--- a +++ b/web/docs/docs.html @@ -0,0 +1,715 @@ +<!DOCTYPE html> +<html lang="en"> + +<head> + <!-- Google tag (gtag.js) --> + <script async src="https://www.googletagmanager.com/gtag/js?id=G-0LTP0WK7EM"></script> + <script> + window.dataLayer = window.dataLayer || []; + function gtag() { dataLayer.push(arguments); } + gtag('js', new Date()); + + gtag('config', 'G-0LTP0WK7EM'); + </script> + <meta charset="UTF-8"> + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + <title>Documentation - DNAnalyzer</title> + <meta name="description" + content="Comprehensive documentation for DNAnalyzer - Get started with our powerful DNA analysis tools and learn how to use all features."> + + <!-- Stylesheets --> + <link rel="stylesheet" href="../style.css"> + <link rel="stylesheet" href="docs.css"> + <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/css/all.min.css"> + <link rel="preconnect" href="https://fonts.googleapis.com"> + <link 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<h2>Documentation</h2> + <button class="mobile-close" id="closeSidebar"> + <i class="fas fa-times"></i> + </button> + </div> + + <div class="sidebar-search"> + <div class="search-input-wrapper"> + <i class="fas fa-search"></i> + <input type="text" id="docsSearch" placeholder="Search documentation..."> + </div> + </div> + + <nav class="sidebar-nav"> + <div class="nav-section"> + <h3>Getting Started</h3> + <ul> + <li><a href="#introduction" class="active">Introduction</a></li> + <li><a href="#installation">Installation</a></li> + <li><a href="#quick-start">Quick Start</a></li> + </ul> + </div> + + <div class="nav-section"> + <h3>Core Concepts</h3> + <ul> + <li><a href="#sequence-analysis">Sequence Analysis</a></li> + <li><a href="#codon-detection">Codon Detection</a></li> + <li><a href="#reading-frames">Reading Frames</a></li> + <li><a href="#protein-prediction">Protein Prediction</a></li> + </ul> + </div> + + <div class="nav-section"> + <h3>Advanced Usage</h3> + <ul> + <li><a href="#server-setup">Server Setup</a></li> + <li><a href="#api-reference">API Reference</a></li> + <li><a href="#cli-usage">CLI Usage</a></li> + </ul> + </div> + + <div class="nav-section"> + <h3>Resources</h3> + <ul> + <li><a href="#faq">FAQ</a></li> + <li><a href="#troubleshooting">Troubleshooting</a></li> + <li><a href="#community">Community</a></li> + </ul> + </div> + </nav> + </aside> + + <!-- Content (Right) --> + <div class="docs-content"> + <div class="docs-mobile-header"> + <button class="sidebar-toggle" id="sidebarToggle"> + <i class="fas fa-bars"></i> + </button> + <h2>Documentation</h2> + </div> + + <div class="docs-container"> + <!-- Introduction --> + <section id="introduction" class="doc-section"> + <h1>Introduction to DNAnalyzer</h1> + <p class="lead">DNAnalyzer is a powerful, privacy-focused DNA analysis tool using advanced machine + learning models for accurate, on-device genomic analysis.</p> + + <p>This documentation will guide you through the installation, setup, and usage of DNAnalyzer for + various DNA analysis tasks. Whether you're a researcher, educator, or bioinformatics enthusiast, + you'll find comprehensive information on all of DNAnalyzer's capabilities.</p> + + <div class="info-box"> + <h3>Key Features</h3> + <ul> + <li><strong>Privacy-First Analysis:</strong> All processing occurs on your device, ensuring + your genetic data never leaves your system.</li> + <li><strong>Machine Learning Powered:</strong> Advanced ML algorithms provide exceptional + accuracy in sequence analysis.</li> + <li><strong>Comprehensive Tools:</strong> From basic sequence statistics to advanced protein + prediction and promoter detection.