🧬 GeneInsight Platform - AI-Enhanced SaaS Edition

Complete SaaS Bioinformatics Platform with LangChain AI, Multi-Tenant Architecture, and Advanced Molecular Analysis

🚀 Latest Major Update - LangChain Integration

✨ New AI Features:

🧠 LangChain AI Assistant: Conversational AI for molecular analysis powered by microsoft/DialoGPT-small
🦠 COVID-19 Specialized Analysis: Expert insights for viral proteins and drug targeting
💬 Context-Aware Chat: Natural language molecular conversations with memory
🎯 Enhanced Docking: AI-powered molecular docking interpretation and optimization
🔬 Automatic Sequence Detection: Paste protein sequences for instant expert analysis
📊 Real-time AI Status: Live LangChain LLM monitoring and capabilities display
🎨 3D + AI Integration: Interactive molecular visualization combined with AI insights

🚀 Live SaaS Platform: [https://geneinsight-platform.vercel.app](https://geneinsight-platform-latest-euwr1g9lf-8packcoders-projects.vercel.app/)
💰 Pricing Plans: View SaaS Pricing
📊 SaaS Dashboard: Multi-tenant with usage analytics & billing management

🤖 LangChain AI Assistant - Revolutionary Molecular Analysis

💬 Conversational AI for Molecular Biology

Experience the future of molecular analysis with our LangChain-powered AI assistant that understands and responds to natural language queries about molecular structures, sequences, and drug interactions.

🧬 What You Can Do:

Paste any protein sequence → Get instant expert analysis with domain identification
Ask "covid 19" → Get specialized viral protein analysis and drug targeting guidance
Query "What does -9.2 kcal/mol mean?" → Get detailed binding affinity explanations
Request "show 3d" → Get 3D visualization guidance and molecular insights
Inquire about domains → Get functional site analysis and drug targeting potential

🎯 AI Capabilities:

Automatic Sequence Recognition: Detects protein sequences in chat (50+ chars, 85% amino acids)
COVID-19 Expertise: Specialized analysis for viral proteins (spike, main protease, etc.)
Context-Aware Responses: Remembers conversation history and provides relevant insights
Scientific Explanations: Expert-level interpretations of molecular data
Drug Discovery Insights: Binding affinity analysis and optimization suggestions

🔗 LangChain Integration:

Model: microsoft/DialoGPT-small for natural language generation
Chains: 2 specialized analysis chains (sequence, docking)
Memory: Conversational context preservation
Hybrid Approach: Rule-based analysis enhanced with LLM insights
Real-time Status: Live monitoring of AI capabilities

🌟 What is GeneInsight Platform?

GeneInsight Platform is a complete Software-as-a-Service (SaaS) bioinformatics platform that combines cutting-edge LangChain AI with advanced molecular visualization. Built for commercial deployment with multi-tenant architecture, subscription billing, and enterprise-grade features.

🔬 What Does GeneInsight Platform Do?

GeneInsight Platform transforms complex genetic analysis into an intuitive, web-based experience. Here's what researchers, students, and biotechnology professionals can accomplish:

🧬 Genetic Sequence Analysis

Upload & Analyze: Simply paste or upload DNA, RNA, or protein sequences in various formats (FASTA, plain text)
Instant Results: Get comprehensive analysis including:
- Nucleotide/Amino Acid Composition: Detailed breakdown of sequence components
- GC Content Analysis: Critical for PCR design and gene expression studies
- Open Reading Frame (ORF) Detection: Identify potential protein-coding regions
- Motif Recognition: Find regulatory elements and binding sites
- Molecular Properties: Calculate molecular weight, isoelectric point, and stability

🎯 AI-Enhanced Molecular Docking

Protein-Ligand Docking: Advanced molecular docking simulations with AI interpretation
Multiple Binding Modes: Generate and analyze multiple ligand binding poses
Binding Affinity Calculation: Accurate kcal/mol scoring with AI explanations
Drug-Likeness Assessment: Lipinski Rule of Five validation and optimization
AI Chat Integration: Ask questions about docking results and get expert insights
3D Visualization: Interactive visualization of docking results with binding sites

