<!DOCTYPE html>
<html lang="en">
<head>
  <meta charset="UTF-8">
  <meta name="viewport" content="width=device-width, initial-scale=1.0">
  <meta name="aspect-ratio" content="4:3">
  <style>
    * {
      box-sizing: border-box;
      margin: 0;
      padding: 0;
      font-family: system-ui, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, sans-serif;
    }

    body {
      background: transparent;
      color: #1e2945;
      padding: 12px;
      display: flex;
      flex-direction: column;
      gap: 12px;
      min-height: 100%;
    }

    /* Step Selector Tabs */
    .step-tabs {
      display: flex;
      gap: 8px;
      width: 100%;
    }

    .tab-btn {
      flex: 1;
      border: 1px solid #e2e8f0;
      background: #ffffff;
      padding: 8px 6px;
      border-radius: 8px;
      font-size: 13px;
      font-weight: 600;
      color: #64748b;
      cursor: pointer;
      display: flex;
      align-items: center;
      justify-content: center;
      gap: 6px;
      transition: all 0.2s ease;
    }

    .tab-btn.active {
      background: #f1f5f9;
      color: #0f172a;
      border-color: #94a3b8;
      box-shadow: 0 1px 3px rgba(0, 0, 0, 0.08);
    }

    /* Comparison Grid */
    .compare-grid {
      display: grid;
      grid-template-columns: 1fr 1fr;
      gap: 10px;
      flex: 1;
    }

    @media (max-width: 440px) {
      .compare-grid {
        grid-template-columns: 1fr;
      }
    }

    /* Cards */
    .side-card {
      border-radius: 10px;
      padding: 12px;
      display: flex;
      flex-direction: column;
      gap: 10px;
      transition: background 0.25s ease, border-color 0.25s ease;
    }

    .card-vague {
      background: #fef2f2;
      border: 1px solid #fecaca;
    }

    .card-rigorous {
      background: #f0fdf4;
      border: 1px solid #bbf7d0;
    }

    .card-header {
      display: flex;
      align-items: center;
      justify-content: space-between;
      font-size: 12px;
      font-weight: 700;
      text-transform: uppercase;
      letter-spacing: 0.5px;
    }

    .card-vague .card-header {
      color: #dc2626;
    }

    .card-rigorous .card-header {
      color: #16a34a;
    }

    .spec-box {
      background: #ffffff;
      border-radius: 8px;
      padding: 10px 12px;
      min-height: 68px;
      display: flex;
      align-items: center;
      font-size: 14px;
      line-height: 1.4;
      font-weight: 500;
      box-shadow: 0 1px 2px rgba(0, 0, 0, 0.04);
    }

    .card-vague .spec-box {
      border-left: 3px solid #ef4444;
      color: #991b1b;
      font-style: italic;
    }

    .card-rigorous .spec-box {
      border-left: 3px solid #22c55e;
      color: #14532d;
      font-family: ui-monospace, SFMono-Regular, Menlo, Monaco, Consolas, monospace;
      font-size: 13px;
    }

    /* Variable Tags */
    .tag-container {
      display: flex;
      flex-wrap: wrap;
      gap: 6px;
    }

    .badge {
      font-size: 11px;
      font-weight: 600;
      padding: 3px 7px;
      border-radius: 5px;
      display: inline-flex;
      align-items: center;
      gap: 4px;
    }

    .badge-missing {
      background: #fee2e2;
      color: #b91c1c;
      border: 1px dashed #f87171;
    }

    .badge-exact {
      background: #dcfce7;
      color: #15803d;
      border: 1px solid #86efac;
    }
  </style>
</head>
<body>

  
  <div class="step-tabs" role="tablist">
    <button class="tab-btn active" onclick="setStep(0)" role="tab" id="tab-0">
      <span>1</span> Incubation
    </button>
    <button class="tab-btn" onclick="setStep(1)" role="tab" id="tab-1">
      <span>2</span> Lysis Buffer
    </button>
    <button class="tab-btn" onclick="setStep(2)" role="tab" id="tab-2">
      <span>3</span> Centrifuge
    </button>
  </div>

