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<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Genomic Data Analysis Platform</title>
<link href="https://cdn.jsdelivr.net/npm/tailwindcss@2.2.19/dist/tailwind.min.css" rel="stylesheet">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/css/all.min.css">
<style>
.upload-area {
border: 2px dashed #4f46e5;
transition: all 0.3s ease;
}
.upload-area:hover {
background-color: #f0f9ff;
border-color: #3b82f6;
}
.file-item {
transition: all 0.2s ease;
}
.file-item:hover {
transform: translateY(-2px);
box-shadow: 0 4px 6px rgba(0, 0, 0, 0.1);
}
.progress-bar {
transition: width 0.5s ease;
}
.pulse {
animation: pulse 2s infinite;
}
@keyframes pulse {
0% { opacity: 1; }
50% { opacity: 0.5; }
100% { opacity: 1; }
}
</style>
</head>
<body class="bg-gradient-to-br from-blue-50 to-indigo-100 min-h-screen">
<div class="container mx-auto px-4 py-8">
<!-- Header -->
<header class="text-center mb-12">
<h1 class="text-4xl md:text-5xl font-bold text-gray-800 mb-4">
<span class="bg-clip-text text-transparent bg-gradient-to-r from-blue-600 to-indigo-600">
Genomic Data Analysis Platform
</span>
</h1>
<p class="text-lg text-gray-600 max-w-3xl mx-auto">
Upload genomic data files and perform semantic analysis to find matching research from NIH and Semantic Scholar. Generate comprehensive AI-powered reports.
</p>
</header>
<!-- Main Content -->
<div class="grid grid-cols-1 lg:grid-cols-2 gap-8">
<!-- Upload Section -->
<div class="bg-white rounded-2xl shadow-xl p-6">
<h2 class="text-2xl font-bold text-gray-800 mb-6 flex items-center">
<i class="fas fa-cloud-upload-alt text-indigo-600 mr-3"></i>
Upload Files
</h2>
<!-- File Upload Area -->
<div id="uploadArea" class="upload-area rounded-xl p-8 text-center cursor-pointer mb-6">
<i class="fas fa-file-upload text-4xl text-indigo-500 mb-4"></i>
<h3 class="text-xl font-semibold text-gray-700 mb-2">Drag & Drop Files</h3>
<p class="text-gray-500 mb-4">Supports: txt, csv, gz, vcf, json</p>
<button id="browseBtn" class="bg-indigo-600 hover:bg-indigo-700 text-white font-medium py-2 px-6 rounded-lg transition duration-300">
Browse Files
</button>
<input type="file" id="fileInput" multiple class="hidden" accept=".txt,.csv,.gz,.vcf,.json">
</div>
<!-- File List -->
<div id="fileList" class="space-y-3 mb-6">
<!-- Files will be listed here -->
</div>
<!-- Knowledge JSON Toggle -->
<div class="flex items-center justify-between bg-blue-50 rounded-lg p-4 mb-6">
<div>
<h3 class="font-medium text-gray-800">Include Knowledge JSON</h3>
<p class="text-sm text-gray-600">Optional: Upload domain-specific knowledge base</p>
</div>
<div class="relative inline-block w-12 mr-2 align-middle select-none">
<input type="checkbox" id="knowledgeToggle" class="sr-only">
<label for="knowledgeToggle" class="block h-6 w-12 rounded-full bg-gray-300 cursor-pointer transition duration-300 ease-in-out">
<span class="block h-4 w-4 mt-1 ml-1 rounded-full bg-white shadow transform transition duration-300 ease-in-out"></span>
</label>
</div>
</div>
<!-- Analysis Button -->
<button id="analyzeBtn" class="w-full bg-gradient-to-r from-indigo-600 to-purple-600 hover:from-indigo-700 hover:to-purple-700 text-white font-bold py-4 px-6 rounded-xl shadow-lg transition duration-300 transform hover:scale-[1.02] disabled:opacity-50 disabled:cursor-not-allowed">
<i class="fas fa-dna mr-2"></i>
Start Genomic Analysis
</button>
</div>
<!-- Results Section -->
<div class="bg-white rounded-2xl shadow-xl p-6">
<h2 class="text-2xl font-bold text-gray-800 mb-6 flex items-center">
<i class="fas fa-chart-bar text-indigo-600 mr-3"></i>
Analysis Results
</h2>
<!-- Status Indicators -->
<div id="statusContainer" class="space-y-4 mb-6">