</li> + <li><strong>Open Source:</strong> DNAnalyzer is completely open source under the MIT + License.</li> + </ul> + </div> + + <h2>System Requirements</h2> + <p>Before getting started, ensure your system meets the following requirements:</p> + + <div class="code-block"> + <div class="code-header"> + <span class="code-label">System Requirements</span> + <button class="copy-button">Copy</button> + </div> + <pre><code>- Operating System: Windows 10+, macOS 10.14+, or Linux (Ubuntu 18.04+) +- Memory: 2GB RAM minimum (4GB+ recommended for large sequences) +- Storage: 200MB for application, additional space for sequence files +- Browser: Chrome 80+, Firefox 75+, Safari 13+, Edge 80+ (for web interface) +- Java Runtime: Java 17+ (for server mode)</code></pre> + </div> + </section> + + <!-- Installation --> + <section id="installation" class="doc-section"> + <h1>Installation</h1> + <p>DNAnalyzer can be installed and used in multiple ways depending on your needs and technical + preferences.</p> + + <h2>Web Interface (No Installation)</h2> + <p>The simplest way to use DNAnalyzer is through our web interface, which requires no installation: + </p> + <ol> + <li>Visit <a href="../analyzer/analyzer.html">DNAnalyzer Web App</a></li> + <li>Upload your DNA sequence files</li> + <li>Select analysis options and get results</li> + </ol> + <p>The web interface runs entirely in your browser, ensuring your data never leaves your device.</p> + + <h2>Local Server Installation</h2> + <p>For more advanced usage or batch processing, you can install DNAnalyzer as a local server:</p> + + <div class="tabs"> + <div class="tab-header"> + <button class="tab-button active" data-tab="windows">Windows</button> + <button class="tab-button" data-tab="macos">macOS</button> + <button class="tab-button" data-tab="linux">Linux</button> + </div> + + <div class="tab-content active" id="windows"> + <ol> + <li>Download the latest <a + href="https://github.com/VerisimilitudeX/DNAnalyzer/releases">DNAnalyzer + release</a> for Windows</li> + <li>Extract the ZIP file to your preferred location</li> + <li>Ensure Java 17 or newer is installed on your system</li> + <li>Double-click on <code>dnanalyzer.bat</code> to start the server</li> + <li>Access the interface at <code>http://localhost:8080</code> in your browser</li> + </ol> + </div> + + <div class="tab-content" id="macos"> + <ol> + <li>Download the latest <a + href="https://github.com/VerisimilitudeX/DNAnalyzer/releases">DNAnalyzer + release</a> for macOS</li> + <li>Extract the ZIP file to your preferred location</li> + <li>Ensure Java 17 or newer is installed on your system</li> + <li>Open Terminal and navigate to the extracted folder</li> + <li>Run <code>chmod +x dnanalyzer.sh</code> to make the script executable</li> + <li>Execute <code>./dnanalyzer.sh</code> to start the server</li> + <li>Access the interface at <code>http://localhost:8080</code> in your browser</li> + </ol> + </div> + + <div class="tab-content" id="linux"> + <ol> + <li>Download the latest <a + href="https://github.com/VerisimilitudeX/DNAnalyzer/releases">DNAnalyzer + release</a> for Linux</li> + <li>Extract the archive to your preferred location</li> + <li>Ensure Java 17 or newer is installed on your system</li> + <li>Open Terminal and navigate to the extracted folder</li> + <li>Run <code>chmod +x dnanalyzer.sh</code> to make the script executable</li> + <li>Execute <code>./dnanalyzer.sh</code> to start the server</li> + <li>Access the interface at <code>http://localhost:8080</code> in your browser</li> + </ol> + </div> + </div> + + <h2>Building from Source</h2> + <p>For developers or those who want the latest features, you can build DNAnalyzer from source:</p> + + <div class="code-block"> + <div class="code-header"> + <span class="code-label">Building from Source</span> + <button class="copy-button">Copy</button> + </div> + <pre><code># Clone the repository +git clone https://github.com/VerisimilitudeX/DNAnalyzer.git +cd DNAnalyzer + +# Make the Gradle wrapper executable +chmod +x ./gradlew + +# Build the project +./gradlew clean bootJar + +# Run the server +java -jar build/libs/DNAnalyzer.jar</code></pre> + </div> + </section> + + <!