  
  <div class="compare-grid">
    
    <div class="side-card card-vague">
      <div class="card-header">
        <span>⚠ Ambiguous Protocol</span>
        <span>25% Reproducible</span>
      </div>
      <div class="spec-box" id="vague-text">
        "Incubate sample at room temp"
      </div>
      <div class="tag-container" id="missing-tags">
        <span class="badge badge-missing">✕ Temp (°C)</span>
        <span class="badge badge-missing">✕ Apparatus</span>
        <span class="badge badge-missing">✕ Tolerance</span>
      </div>
    </div>

    
    <div class="side-card card-rigorous">
      <div class="card-header">
        <span>✓ Rigorous Specification</span>
        <span>Quantified</span>
      </div>
      <div class="spec-box" id="rigorous-text">
        Incubate in circulating water bath at 22.5 ± 0.5 °C
      </div>
      <div class="tag-container" id="exact-tags">
        <span class="badge badge-exact">✓ 22.5 ± 0.5 °C</span>
        <span class="badge badge-exact">✓ Water bath</span>
      </div>
    </div>
  </div>

  <script>
    const steps = [
      {
        vague: '"Incubate sample at room temp"',
        missing: ['✕ Exact Temp', '✕ Apparatus', '✕ Tolerance (±)'],
        rigorous: 'Incubate in circulating water bath at 22.5 ± 0.5 °C',
        exact: ['✓ 22.5 ± 0.5 °C', '✓ Water bath', '✓ Constant flow']
      },
      {
        vague: '"Add lysis buffer to sample"',
        missing: ['✕ Volume (µL)', '✕ Buffer formula', '✕ Exact pH'],
        rigorous: 'Add 500 µL of 50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1% Triton X-100',
        exact: ['✓ 500 µL', '✓ 50 mM Tris (pH 7.4)', '✓ 150 mM NaCl', '✓ 1% Detergent']
      },
      {
        vague: '"Centrifuge briefly at high speed"',
        missing: ['✕ Force (× g)', '✕ Duration', '✕ Chamber Temp'],
        rigorous: 'Centrifuge at 14,000 × g for 10 min at 4 °C',
        exact: ['✓ 14,000 × g (RCF)', '✓ 10 min', '✓ 4 °C']
      }
    ];

    function setStep(index) {
      // Update active tab styling
      document.querySelectorAll('.tab-btn').forEach((btn, i) => {
        btn.classList.toggle('active', i === index);
      });

      const data = steps[index];

      // Update vague side
      document.getElementById('vague-text').textContent = data.vague;
      const missingContainer = document.getElementById('missing-tags');
      missingContainer.innerHTML = data.missing
        .map(tag => `<span class="badge badge-missing">${tag}</span>`)
        .join('');

      // Update rigorous side
      document.getElementById('rigorous-text').textContent = data.rigorous;
      const exactContainer = document.getElementById('exact-tags');
      exactContainer.innerHTML = data.exact
        .map(tag => `<span class="badge badge-exact">${tag}</span>`)
        .join('');
    }
  </script>
</body>
</html>

Following and Evaluating Complex Multi-Stage Experimental Protocols

<!DOCTYPE html>
<html lang="en">
<head>
  <meta charset="UTF-8">
  <meta name="viewport" content="width=device-width, initial-scale=1.0">
  <meta name="aspect-ratio" content="4:3">
  <title>RT-qPCR Protocol Breakdown</title>
  <style>
    * { box-sizing: border-box; margin: 0; padding: 0; }
    body {
      font-family: system-ui, -apple-system, sans-serif;
      background: #f8fafc;
      color: #1e2945;
      padding: 10px;
      display: flex;
      flex-direction: column;
      gap: 8px;
    }

    .pipeline-section {
      background: #ffffff;
      border-radius: 8px;
      padding: 8px 10px;
      box-shadow: 0 1px 3px rgba(0,0,0,0.06);
    }

    .section-title {
      font-size: 13px;
      font-weight: 700;
      text-transform: uppercase;
      letter-spacing: 0.5px;
      margin-bottom: 6px;
      display: flex;
      align-items: center;
      justify-content: space-between;
    }