<div id="uploadStatus" class="flex items-center p-3 bg-gray-50 rounded-lg">
<div class="w-3 h-3 rounded-full bg-gray-400 mr-3"></div>
<span class="text-gray-600">Upload genomic data files</span>
</div>
<div id="processStatus" class="flex items-center p-3 bg-gray-50 rounded-lg">
<div class="w-3 h-3 rounded-full bg-gray-400 mr-3"></div>
<span class="text-gray-600">Processing genomic data</span>
</div>
<div id="researchStatus" class="flex items-center p-3 bg-gray-50 rounded-lg">
<div class="w-3 h-3 rounded-full bg-gray-400 mr-3"></div>
<span class="text-gray-600">Finding matching research</span>
</div>
<div id="reportStatus" class="flex items-center p-3 bg-gray-50 rounded-lg">
<div class="w-3 h-3 rounded-full bg-gray-400 mr-3"></div>
<span class="text-gray-600">Generating comprehensive report</span>
</div>
</div>
<!-- Progress Bar -->
<div class="mb-6">
<div class="flex justify-between text-sm text-gray-600 mb-1">
<span>Analysis Progress</span>
<span id="progressText">0%</span>
</div>
<div class="h-3 bg-gray-200 rounded-full overflow-hidden">
<div id="progressBar" class="h-full bg-gradient-to-r from-blue-500 to-indigo-600 rounded-full progress-bar" style="width: 0%"></div>
</div>
</div>
<!-- Results Summary -->
<div id="resultsSummary" class="hidden">
<div class="grid grid-cols-2 gap-4 mb-6">
<div class="bg-blue-50 p-4 rounded-lg">
<div class="text-2xl font-bold text-indigo-700">24</div>
<div class="text-sm text-gray-600">Research Papers Found</div>
</div>
<div class="bg-green-50 p-4 rounded-lg">
<div class="text-2xl font-bold text-green-700">8</div>
<div class="text-sm text-gray-600">Highly Relevant</div>
</div>
</div>
<div class="mb-6">
<h3 class="font-bold text-gray-800 mb-3">Top Research Matches</h3>
<div class="space-y-3">
<div class="p-3 bg-gray-50 rounded-lg">
<div class="font-medium text-gray-800">Genome-wide association study of...</div>
<div class="text-sm text-gray-600">NIH Database • 2023</div>
</div>
<div class="p-3 bg-gray-50 rounded-lg">
<div class="font-medium text-gray-800">Semantic analysis of genetic variants...</div>
<div class="text-sm text-gray-600">Semantic Scholar • 2022</div>
</div>
</div>
</div>
<button id="downloadBtn" class="w-full bg-gradient-to-r from-green-500 to-emerald-600 hover:from-green-600 hover:to-emerald-700 text-white font-bold py-3 px-6 rounded-xl shadow-lg transition duration-300 flex items-center justify-center">
<i class="fas fa-download mr-2"></i>
Download DOCX Report
</button>
</div>
<!-- Placeholder when no results -->
<div id="noResults" class="text-center py-12">
<i class="fas fa-microscope text-5xl text-gray-300 mb-4"></i>
<p class="text-gray-500">Upload files and start analysis to see results</p>
</div>
</div>
</div>
<!-- Features Section -->
<div class="mt-16">
<h2 class="text-3xl font-bold text-center text-gray-800 mb-12">How It Works</h2>
<div class="grid grid-cols-1 md:grid-cols-3 gap-8">
<div class="bg-white p-6 rounded-2xl shadow-lg text-center">
<div class="w-16 h-16 bg-blue-100 rounded-full flex items-center justify-center mx-auto mb-4">
<i class="fas fa-file-upload text-blue-600 text-2xl"></i>
</div>
<h3 class="text-xl font-bold text-gray-800 mb-2">Upload Data</h3>
<p class="text-gray-600">Upload genomic files in various formats including VCF, CSV, and TXT</p>
</div>
<div class="bg-white p-6 rounded-2xl shadow-lg text-center">
<div class="w-16 h-16 bg-indigo-100 rounded-full flex items-center justify-center mx-auto mb-4">
<i class="fas fa-brain text-indigo-600 text-2xl"></i>
</div>
<h3 class="text-xl font-bold text-gray-800 mb-2">AI Analysis</h3>
<p class="text-gray-600">Semantic analysis using advanced AI to interpret genomic data</p>
</div>