-- Quick Start --> + <section id="quick-start" class="doc-section"> + <h1>Quick Start Guide</h1> + <p>This guide will help you quickly get started with DNAnalyzer's basic features.</p> + + <h2>Analyzing Your First DNA Sequence</h2> + <p>Follow these steps to perform your first DNA sequence analysis:</p> + + <div class="steps"> + <div class="step"> + <div class="step-number">1</div> + <div class="step-content"> + <h3>Upload a Sequence</h3> + <p>Navigate to the <a href="../analyzer/analyzer.html">DNA Analyzer</a> page and upload + your FASTA or FASTQ file by dragging it to the upload area or clicking to browse. + </p> + <p><strong>Don't have a sequence file?</strong> Click "Import Sample" to use a + pre-loaded sample sequence.</p> + </div> + </div> + + <div class="step"> + <div class="step-number">2</div> + <div class="step-content"> + <h3>Select Analysis Options</h3> + <p>Choose which analysis features you want to run:</p> + <ul> + <li><strong>Basic Analysis:</strong> Sequence length, GC content, base composition + </li> + <li><strong>Codon Analysis:</strong> Start codons, stop codons, reading frames</li> + <li><strong>Advanced Features:</strong> Coverage analysis, protein prediction, + promoter detection</li> + </ul> + </div> + </div> + + <div class="step"> + <div class="step-number">3</div> + <div class="step-content"> + <h3>Run Analysis</h3> + <p>Click the "Start Analysis" button to process your sequence. The analysis time depends + on the sequence length and selected options.</p> + </div> + </div> + + <div class="step"> + <div class="step-number">4</div> + <div class="step-content"> + <h3>Review Results</h3> + <p>Examine the analysis results, which include visualizations, statistics, and detailed + information about your sequence.</p> + <p>You can export the results in JSON, CSV, or text format for further processing or + documentation.</p> + </div> + </div> + </div> + + <div class="info-box tip"> + <h3>Pro Tip</h3> + <p>For large sequences (>1MB), consider using the local server installation for better + performance and additional analysis options.</p> + </div> + </section> + + <!-- Sequence Analysis --> + <section id="sequence-analysis" class="doc-section"> + <h1>Sequence Analysis</h1> + <p>DNAnalyzer provides comprehensive tools to analyze the basic properties of DNA sequences.</p> + + <h2>Base Composition Analysis</h2> + <p>One of the fundamental analyses is determining the nucleotide composition of your DNA sequence: + </p> + + <ul> + <li><strong>Nucleotide Counts:</strong> Total count of A, T, G, C, and any other bases (N) in + the sequence</li> + <li><strong>Percentage Distribution:</strong> Proportion of each nucleotide type</li> + <li><strong>Visualization:</strong> Interactive bar chart showing the distribution</li> + </ul> + + <h2>GC Content Analysis</h2> + <p>GC content is the percentage of nitrogenous bases in a DNA molecule that are either guanine (G) + or cytosine (C):</p> + + <div class="code-block"> + <div class="code-header"> + <span class="code-label">GC Content Formula</span> + <button class="copy-button">Copy</button> + </div> + <pre><code>GC Content (%) = (G + C) / (A + T + G + C) × 100</code></pre> + </div> + + <p>GC content is important because:</p> + <ul> + <li>It affects DNA stability (higher GC content = more stable)</li> + <li>GC-rich regions often indicate regulatory elements and gene-dense areas</li> + <li>Different organisms have characteristic GC content ranges</li> + </ul> + + <div class="info-box"> + <h3>Interpreting GC Content</h3> + <ul> + <li><strong>Low GC (< 40%):</strong> Common in AT-rich genomes like certain bacteria</li> + <li><strong>Medium GC (40-60%):</strong> Typical of many eukaryotic genomes, including + humans</li> + <li><strong>High GC (> 60%):</strong> Often found in gene-rich regions and certain + prokaryotes</li> + </ul> + </div> + </section> + + <!-- More sections would continue here... --> + + <!-- API Reference --> + <section id="api-reference" class="doc-section"> + <h1>API Reference</h1> + <p>DNAnalyzer provides a RESTful API when running in server mode, allowing programmatic access to + all analysis features.</p> + + <h2>API Endpoints</h2> + <p>The following endpoints are available when the server is running:</p> + + <div class="api-endpoint"> + <div class="endpoint-method get">GET</div> + <div class="endpoint-path">/api/v1/status</div> + <div class="endpoint-description"> + <p>Check server status and version information</p> + <h4>Response</h4> + <div class="code-block"> + <pre><code>{ + "status": "running", + "version": "1.0.0", + "uptime": "12h 34m 56s" +}</code></pre> + </div> + </div> + </div> + + <div class="api-endpoint"> + <div class="endpoint-method post">POST</div> + <div class="endpoint-path">/api/v1/analyze</div> + <div class="endpoint-description"> + <p>Analyze a DNA sequence file</p> + <h4>Request</h4> + <p>Form data with the following parameters:</p> + <ul> + <li><code>dnaFile</code> (required): The DNA sequence file to analyze</li> + <li><code>options</code>: JSON string with analysis options</li> + </ul> + <h4>Response</h4> + <div class="code-block"> + <pre><code>{ + "sequence": { + "length": 1234, + "filename": "example.fa" + }, + "basePairs": { + "counts": { "A": 300, "T": 310, "G": 320, "C": 304 }, + "percentages": { "A": 24.3, "T": 25.1, "G": 25.9, "C": 24.7 }, + "gcContent": 50.6 + }, + "analysis": { + // Additional analysis results based on options + } +}</code></pre> + </div> + </div> + </div> + + <div class="api-endpoint"> + <div class="endpoint-method post">POST</div> + <div class="endpoint-path">/api/v1/base-pairs</div> + <div class="endpoint-description"> + <p>Analyze base pair composition of a DNA sequence</p> + <h4>Request</h4> + <div class="code-block"> + <pre><code>{ + "sequence": "ATGCATGCATGC" +}</code></pre> + </div> + <h4>Response</h4> + <div class="code-block"> + <pre><code>{ + "counts": { "A": 3, "T": 3, "G": 3, "C": 3 }, + "percentages": { "A": 25, "T": 25, "G": 25, "C": 25 }, + "gcContent": 50 +}</code></pre> + </div> + </div> + </div> + + <h2>Python Client Example</h2> + <p>Here's a simple Python example to interact with the DNAnalyzer API:</p> + + <div class="code-block"> + <div class="code-header"> + <span class="code-label">Python</span> + <button class="copy-button">Copy</button> + </div> + <pre><code>import requests + +# API base URL +BASE_URL = "http://localhost:8080/api/v1" + +# Check server status +response = requests.get(f"{BASE_URL}/status") +print("Server status:", response.json()) + +# Analyze a sequence +with open("sequence.fa", "rb") as f: + files = {"dnaFile": f} + options = { + "sequence-length": True, + "gc-content": True, + "base-composition": True, + "start-codons": True, + "stop-codons": True + } + data = {"options": json.dumps(options)} + response = requests.post(f"{BASE_URL}/analyze", files=files, data=data) + + # Print results + result = response.json() + print(f"Sequence length: {result['sequence']['length']}") + print(f"GC content: {result['basePairs']['gcContent']}%")</code></pre> + </div> + </section> + + <!