GeneForgeLang Documentation

Welcome to the comprehensive documentation for GeneForgeLang (GFL), a domain-specific language for genomic workflow specification, validation, and AI-powered analysis.

🧬 Now live on GitHub Pages!

🚀 Quick Start

• Installation Guide - Get started with GeneForgeLang
• Getting Started Tutorial - Your first GFL workflow
• API Reference - Complete API documentation
• CLI Tools Guide - Command-line interface usage

📖 Core Documentation

User Guides

• Language Specification
• GFL Syntax Reference
• Workflow Examples

• Best Practices

• Web Interface

• Getting Started
• Advanced Features
• Troubleshooting

Developer Documentation

• API Documentation
• REST API Reference
• Client SDK

• Authentication

• Architecture

• System Overview
• Plugin System
• Inference Engine

🔬 Advanced Features

AI & Machine Learning

• Enhanced Inference Engine
• Model Integration
• Custom Models
• Performance Tuning

Symbolic Reasoning

• Knowledge Representation
• Rules and Hypotheses
• Temporal Orchestration
• Biological Entities

Web & API Platform

• Platform Features
• Web Interface Overview
• Server Deployment
• Monitoring & Analytics

🔒 Security & Operations

• Security
• Security Advisory
• Best Practices

• Vulnerability Management

• Deployment

• Production Setup
• Docker & Kubernetes
• Cloud Deployment

🛣️ Roadmap & Development

• Development
• Contributing Guide
• Development Setup

• Testing Guide

• Roadmap

• Phase 4 Planning
• Feature Requests
• Release Notes

📚 Reference Materials

Academic & Research

• Research Paper - Academic publication
• Citations - How to cite GeneForgeLang
• Bibliography - Related research

Technical Specifications

• Schema Reference - JSON Schema definitions
• Examples Collection - Code examples and demos
• Testing Suite - Comprehensive test examples

🎯 Use Cases & Applications

Genomics Applications

• CRISPR Gene Editing - Design and validate CRISPR experiments
• RNA-seq Analysis - Differential expression workflows
• Variant Analysis - Genomic variant interpretation
• Protein Analysis - Structure prediction and analysis

Industry Solutions

• Clinical Genomics - Diagnostic workflow automation
• Agricultural Genomics - Crop improvement pipelines
• Pharmaceutical Research - Drug discovery workflows
• Research Collaboration - Standardized workflow sharing

🆘 Support & Community

• FAQ - Frequently asked questions
• Troubleshooting - Common issues and solutions
• Community - Forums, discussions, and help
• Contact - Get in touch with the team

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Version Information

• Current Version: 0.1.0
• Documentation Version: 2025.1
• Last Updated: {{ current_date }}
• License: MIT License

Quick Navigation

Component	Documentation	Status
🔤 Language Core	Syntax	✅ Stable
🌐 Web Interface	Platform Docs	✅ Production Ready
🤖 AI Engine	Inference Docs	✅ Advanced Features
🔧 CLI Tools	CLI Guide	✅ Full Featured
📡 REST API	API Reference	✅ Complete
🔌 Plugin System	Plugin Guide	✅ Extensible

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GeneForgeLang - Empowering genomic research through structured workflows and AI-powered analysis.