    .title-flawed { color: #dc2626; }
    .title-robust { color: #059669; }

    .track {
      display: grid;
      grid-template-columns: repeat(4, 1fr);
      gap: 6px;
      position: relative;
    }

    .step-card {
      background: #f1f5f9;
      border: 1.5px solid #cbd5e1;
      border-radius: 6px;
      padding: 6px 4px;
      text-align: center;
      cursor: pointer;
      transition: box-shadow 0.2s ease, border-color 0.2s ease;
      min-height: 72px;
      display: flex;
      flex-direction: column;
      justify-content: center;
      align-items: center;
      user-select: none;
    }

    .step-card:hover {
      box-shadow: 0 2px 6px rgba(0,0,0,0.1);
    }

    .step-card.active {
      border-color: #2563eb;
      box-shadow: 0 0 0 2px #93c5fd;
    }

    .step-num {
      font-size: 11px;
      font-weight: 700;
      color: #64748b;
      margin-bottom: 2px;
    }

    .step-label {
      font-size: 12px;
      font-weight: 600;
      line-height: 1.2;
    }

    /* Flawed styling */
    .card-fail {
      background: #fef2f2;
      border-color: #fca5a5;
    }
    .badge-fail {
      background: #fee2e2;
      color: #b91c1c;
      font-size: 11px;
      font-weight: 700;
      padding: 2px 4px;
      border-radius: 4px;
      margin-top: 3px;
    }

    /* Corrected styling */
    .card-pass {
      background: #f0fdf4;
      border-color: #86efac;
    }
    .badge-pass {
      background: #dcfce7;
      color: #15803d;
      font-size: 11px;
      font-weight: 700;
      padding: 2px 4px;
      border-radius: 4px;
      margin-top: 3px;
    }

    .outcome-box {
      background: #ffffff;
      border-radius: 8px;
      padding: 8px 12px;
      border: 1px solid #e2e8f0;
      display: flex;
      align-items: center;
      gap: 12px;
      min-height: 60px;
    }

    .outcome-icon {
      font-size: 24px;
      flex-shrink: 0;
    }

    .outcome-text {
      flex: 1;
    }

    .outcome-header {
      font-size: 13px;
      font-weight: 700;
      margin-bottom: 2px;
    }

    .outcome-desc {
      font-size: 12px;
      color: #475569;
      line-height: 1.3;
    }

    .controls-row {
      display: flex;
      justify-content: center;
      gap: 8px;
      align-items: center;
    }

    .btn-nav {
      background: #ffffff;
      border: 1px solid #cbd5e1;
      padding: 4px 10px;
      border-radius: 6px;
      font-size: 12px;
      font-weight: 600;
      cursor: pointer;
      color: #334155;
    }

    .btn-nav:hover {
      background: #f8fafc;
    }

    .dot {
      width: 8px;
      height: 8px;
      border-radius: 50%;
      background: #cbd5e1;
      cursor: pointer;
      transition: background 0.2s;
    }

    .dot.active {
      background: #2563eb;
      transform: scale(1.2);
    }
  </style>
</head>
<body>

  
  <div class="pipeline-section">
    <div class="section-title title-flawed">
      <span>⚠️ Flawed Protocol</span>
      <span style="font-size:11px; font-weight:600;">Omitted Controls</span>
    </div>
    <div class="track">
      <div class="step-card card-fail" data-idx="0">
        <span class="step-num">Step 1</span>
        <span class="step-label">RNA Extract</span>
        <span class="badge-fail">No DNase</span>
      </div>
      <div class="step-card card-fail" data-idx="1">
        <span class="step-num">Step 2</span>
        <span class="step-label">Quantify</span>
        <span class="badge-fail">No A260/280</span>
      </div>
      <div class="step-card card-fail" data-idx="2">
        <span class="step-num">Step 3</span>
        <span class="step-label">Reverse Tx</span>
        <span class="badge-fail">No -RT Tube</span>
      </div>
      <div class="step-card card-fail" data-idx="3">
        <span class="step-num">Step 4</span>
        <span class="step-label">qPCR Run</span>
        <span class="badge-fail">Artifact ❌</span>
      </div>
    </div>
  </div>