-- FAQ Section --> + <section id="faq" class="doc-section"> + <h1>Frequently Asked Questions</h1> + + <div class="faq-item"> + <div class="faq-question"> + <h3>Is my DNA data secure when using DNAnalyzer?</h3> + <i class="fas fa-chevron-down"></i> + </div> + <div class="faq-answer"> + <p>Yes, DNAnalyzer is designed with privacy as a fundamental principle. All processing + occurs locally on your device, and your DNA sequence data never leaves your system. In + web mode, analysis runs directly in your browser, and in server mode, it runs only on + your local machine. We don't collect, store, or transmit any of your sequence data.</p> + </div> + </div> + + <div class="faq-item"> + <div class="faq-question"> + <h3>What file formats does DNAnalyzer support?</h3> + <i class="fas fa-chevron-down"></i> + </div> + <div class="faq-answer"> + <p>DNAnalyzer supports the following file formats:</p> + <ul> + <li>FASTA (.fa, .fasta)</li> + <li>FASTQ (.fastq)</li> + <li>Plain text (.txt) containing DNA sequences</li> + </ul> + <p>The sequences should contain only A, T, G, C, and N (unknown) nucleotides. Other + characters will be treated as unknown bases.</p> + </div> + </div> + + <div class="faq-item"> + <div class="faq-question"> + <h3>How large of a sequence can DNAnalyzer handle?</h3> + <i class="fas fa-chevron-down"></i> + </div> + <div class="faq-answer"> + <p>The size limitations depend on the mode of operation:</p> + <ul> + <li><strong>Web Interface:</strong> Up to around 5MB sequence files, depending on your + browser and device memory</li> + <li><strong>Local Server:</strong> Can handle much larger sequences, typically up to + several hundred MB</li> + </ul> + <p>For very large genomes (e.g., human genome), we recommend using the local server + installation with a machine that has at least 8GB of RAM.</p> + </div> + </div> + + <div class="faq-item"> + <div class="faq-question"> + <h3>Can DNAnalyzer analyze my 23andMe or Ancestry DNA data?</h3> + <i class="fas fa-chevron-down"></i> + </div> + <div class="faq-answer"> + <p>Not directly in the current version. DNAnalyzer is designed to work with full DNA + sequences rather than SNP genotype data from consumer genetics services. However, we're + developing a feature to support genotype data analysis in an upcoming version.</p> + <p>If you have raw data from these services, you would need to convert it to a suitable + format before using it with DNAnalyzer.</p> + </div> + </div> + + <div class="faq-item"> + <div class="faq-question"> + <h3>Is DNAnalyzer open source?</h3> + <i class="fas fa-chevron-down"></i> + </div> + <div class="faq-answer"> + <p>Yes, DNAnalyzer is completely open source under the MIT License. You can view, modify, + and contribute to the code on our <a + href="https://github.com/VerisimilitudeX/DNAnalyzer">GitHub repository</a>.</p> + </div> + </div> + </section> + + <!-- Community Section --> + <section id="community" class="doc-section"> + <h1>Community & Support</h1> + <p>DNAnalyzer has an active community of users and developers. Here's how you can get involved and + find support.</p> + + <h2>Getting Help</h2> + <p>If you need assistance with DNAnalyzer, there are several resources available:</p> + + <div class="community-resources"> + <div class="resource-card"> + <i class="fab fa-discord"></i> + <h3>Discord Community</h3> + <p>Join our Discord server for real-time assistance and discussions about DNAnalyzer.</p> + <a href="https://discord.gg/xNpujz49gj" class="btn btn-secondary btn-sm">Join Discord</a> + </div> + + <div class="resource-card"> + <i class="fab fa-github"></i> + <h3>GitHub Issues</h3> + <p>Report bugs or request features through our GitHub issue tracker.