><span class="rule-text">Canonical unsigned decimal counts</span><span class="rule-status pass"></span> | |
| <span class="rule-num">04</span><span class="rule-text">Finite decimals with units</span><span class="rule-status pass"></span> | |
| <span class="rule-num">05</span><span class="rule-text">Sample/gene reference resolution</span><span class="rule-status pass"></span> | |
| <span class="rule-num">06</span><span class="rule-text">Quantity kind integrity</span><span class="rule-status pass"></span> | |
| <span class="rule-num">07</span><span class="rule-text">Exclusion map preservation</span><span class="rule-status pass"></span> | |
| <span class="rule-num">08</span><span class="rule-text">Source byte completeness</span><span class="rule-status pending"></span> | |
| <span class="rule-num">09</span><span class="rule-text">Synthetic origin propagation</span><span class="rule-status pass"></span> | |
| <span class="rule-num">10</span><span class="rule-text">No phantom model results</span><span class="rule-status pass"></span> | |
| </div> | |
| </div> | |
| </div> | |
| <!-- CENTER COLUMN --> | |
| <div style="display:flex;flex-direction:column;gap:16px;"> | |
| <!-- Architecture Flow --> | |
| <div class="panel"> | |
| <h2>Architecture Pipeline</h2> | |
| <div class="flow"> | |
| <div class="flow-node" style="border-color:rgba(105,240,174,.3);color:var(--green);">BIOLOGICAL OBSERVATIONS</div> | |
| <div class="flow-arrow">↓</div> | |
| <div class="flow-node" style="border-color:rgba(105,240,174,.2);">cDNA EXPRESSION DATA</div> | |
| <div class="flow-arrow">↓</div> | |
| <div class="flow-node">DATA VALIDATION</div> | |
| <div class="flow-arrow">↓</div> | |
| <div class="flow-node">GENE EXPRESSION</div> | |
| <div class="flow-arrow">↓</div> | |
| <div class="flow-node" style="border-color:rgba(179,136,255,.3);color:var(--violet);">STAN MODEL</div> | |
| <div class="flow-arrow">↓</div> | |
| <div class="flow-node" style="border-color:rgba(179,136,255,.2);">POSTERIOR STATE</div> | |
| <div class="flow-arrow">↓</div> | |
| <div class="flow-node" style="border-color:rgba(0,229,255,.3);">MINIZINC MODEL</div> | |
| <div class="flow-arrow">↓</div> | |
| <div class="flow-node">COMPUTATIONAL RESULT</div> | |
| <div class="flow-arrow">↓</div> | |
| <div class="flow-node" style="border-color:rgba(255,215,64,.3);color:var(--amber);">VISUALIZER</div> | |
| <div class="flow-arrow">↓</div> | |
| <div class="flow-node" style="border-color:rgba(0,229,255,.4);color:var(--cyan);">HUMAN-READABLE MODEL</div> | |
| </div> | |
| </div> | |
| <!-- Quantity Kinds --> | |
| <div class="panel"> | |
| <h2>Semantic Quantity Classification</h2> | |
| <div style="display:flex;flex-wrap:wrap;gap:8px;margin-top:4px;"> | |
| <span class="tag tag-observed">OBSERVED — measurement</span> | |
| <span class="tag tag-inferred">INFERRED — posterior</span> | |
| <span class="tag tag-derived">DERIVED — transformation</span> | |
| <span class="tag tag-predicted">PREDICTED — model output</span> | |
| <span class="tag tag-constrained">CONSTRAINED — solver</span> | |
| <span class="tag tag-encoded">ENCODED — representation</span> | |
| <span class="tag tag-executed">EXECUTED — run evidence</span> | |
| </div> | |
| <div style="margin-top:12px;font:.7rem var(--sans);color:var(--dim);line-height:1.8;"> | |