<div class="bg-white p-6 rounded-2xl shadow-lg text-center">
<div class="w-16 h-16 bg-green-100 rounded-full flex items-center justify-center mx-auto mb-4">
<i class="fas fa-file-medical text-green-600 text-2xl"></i>
</div>
<h3 class="text-xl font-bold text-gray-800 mb-2">Research Matching</h3>
<p class="text-gray-600">Find relevant research from NIH and Semantic Scholar databases</p>
</div>
</div>
</div>
</div>
<script>
document.addEventListener('DOMContentLoaded', function() {
// Elements
const uploadArea = document.getElementById('uploadArea');
const fileInput = document.getElementById('fileInput');
const browseBtn = document.getElementById('browseBtn');
const fileList = document.getElementById('fileList');
const analyzeBtn = document.getElementById('analyzeBtn');
const downloadBtn = document.getElementById('downloadBtn');
const knowledgeToggle = document.getElementById('knowledgeToggle');
const progressBar = document.getElementById('progressBar');
const progressText = document.getElementById('progressText');
const resultsSummary = document.getElementById('resultsSummary');
const noResults = document.getElementById('noResults');
const statusContainer = document.getElementById('statusContainer');
// Status indicators
const uploadStatus = document.getElementById('uploadStatus').querySelector('div');
const processStatus = document.getElementById('processStatus').querySelector('div');
const researchStatus = document.getElementById('researchStatus').querySelector('div');
const reportStatus = document.getElementById('reportStatus').querySelector('div');
// File storage
let uploadedFiles = [];
// Event Listeners
browseBtn.addEventListener('click', () => fileInput.click());
fileInput.addEventListener('change', handleFileSelect);
uploadArea.addEventListener('dragover', handleDragOver);
uploadArea.addEventListener('drop', handleDrop);
analyzeBtn.addEventListener('click', startAnalysis);
downloadBtn.addEventListener('click', downloadReport);
// Functions
function handleDragOver(e) {
e.preventDefault();
e.stopPropagation();
uploadArea.classList.add('bg-blue-50');
}
function handleDrop(e) {
e.preventDefault();
e.stopPropagation();
uploadArea.classList.remove('bg-blue-50');
const files = e.dataTransfer.files;
handleFiles(files);
}
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const files = e.target.files;
handleFiles(files);
}
function handleFiles(files) {
for (let i = 0; i < files.length; i++) {
const file = files[i];
if (validateFile(file)) {
uploadedFiles.push(file);
addFileToList(file);
}
}
updateAnalyzeButton();
}
function validateFile(file) {
const validExtensions = ['.txt', '.csv', '.gz', '.vcf', '.json'];
const extension = '.' + file.name.split('.').pop().toLowerCase();
return validExtensions.includes(extension);
}
function addFileToList(file) {
const fileItem = document.createElement('div');
fileItem.className = 'file-item flex items-center justify-between p-3 bg-gray-50 rounded-lg';
const fileInfo = document.createElement('div');
fileInfo.className = 'flex items-center';
const fileIcon = document.createElement('i');
fileIcon.className = getFileIcon(file.name);
fileIcon.classList.add('text-indigo-500', 'mr-3');
const fileName = document.createElement('span');
fileName.className = 'text-gray-700 truncate max-w-xs';
fileName.textContent = file.name;
fileInfo.appendChild(fileIcon);
fileInfo.appendChild(fileName);
const fileSize = document.createElement('span');
fileSize.className = 'text-sm text-gray-500 ml-2';
fileSize.textContent = formatFileSize(file.size);
const removeBtn = document.createElement('button');
removeBtn.className = 'text-red-500 hover:text-red-700 ml-2';
removeBtn.innerHTML = '<i class="fas fa-times"></i>';
removeBtn.addEventListener('click', () => {