  
  <div class="pipeline-section">
    <div class="section-title title-robust">
      <span>✓ Validated Protocol</span>
      <span style="font-size:11px; font-weight:600;">Full Verification</span>
    </div>
    <div class="track">
      <div class="step-card card-pass" data-idx="0">
        <span class="step-num">Step 1</span>
        <span class="step-label">RNA Extract</span>
        <span class="badge-pass">+ DNase I</span>
      </div>
      <div class="step-card card-pass" data-idx="1">
        <span class="step-num">Step 2</span>
        <span class="step-label">NanoDrop</span>
        <span class="badge-pass">A260/280 ≥ 2.0</span>
      </div>
      <div class="step-card card-pass" data-idx="2">
        <span class="step-num">Step 3</span>
        <span class="step-label">RT + No-RT</span>
        <span class="badge-pass">Twin Controls</span>
      </div>
      <div class="step-card card-pass" data-idx="3">
        <span class="step-num">Step 4</span>
        <span class="step-label">qPCR Run</span>
        <span class="badge-pass">True Signal ✓</span>
      </div>
    </div>
  </div>

  
  <div class="outcome-box" id="outcomeBox">
    <div class="outcome-icon" id="outcomeIcon">🧬</div>
    <div class="outcome-text">
      <div class="outcome-header" id="outcomeHeader">Stage 1: Genomic DNA Contamination</div>
      <div class="outcome-desc" id="outcomeDesc">Skipping DNase leaves gDNA carryover, yielding false amplification signals.</div>
    </div>
  </div>

  
  <div class="controls-row">
    <button class="btn-nav" id="prevBtn">◀ Prev</button>
    <div class="dot active" data-idx="0"></div>
    <div class="dot" data-idx="1"></div>
    <div class="dot" data-idx="2"></div>
    <div class="dot" data-idx="3"></div>
    <button class="btn-nav" id="nextBtn">Next ▶</button>
  </div>

  <script>
    const stepsData = [
      {
        icon: "🧬",
        header: "Stage 1: Nuclease Digestion",
        desc: "Without DNase I, genomic DNA (gDNA) amplifies alongside target mRNA, creating severe false-positive artifacts."
      },
      {
        icon: "🧪",
        header: "Stage 2: Purity Verification",
        desc: "Skipping NanoDrop A260/280 checks masks phenol/salt carryover that poisons RT polymerase enzymes."
      },
      {
        icon: "🧫",
        header: "Stage 3: Negative RT Control",
        desc: "Omitting the No-RT control makes it impossible to distinguish true cDNA from background gDNA amplification."
      },
      {
        icon: "📊",
        header: "Stage 4: Quantitative qPCR Result",
        desc: "Uncontrolled protocols produce irreproducible Cq curves; validated protocols confirm authentic target expression."
      }
    ];

    let currentStep = 0;
    const allCards = document.querySelectorAll('.step-card');
    const dots = document.querySelectorAll('.dot');
    const outcomeIcon = document.getElementById('outcomeIcon');
    const outcomeHeader = document.getElementById('outcomeHeader');
    const outcomeDesc = document.getElementById('outcomeDesc');

    function showStep(idx) {
      currentStep = (idx + stepsData.length) % stepsData.length;

      allCards.forEach(card => {
        const cardIdx = parseInt(card.getAttribute('data-idx'), 10);
        if (cardIdx === currentStep) {
          card.classList.add('active');
        } else {
          card.classList.remove('active');
        }
      });

      dots.forEach((dot, dIdx) => {
        dot.classList.toggle('active', dIdx === currentStep);
      });

      const data = stepsData[currentStep];
      outcomeIcon.textContent = data.icon;
      outcomeHeader.textContent = data.header;
      outcomeDesc.textContent = data.desc;
    }

    allCards.forEach(card => {
      card.addEventListener('click', () => {
        showStep(parseInt(card.getAttribute('data-idx'), 10));
      });
    });