| Observed measurements ≠ inferred posteriors.<br> | |
| Inferred posteriors ≠ deterministic derivations.<br> | |
| Derivations ≠ binary representations.<br> | |
| Representations ≠ execution evidence. | |
| </div> | |
| </div> | |
| <!-- PTM --> | |
| <div class="panel"> | |
| <h2>PTM — Bit Parity / 1</h2> | |
| <div style="display:flex;gap:12px;align-items:center;margin-bottom:8px;"> | |
| <span class="state-badge state-even">q_even</span> | |
| <span class="state-badge state-odd">q_odd</span> | |
| <span class="state-badge state-accept">q_accept</span> | |
| </div> | |
| <div class="tape"> | |
| <div class="tape-cell">1</div> | |
| <div class="tape-cell">0</div> | |
| <div class="tape-cell head">1</div> | |
| <div class="tape-cell">1</div> | |
| <div class="tape-cell">0</div> | |
| <div class="tape-cell">1</div> | |
| <div class="tape-cell">0</div> | |
| <div class="tape-cell blank">_</div> | |
| </div> | |
| <table style="margin-top:8px;"> | |
| <thead><tr><th>STATE</th><th>READ</th><th>WRITE</th><th>MOVE</th><th>NEXT</th></tr></thead> | |
| <tbody> | |
| <tr><td>q_even</td><td>0</td><td>0</td><td>R</td><td>q_even</td></tr> | |
| <tr><td>q_even</td><td>1</td><td>1</td><td>R</td><td>q_odd</td></tr> | |
| <tr><td>q_odd</td><td>0</td><td>0</td><td>R</td><td>q_odd</td></tr> | |
| <tr><td>q_odd</td><td>1</td><td>1</td><td>R</td><td>q_even</td></tr> | |
| <tr><td>q_even</td><td>_</td><td>0</td><td>Stay</td><td>q_accept</td></tr> | |
| <tr><td>q_odd</td><td>_</td><td>1</td><td>Stay</td><td>q_accept</td></tr> | |
| </tbody> | |
| </table> | |
| <div style="margin-top:8px;font:.65rem var(--mono);color:var(--dim);"> | |
| n INPUT SYMBOLS · n+1 TRANSITIONS · O(1) AUXILIARY STORAGE | |
| </div> | |
| </div> | |
| </div> | |
| <!-- RIGHT COLUMN --> | |
| <div style="display:flex;flex-direction:column;gap:16px;"> | |
| <!-- Stan --> | |
| <div class="panel"> | |
| <h2>Stan — Bayesian Inference</h2> | |
| <span class="tag tag-inferred">INFERRED</span> | |
| <h3>Prior → Likelihood → Posterior</h3> | |
| <div style="margin-top:8px;"> | |
| <div class="dist-bar"> | |
| <span class="dist-label">baseline</span> | |
| <div class="dist-track"><div class="dist-fill" style="width:72%;"></div><div class="dist-ci" style="left:28%;width:44%;"></div></div> | |
| <span class="dist-val">6.84</span> | |
| </div> | |
| <div class="dist-bar"> | |
| <span class="dist-label">cond_eff</span> | |
| <div class="dist-track"><div class="dist-fill" style="width:45%;"></div><div class="dist-ci" style="left:15%;width:30%;"></div></div> | |
| <span class="dist-val">1.23</span> | |
| </div> | |
| <div class="dist-bar"> | |
| <span class="dist-label">time_eff</span> | |
| <div class="dist-track"><div class="dist-fill" style="width:31%;"></div><div class="dist-ci" style="left:10%;width:21%;"></div></div> | |
| <span class="dist-val">0.47</span> | |
| </div> | |
| <div class="dist-bar"> | |
| <span class="dist-label">sigma</span> | |
| <div class="dist-track"><div class="dist-fill" style="width:58%;"></div><div class="dist-ci" style="left:38%;width:20%;"></div></div> | |
| <span class="dist-val">2.11</span> | |
| </div> | |
| </div> | |
| <table style="margin-top:12px;"> | |
| <thead><tr><th>PARAM</th><th>MEAN</th><th>SD</th><th>95% CI</th><th>R-HAT</th><th>ESS</th></tr></thead> | |