const index = uploadedFiles.indexOf(file);
if (index > -1) {
uploadedFiles.splice(index, 1);
fileItem.remove();
updateAnalyzeButton();
}
});
fileItem.appendChild(fileInfo);
fileItem.appendChild(fileSize);
fileItem.appendChild(removeBtn);
fileList.appendChild(fileItem);
}
function getFileIcon(filename) {
const extension = filename.split('.').pop().toLowerCase();
switch (extension) {
case 'vcf': return 'fas fa-dna';
case 'csv': return 'fas fa-table';
case 'txt': return 'fas fa-file-alt';
case 'gz': return 'fas fa-file-archive';
case 'json': return 'fas fa-code';
default: return 'fas fa-file';
}
}
function formatFileSize(bytes) {
if (bytes === 0) return '0 Bytes';
const k = 1024;
const sizes = ['Bytes', 'KB', 'MB', 'GB'];
const i = Math.floor(Math.log(bytes) / Math.log(k));
return parseFloat((bytes / Math.pow(k, i)).toFixed(2)) + ' ' + sizes[i];
}
function updateAnalyzeButton() {
const hasGenomicFiles = uploadedFiles.some(file => {
const ext = file.name.split('.').pop().toLowerCase();
return ['vcf', 'txt', 'csv', 'gz'].includes(ext);
});
analyzeBtn.disabled = !hasGenomicFiles || uploadedFiles.length === 0;
}
function startAnalysis() {
if (uploadedFiles.length === 0) return;
// Reset UI
resetStatusIndicators();
resultsSummary.classList.add('hidden');
noResults.classList.add('hidden');
// Show processing
uploadArea.classList.add('opacity-50', 'pointer-events-none');
analyzeBtn.disabled = true;
analyzeBtn.innerHTML = '<i class="fas fa-spinner fa-spin mr-2"></i> Analyzing...';
// Simulate analysis process
simulateAnalysis();
}
function resetStatusIndicators() {
// Reset all status indicators
const indicators = statusContainer.querySelectorAll('div > div:first-child');
indicators.forEach(indicator => {
indicator.className = 'w-3 h-3 rounded-full bg-gray-400 mr-3';
});
// Reset progress
progressBar.style.width = '0%';
progressText.textContent = '0%';
}
function simulateAnalysis() {
let progress = 0;
const steps = [
{ duration: 1000, status: 'uploadStatus' },
{ duration: 2000, status: 'processStatus' },
{ duration: 2500, status: 'researchStatus' },
{ duration: 1500, status: 'reportStatus' }
];
function updateStep(stepIndex) {
if (stepIndex >= steps.length) {
// Analysis complete
finishAnalysis();
return;
}
const step = steps[stepIndex];
const statusElement = document.getElementById(step.status).querySelector('div');
statusElement.className = 'w-3 h-3 rounded-full bg-blue-500 mr-3 pulse';
const interval = setInterval(() => {
if (progress < ((stepIndex + 1) / steps.length) * 100) {
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progressBar.style.width = `${progress}%`;
progressText.textContent = `${Math.min(progress, 100)}%`;
} else {
clearInterval(interval);
statusElement.className = 'w-3 h-3 rounded-full bg-green-500 mr-3';
setTimeout(() => updateStep(stepIndex + 1), 300);
}
}, step.duration / 50);
}
updateStep(0);
}
function finishAnalysis() {
uploadArea.classList.remove('opacity-50', 'pointer-events-none');
analyzeBtn.disabled = false;
analyzeBtn.innerHTML = '<i class="fas fa-dna mr-2"></i> Start Genomic Analysis';
// Show results
setTimeout(() => {
resultsSummary.classList.remove('hidden');
noResults.classList.add('hidden');
}, 500);
}
function downloadReport() {
// Simulate download
downloadBtn.innerHTML = '<i class="fas fa-spinner fa-spin mr-2"></i> Preparing...';
setTimeout(() => {
downloadBtn.innerHTML = '<i class="fas fa-download mr-2"></i> Download DOCX Report';
// In a real app, this would trigger the actual download
alert('Report download would start now. In a real application, this would download the generated DOCX file.');
}, 1500);
}
// Initialize
updateAnalyzeButton();
});
</script>
</body>
</html> |