    dots.forEach(dot => {
      dot.addEventListener('click', () => {
        showStep(parseInt(dot.getAttribute('data-idx'), 10));
      });
    });

    document.getElementById('prevBtn').addEventListener('click', () => showStep(currentStep - 1));
    document.getElementById('nextBtn').addEventListener('click', () => showStep(currentStep + 1));

    showStep(0);
  </script>
</body>
</html>

<!DOCTYPE html>
<html lang="en">
<head>
  <meta charset="UTF-8">
  <meta name="viewport" content="width=device-width, initial-scale=1.0">
  <meta name="aspect-ratio" content="4:3">
  <title>Multi-Stage Experimental Protocol</title>
  <style>
    * { box-sizing: border-box; margin: 0; padding: 0; }
    body {
      font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, sans-serif;
      background: #f8f9fa;
      color: #1e2945;
      padding: 12px;
      display: flex;
      flex-direction: column;
      gap: 12px;
      user-select: none;
    }

    /* Step Selector / Controls Header */
    .stepper-nav {
      display: flex;
      justify-content: space-between;
      align-items: center;
      gap: 8px;
    }
    .step-buttons {
      display: flex;
      gap: 6px;
      flex-wrap: wrap;
    }
    .btn-step {
      background: #ffffff;
      border: 1.5px solid #e2e8f0;
      color: #1e2945;
      padding: 5px 12px;
      border-radius: 20px;
      font-size: 13px;
      font-weight: 600;
      cursor: pointer;
      transition: all 0.25s ease;
    }
    .btn-step.active {
      background: #22b7ff;
      border-color: #22b7ff;
      color: #ffffff;
      box-shadow: 0 2px 8px rgba(34, 183, 255, 0.35);
    }
    .play-btn {
      background: #ffffff;
      border: 1.5px solid #e2e8f0;
      color: #1e2945;
      padding: 5px 10px;
      border-radius: 8px;
      font-size: 13px;
      font-weight: 600;
      cursor: pointer;
    }

    /* Pipeline Grid */
    .pipeline {
      display: grid;
      grid-template-columns: repeat(3, 1fr);
      gap: 10px;
      position: relative;
    }

    .stage-col {
      display: flex;
      flex-direction: column;
      align-items: center;
      gap: 6px;
      transition: opacity 0.3s ease;
    }
    .stage-col.dimmed {
      opacity: 0.35;
    }

    /* Input Tag */
    .input-tag {
      background: #e0f2fe;
      color: #0369a1;
      border: 1px solid #bae6fd;
      border-radius: 12px;
      font-size: 11px;
      font-weight: 700;
      padding: 3px 8px;
      display: flex;
      align-items: center;
      gap: 4px;
      white-space: nowrap;
    }

    /* Stage Card */
    .stage-card {
      width: 100%;
      background: #ffffff;
      border: 1.5px solid #e2e8f0;
      border-radius: 10px;
      padding: 10px 6px;
      text-align: center;
      font-size: 13px;
      font-weight: 700;
      color: #1e2945;
      box-shadow: 0 1px 3px rgba(0,0,0,0.04);
      position: relative;
      transition: border-color 0.25s ease, box-shadow 0.25s ease;
    }
    .stage-col.active .stage-card {
      border-color: #22b7ff;
      box-shadow: 0 0 0 2px rgba(34, 183, 255, 0.25);
    }
    .stage-icon {
      font-size: 18px;
      display: block;
      margin-bottom: 2px;
    }

    /* Checkpoint Diamond / Badge */
    .checkpoint {
      width: 100%;
      background: #ecfdf5;
      border: 1.5px solid #10b981;
      border-radius: 8px;
      padding: 6px 4px;
      text-align: center;
      font-size: 11px;
      font-weight: 700;
      color: #065f46;
      display: flex;
      flex-direction: column;
      align-items: center;
      gap: 2px;
    }
    .checkpoint-tag {
      font-size: 9px;
      text-transform: uppercase;
      letter-spacing: 0.5px;
      color: #059669;
      display: flex;
      align-items: center;
      gap: 3px;
    }