| <tbody> | |
| <tr><td>baseline</td><td>6.84</td><td>0.42</td><td>[6.02, 7.66]</td><td>1.00</td><td>4200</td></tr> | |
| <tr><td>cond_eff</td><td>1.23</td><td>0.31</td><td>[0.63, 1.84]</td><td>1.00</td><td>3800</td></tr> | |
| <tr><td>time_eff</td><td>0.47</td><td>0.18</td><td>[0.12, 0.82]</td><td>1.01</td><td>2900</td></tr> | |
| <tr><td>sigma</td><td>2.11</td><td>0.15</td><td>[1.82, 2.41]</td><td>1.00</td><td>4100</td></tr> | |
| </tbody> | |
| </table> | |
| <div style="margin-top:8px;font:.6rem var(--mono);color:var(--dim);">0 divergences · run_id: not_run</div> | |
| </div> | |
| <!-- MiniZinc --> | |
| <div class="panel"> | |
| <h2>MiniZinc — Constraints</h2> | |
| <span class="tag tag-constrained">CONSTRAINED</span> | |
| <table style="margin-top:8px;"> | |
| <thead><tr><th>VARIABLE</th><th>DOMAIN</th><th>CONSTRAINT</th><th>STATUS</th></tr></thead> | |
| <tbody> | |
| <tr><td>sample_assign</td><td>{0,1}</td><td>balanced groups</td><td style="color:var(--green);">feasible</td></tr> | |
| <tr><td>batch_block</td><td>1..4</td><td>no confounding</td><td style="color:var(--green);">feasible</td></tr> | |
| <tr><td>gene_select</td><td>{0,1}</td><td>top-k variance</td><td style="color:var(--amber);">not_run</td></tr> | |
| </tbody> | |
| </table> | |
| <div style="margin-top:8px;font:.6rem var(--mono);color:var(--dim);">solver_outcome: not_run</div> | |
| </div> | |
| <!-- Quipper --> | |
| <div class="panel"> | |
| <h2>Quipper — Quantum Circuit</h2> | |
| <div class="circuit">q0: ─── H ──── ● ──── M ─── | |
| q1: ──────── X ──── M ─── | |
| q2: ─── H ──────── M ─── | |
| DEPTH: 3 QUBITS: 3 GATES: 4 | |
| MEASUREMENTS: 3 ANCILLAS: 0</div> | |
| <div style="margin-top:8px;font:.6rem var(--mono);color:var(--dim);">generation: specified · validation: not_run · execution: not_run</div> | |
| </div> | |
| <!-- Binary Semantics --> | |
| <div class="panel"> | |
| <h2>Binary Semantics</h2> | |
| <span class="tag tag-encoded">ENCODED</span> | |
| <div style="margin-top:8px;font:.7rem var(--mono);color:var(--text);"> | |
| <div>PROFILE: u32-checked/1</div> | |
| <div style="color:var(--dim);margin-top:4px;">unsigned 32-bit · big-endian · 0..4294967295</div> | |
| <div style="color:var(--dim);">overflow: trap · div-by-zero: trap</div> | |
| </div> | |
| <h3>State Transition</h3> | |
| <div style="font:.65rem var(--mono);color:var(--text);margin-top:4px;"> | |
| <div>SEMANTIC VALUE → ENCODING → BITS → STATE → TRANSITION</div> | |
| <div style="margin-top:4px;color:var(--cyan);letter-spacing:.15em;">00000000 00000000 00010011 10110010</div> | |
| <div style="color:var(--dim);margin-top:2px;">present zero ≠ missing · distinct encodings</div> | |
| </div> | |
| </div> | |
| </div> | |
| </div> | |
| <!-- BOTTOM BAR --> | |
| <div class="bottom-bar"> | |
| <!-- Provenance --> | |
| <div class="panel"> | |
| <h2>Immutable Provenance</h2> | |
| <div class="chain-link"> | |
| <div class="chain-dot"></div> | |
| <div class="chain-info"> | |
| <div class="chain-id">art_001_source_cdna</div> | |
| <div class="chain-meta">sha256: a3f8c1...9e2d · SOURCE</div> | |
| </div> | |
| </div> | |
| <div class="chain-link"> | |
| <div class="chain-dot" style="background:var(--green);"></div> | |
