Cloud Infrastructure Workflow
Interactive Analysis Demo
Start Demo Analysis
Step 1: Data Upload
Uploading sample genomic sequencing data (FASTQ files)…
Step 2: Quality Control
Running FastQC and trimming low-quality reads…
Step 3: Genome Alignment
Aligning reads to reference genome using BWA-MEM…
Step 4: Variant Calling
Identifying genomic variants using GATK HaplotypeCaller…
Step 5: Variant Annotation
Annotating variants with functional information using SnpEff…
Analysis Results
Variant Type Distribution
Top Significant Variants
| Chromosome |
Position |
Reference |
Alternate |
Gene |
Impact |
Clinical Significance |
Data Upload Interface
Drag & Drop Your Genomic Data Files Here
or
Browse Files
Supported formats: FASTQ, BAM, VCF
This is a demonstration only – please don’t upload actual data here!
https://cdn.jsdelivr.net/npm/chart.js
document.addEventListener(‘DOMContentLoaded’, function() {
// Create AWS Flow Chart
const awsFlowChart = `
S3
Data Storage
Lambda
Processing
Batch
Analysis
DynamoDB
Results
Raw Data
QC & Preprocessing
Genomic Analysis
Structured Results
AWS Serverless Genomics Pipeline
Scalable, Cost-Effective Data Processing
`;
document.getElementById(‘genoma-aws-flow-chart’) .innerHTML = awsFlowChart;
// Sample variant data for the table
const variantData = [
{ chrom: “chr1”, pos: “69511”, ref: “A”, alt: “G”, gene: “OR4F5”, impact: “MODERATE”, clinical: “Likely benign” },
{ chrom: “chr1”, pos: “865694”, ref: “G”, alt: “A”, gene: “SAMD11”, impact: “HIGH”, clinical: “Pathogenic” },
{ chrom: “chr2”, pos: “48010488”, ref: “G”, alt: “A”, gene: “MSH2”, impact: “HIGH”, clinical: “Pathogenic” },
{ chrom: “chr3”, pos: “41266101”, ref: “C”, alt: “T”, gene: “CTNNB1”, impact: “MODERATE”, clinical: “Likely pathogenic” },
{ chrom: “chr7”, pos: “55259515”, ref: “T”, alt: “G”, gene: “EGFR”, impact: “HIGH”, clinical: “Pathogenic” }
];
// Start Analysis Demo
document.getElementById(‘genoma-start-analysis-btn’).addEventListener(‘click’, function() {
this.disabled = true;
runAnalysisDemo();
});
function runAnalysisDemo() {
// Show first step
document.getElementById(‘genoma-step1’).style.opacity = ‘1’;
// Simulate upload progress
simulateProgress(‘genoma-upload-progress’, 100, 3000, function() {
// Show second step
document.getElementById(‘genoma-step2’).style.opacity = ‘1’;
// Simulate QC progress
simulateProgress(‘genoma-qc-progress’, 100, 4000, function() {
// Show third step
document.getElementById(‘genoma-step3’).style.opacity = ‘1’;
// Simulate alignment progress
simulateProgress(‘genoma-alignment-progress’, 100, 5000, function() {
// Show fourth step
document.getElementById(‘genoma-step4’).style.opacity = ‘1’;
// Simulate variant calling progress
simulateProgress(‘genoma-variant-progress’, 100, 4000, function() {
// Show fifth step
document.getElementById(‘genoma-step5’).style.opacity = ‘1’;
// Simulate annotation progress
simulateProgress(‘genoma-annotation-progress’, 100, 3000, function() {
// Show results
showResults();
});
});
});
});
});
}
function simulateProgress(elementId, targetValue, duration, callback) {
const progressBar = document.getElementById(elementId);
let currentValue = 0;
const interval = 50;
const steps = duration / interval;
const increment = targetValue / steps;
const timer = setInterval(function() {
currentValue += increment;
const roundedValue = Math.min(Math.round(currentValue), targetValue);
progressBar.style.width = roundedValue + ‘%’;
if (roundedValue >= targetValue) {
clearInterval(timer);
if (callback) callback();
}
}, interval);
}
function showResults() {
// Display results container
document.getElementById(‘genoma-results-container’).style.display = ‘block’;
// Populate variant table
const tableBody = document.getElementById(‘genoma-variant-table-body’);
variantData.forEach(function(variant, index) {
const row = document.createElement(‘tr’);
if (variant.impact === ‘HIGH’) {
row.style.backgroundColor = ‘rgba(52, 152, 219, 0.1)’;
}
row.innerHTML = `
${variant.chrom} |
${variant.pos} |
${variant.ref} |
${variant.alt} |
${variant.gene} |
${variant.impact} |
${variant.clinical} |
`;
tableBody.appendChild(row);
});
// Show result cards with animation
const resultCards = [
document.getElementById(‘genoma-variant-chart-card’),
document.getElementById(‘genoma-impact-chart-card’),
document.getElementById(‘genoma-variant-table-card’),
document.getElementById(‘genoma-summary-card’)
];
resultCards.forEach(function(card, index) {
setTimeout(function() {
card.style.opacity = ‘1’;
card.style.transform = ‘translateY(0)’;
}, 300 * index);
});
// Create charts
createVariantChart();
createImpactChart();
}
function createVariantChart() {
const ctx = document.getElementById(‘genoma-variant-chart’).getContext(‘2d’);
new Chart(ctx, {
type: ‘pie’,
data: {
labels: [‘SNP’, ‘Insertion’, ‘Deletion’, ‘Complex’],
datasets: [{
data: [65, 15, 12, 8],
backgroundColor: [
‘#3498db’,
‘#2ecc71’,
‘#e74c3c’,
‘#f39c12’
],
borderWidth: 1
}]
},
options: {
responsive: true,
maintainAspectRatio: false,
plugins: {
legend: {
position: ‘right’,
},
title: {
display: true,
text: ‘Variant Types’
}
}
}
});
}
function createImpactChart() {
const ctx = document.getElementById(‘genoma-impact-chart’).getContext(‘2d’);
new Chart(ctx, {
type: ‘bar’,
data: {
labels: [‘HIGH’, ‘MODERATE’, ‘LOW’, ‘MODIFIER’],
datasets: [{
label: ‘Number of Variants’,
data: [427, 1253, 2104, 544],
backgroundColor: [
‘#e74c3c’,
‘#f39c12’,
‘#3498db’,
‘#2ecc71’
],
borderWidth: 1
}]
},
options: {
responsive: true,
maintainAspectRatio: false,
scales: {
y: {
beginAtZero: true
}
},
plugins: {
title: {
display: true,
text: ‘Variant Impact Distribution’
}
}
}
});
}
// Make upload box interactive
const uploadBox = document.getElementById(‘genoma-upload-box’);
uploadBox.addEventListener(‘dragover’, function(e) {
e.preventDefault();
this.style.borderColor = ‘#3498db’;
this.style.backgroundColor = ‘#eaf2f8’;
});
uploadBox.addEventListener(‘dragleave’, function(e) {
e.preventDefault();
this.style.borderColor = ‘#ccc’;
this.style.backgroundColor = ‘#f8f9fa’;
});
uploadBox.addEventListener(‘drop’, function(e) {
e.preventDefault();
this.style.borderColor = ‘#ccc’;
this.style.backgroundColor = ‘#f8f9fa’;
alert(‘This is a demonstration only. Please do not upload actual data here.’);
});
uploadBox.querySelector(‘button’).addEventListener(‘click’, function(e) {
e.preventDefault();
alert(‘This is a demonstration only. Please do not upload actual data here.’);
});
});
Genoma Bioinformatics 