    /* Controls Track */
    .controls-container {
      background: #ffffff;
      border: 1.5px dashed #cbd5e1;
      border-radius: 10px;
      padding: 10px 12px;
      display: flex;
      flex-direction: column;
      gap: 8px;
    }
    .controls-title {
      font-size: 11px;
      font-weight: 800;
      text-transform: uppercase;
      letter-spacing: 0.6px;
      color: #64748b;
      display: flex;
      justify-content: space-between;
    }

    .control-row {
      display: grid;
      grid-template-columns: 100px 1fr auto;
      align-items: center;
      gap: 8px;
      font-size: 12px;
      font-weight: 600;
      padding: 4px 8px;
      border-radius: 6px;
      background: #f8fafc;
      border: 1px solid #f1f5f9;
    }
    .control-badge {
      display: inline-flex;
      align-items: center;
      gap: 4px;
      font-size: 11px;
      font-weight: 700;
    }
    .badge-pos { color: #0284c7; }
    .badge-neg { color: #64748b; }
    .control-desc {
      color: #475569;
      font-size: 11px;
    }
    .control-status {
      font-size: 11px;
      font-weight: 700;
      padding: 2px 8px;
      border-radius: 12px;
      white-space: nowrap;
    }
    .status-pos { background: #dcfce7; color: #15803d; }
    .status-neg { background: #f1f5f9; color: #475569; }

    @media (max-width: 420px) {
      .pipeline { gap: 6px; }
      .stage-card { font-size: 11px; padding: 6px 2px; }
      .checkpoint { font-size: 10px; }
      .input-tag { font-size: 9px; padding: 2px 4px; }
      .control-row { grid-template-columns: 80px 1fr auto; font-size: 10px; gap: 4px; }
      .control-desc { font-size: 9px; }
    }
  </style>
</head>
<body>

  
  <div class="stepper-nav">
    <div class="step-buttons">
      <button class="btn-step active" onclick="setStep(0)">Stage 1</button>
      <button class="btn-step" onclick="setStep(1)">Stage 2</button>
      <button class="btn-step" onclick="setStep(2)">Stage 3</button>
      <button class="btn-step" onclick="setStep(3)">Full Pipeline</button>
    </div>
    <button class="play-btn" id="playBtn" onclick="togglePlay()">⏸</button>
  </div>

  
  <div class="pipeline">
    
    <div class="stage-col active" id="col-0">
      <div class="input-tag">↓ Lysis Reagent</div>
      <div class="stage-card">
        <span class="stage-icon">🧫</span>
        1. Cell Lysis
      </div>
      <div class="checkpoint">
        <span class="checkpoint-tag">✦ Gate 1</span>
        Pellet Clarity
      </div>
    </div>

    
    <div class="stage-col active" id="col-1">
      <div class="input-tag">↓ Spin Column</div>
      <div class="stage-card">
        <span class="stage-icon">🧪</span>
        2. Purification
      </div>
      <div class="checkpoint">
        <span class="checkpoint-tag">✦ Gate 2</span>
        A260/280 Ratio
      </div>
    </div>

    
    <div class="stage-col active" id="col-2">
      <div class="input-tag">↓ UV Beam</div>
      <div class="stage-card">
        <span class="stage-icon">📊</span>
        3. Quantitation
      </div>
      <div class="checkpoint">
        <span class="checkpoint-tag">✦ Gate 3</span>
        Yield &gt; 50 ng/µL
      </div>
    </div>
  </div>

  
  <div class="controls-container">
    <div class="controls-title">
      <span>Parallel Control Tracks</span>
      <span>Omission Prevention</span>
    </div>
    
    <div class="control-row">
      <div class="control-badge badge-pos">✦ Positive</div>
      <div class="control-desc">Known Reference Standard</div>
      <div class="control-status status-pos">Expected Signal ✓</div>
    </div>

    <div class="control-row">
      <div class="control-badge badge-neg">✦ Blank (Neg)</div>
      <div class="control-desc">Buffer Only (Vehicle)</div>
      <div class="control-status status-neg">Zero Absorbance 0.0</div>
    </div>
  </div>

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OGE.13.RI.6

Aligned learning resources

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