| <div class="chain-info"> | |
| <div class="chain-id">art_002_validated</div> | |
| <div class="chain-meta">sha256: 7b2e4f...c8a1 · parent: art_001 · VALIDATION</div> | |
| </div> | |
| </div> | |
| <div class="chain-link"> | |
| <div class="chain-dot" style="background:var(--violet);"></div> | |
| <div class="chain-info"> | |
| <div class="chain-id">art_003_stan_model</div> | |
| <div class="chain-meta">sha256: unavailable · parent: art_002 · INFERENCE</div> | |
| </div> | |
| </div> | |
| <div class="chain-link"> | |
| <div class="chain-dot" style="background:var(--amber);"></div> | |
| <div class="chain-info"> | |
| <div class="chain-id">art_004_minizinc</div> | |
| <div class="chain-meta">sha256: unavailable · parent: art_003 · CONSTRAINT</div> | |
| </div> | |
| </div> | |
| </div> | |
| <!-- RPG/JCL --> | |
| <div class="panel"> | |
| <h2>RPG / JCL Integration</h2> | |
| <div class="mainframe-box"> | |
| <div><span class="job-id">WORKFLOW:</span> RUNSTAGE</div> | |
| <div>STAGE: PYTHON_PIPELINE</div> | |
| <div>STATUS: <span style="color:var(--amber);">NOT_RUN</span></div> | |
| <div style="margin-top:8px;border-top:1px solid var(--border);padding-top:8px;"> | |
| <span class="job-id">//VAULTJOB</span> JOB (ACCOUNT) | |
| <div><span class="dsn">DSN=YOURHLQ.VAULT.RUN0001.REPORT</span></div> | |
| <div><span class="dsn">DSN=YOURHLQ.VAULT.RUN0001.MANIFEST</span></div> | |
| <div style="margin-top:4px;">STATUS: <span style="color:var(--amber);">TEMPLATE ONLY</span></div> | |
| </div> | |
| </div> | |
| </div> | |
| <!-- Repository --> | |
| <div class="panel"> | |
| <h2>Repository Structure</h2> | |
| <div style="font:.7rem var(--mono);color:var(--text);line-height:2;"> | |
| <div style="color:var(--cyan);">bio-semantics/</div> | |
| <div> src/</div> | |
| <div> <span style="color:var(--green);">semantics.py</span></div> | |
| <div> <span style="color:var(--green);">test_semantics.py</span></div> | |
| <div> <span style="color:var(--amber);">dashboard.html</span></div> | |
| <div> <span style="color:var(--cyan);">index.html</span></div> | |
| <div> spec/</div> | |
| <div> <span style="color:var(--blue);">types.ts</span></div> | |
| <div> <span style="color:var(--dim);">contract.md</span></div> | |
| <div> <span style="color:var(--dim);">system_prompt.md</span></div> | |
| <div> templates/</div> | |
| <div> <span style="color:var(--violet);">workflow.rpgle</span></div> | |
| <div> <span style="color:var(--violet);">vault.jcl</span></div> | |
| </div> | |
| </div> | |
| <!-- Gate Status --> | |
| <div class="panel"> | |
| <h2>Gated Phases</h2> | |
| <table> | |
| <thead><tr><th>GATE</th><th>STATUS</th><th>EVIDENCE</th></tr></thead> | |
| <tbody> | |
| <tr><td>1. CONTRACT</td><td style="color:var(--green);">READY</td><td>Contracts specified, validators written</td></tr> | |
| <tr><td>2. ENGINE</td><td style="color:var(--amber);">NOT STARTED</td><td>Stan/MiniZinc/Quipper sources pending</td></tr> | |
| <tr><td>3. INTEGRATION</td><td style="color:var(--amber);">NOT STARTED</td><td>Panels, WORM, governance pending</td></tr> | |
| </tbody> | |
| </table> | |
| </div> | |
| </div> | |
| <footer> | |
| BSL-1.1 / AGPL-3.0 / MPL-2.0 · SNAPKITTY WEST / SNAPKITTYWEST · EVIDENCE OR SILENCE · 2026 | |
| </footer> | |
| </body> | |
| </html> | |