</p> + <a href="https://github.com/VerisimilitudeX/DNAnalyzer/issues" + class="btn btn-secondary btn-sm">GitHub Issues</a> + </div> + + <div class="resource-card"> + <i class="fas fa-book"></i> + <h3>Documentation</h3> + <p>Browse comprehensive guides and tutorials in our documentation.</p> + <a href="docs.html" class="btn btn-secondary btn-sm">View Docs</a> + </div> + </div> + + <h2>Contributing</h2> + <p>DNAnalyzer is an open-source project, and we welcome contributions from the community. There are + many ways to contribute:</p> + + <ul> + <li><strong>Code Contributions:</strong> Help improve DNAnalyzer by fixing bugs or adding new + features</li> + <li><strong>Documentation:</strong> Improve our guides, tutorials, and API documentation</li> + <li><strong>Testing:</strong> Test DNAnalyzer and report issues or suggest improvements</li> + <li><strong>Translations:</strong> Help translate DNAnalyzer into different languages</li> + </ul> + + <p>To get started with contributing, please read our <a + href="https://github.com/VerisimilitudeX/DNAnalyzer/blob/main/CONTRIBUTING.md">contribution + guidelines</a>.</p> + + <div class="info-box"> + <h3>Code of Conduct</h3> + <p>We're committed to providing a welcoming and inclusive environment for all contributors. + Please read and follow our <a + href="https://github.com/VerisimilitudeX/DNAnalyzer/blob/main/CODE_OF_CONDUCT.md">Code + of Conduct</a>.</p> + </div> + </section> + </div> + </div> + </div> + + <!-- Footer --> + <footer class="footer"> + <div class="container"> + <div class="footer-grid"> + <div class="footer-brand"> + <img src="../assets/icons/Icon_Dark_BG.svg" alt="DNAnalyzer Logo"> + <p>DNAnalyzer is a powerful, privacy-focused DNA analysis tool using cutting-edge machine learning + models for accurate, on-device genomic analysis.</p> + + <div class="footer-social"> + <a href="https://www.twitter.com/DNAnalyzer_" class="social-link"> + <i class="fab fa-twitter"></i> + </a> + <a href="https://github.com/VerisimilitudeX/DNAnalyzer" class="social-link"> + <i class="fab fa-github"></i> + </a> + <a href="#" class="social-link"> + <i class="fab fa-twitter"></i> + </a> + </div> + </div> + + <div class="footer-nav"> + <h4>Product</h4> + <ul> + <li><a href="../features/features.html">Features</a></li> + <li><a href="../analyzer/analyzer.html">DNA Analyzer</a></li> + <li><a href="../server/server.html">Server</a></li> + <li><a href="docs.html">Documentation</a></li> + </ul> + </div> + + <div class="footer-nav"> + <h4>Resources</h4> + <ul> + <li><a href="getting-started.md">Getting Started</a></li> + <li><a href="citations.md">Citations</a></li> + <li><a href="research/genes.md">Gene Research</a></li> + <li><a href="samples/cli-arguments-examples.md">CLI Examples</a></li> + </ul> + </div> + + <div class="footer-nav"> + <h4>Community</h4> + <ul> + <li><a href="https://github.com/VerisimilitudeX/DNAnalyzer">GitHub</a></li> + <li><a href="https://discord.gg/xNpujz49gj">Discord</a></li> + <li><a href="contributing/CONTRIBUTING.md">Contributing</a></li> + <li><a href="../CODE_OF_CONDUCT.md">Code of Conduct</a></li> + </ul> + </div> + </div> + + <div class="footer-bottom"> + <div class="footer-copyright"> + Copyright © Piyush Acharya 2025. DNAnalyzer is a fiscally sponsored 501(c)(3) nonprofit (EIN: + 81-2908499). MIT License. + </div> + + <div class="footer-links"> + <a href="../LICENSE.md">License</a> + <a href="../SECURITY.md">Security</a> + <a href="../CITATION.cff">Citation</a> + </div> + </div> + </div> + </footer> + + <!-- JavaScript --> + <script src="docs.js"></script> +</body> + +</html> \ No newline at end of file