🔬 3D Molecular Visualization

Interactive 3D Structures: View and manipulate protein structures in real-time
Multiple Visualization Modes: Switch between cartoon, surface, stick, and ball-and-stick representations
PDB File Support: Import existing protein structures from the Protein Data Bank
Structure Prediction: AI-powered prediction of 3D protein structures from sequences
AI + 3D Integration: Combine interactive visualization with conversational AI insights
High-Quality Exports: Save publication-ready images and structure files

🤖 LangChain AI-Powered Insights

Conversational AI Assistant: Natural language molecular analysis with LangChain
Automatic Sequence Detection: Paste protein sequences for instant expert analysis
COVID-19 Specialized Analysis: Expert insights for viral proteins and drug targets
Context-Aware Responses: AI remembers conversation history and provides relevant insights
Binding Affinity Explanations: Detailed scientific interpretations of molecular interactions
Domain Analysis: Functional site identification with drug targeting potential
Structure Prediction: Machine learning models predict 3D protein structures
Disease Association: Analyze potential gene-disease relationships
Real-time AI Status: Live monitoring of LangChain LLM capabilities

📊 Professional Workflow Management

Project Organization: Organize analyses into projects and folders
Team Collaboration: Share results with team members and collaborators
Export Options: Download results in PDF, CSV, JSON, and FASTA formats
Analysis History: Track and revisit previous analyses with version control

💼 Commercial SaaS Features

Multi-Tenant Architecture: Secure, isolated workspaces for different organizations
Subscription Plans: Flexible pricing from free tier to enterprise solutions
Usage Analytics: Real-time tracking of analyses, storage, and team activity
API Access: Programmatic access for integration with existing workflows

🎯 Who Benefits from GeneInsight Platform?

🎓 Students: Learn bioinformatics with an intuitive, modern interface
🔬 Researchers: Accelerate genetic analysis with AI-powered tools
🏥 Clinical Labs: Streamline genetic testing workflows
🏢 Biotech Companies: Scale bioinformatics operations with SaaS efficiency
👥 Research Teams: Collaborate seamlessly with shared workspaces

In essence, GeneInsight Platform makes advanced bioinformatics accessible to everyone - from students learning the basics to professional researchers conducting cutting-edge genetic analysis.

🎯 SaaS Business Model

Plan	Price	Users	Analyses/Month	Storage	Target Market
Free	$0	5	100	1GB	Students & Individual Researchers
Pro	$49/mo	25	1,000	10GB	Research Teams & Small Labs
Enterprise	$199/mo	Unlimited	Unlimited	100GB	Large Organizations & Institutions

Annual billing available with 20% discount

💼 Key SaaS Features

🏢 Multi-Tenant Architecture

Organization Management: Complete tenant isolation with custom branding
Team Collaboration: Owner, Admin, Member, Viewer roles with granular permissions
User Invitations: Email-based team member invitations with role assignment
Data Isolation: Secure tenant separation with organization-scoped data access

💳 Subscription & Billing System

3-Tier Pricing: Free, Pro ($49/mo), Enterprise ($199/mo) with clear value propositions
Usage Tracking: Real-time monitoring of analyses, storage, API calls, and team members
Automatic Limits: Usage enforcement with smart upgrade prompts and notifications
Stripe Integration: Ready for payment processing with subscription management

📊 SaaS Dashboard & Analytics

Usage Overview: Real-time usage statistics with progress bars and percentages
Billing Information: Current plan, billing cycle, subscription status display
Upgrade Prompts: Smart notifications when approaching usage limits
Team Analytics: Member activity and organization usage insights

🔬 Core Scientific Features

Multi-format Support: Analyze DNA, RNA, and protein sequences with usage tracking
Comprehensive Analysis: Nucleotide composition, GC content, ORF detection, motif identification
3D Molecular Visualization: Interactive 3D viewer powered by 3DMol.js
Real-time Results: Instant analysis with detailed visualizations and usage metering
Export Options: Download results in multiple formats with plan-based limits

📁 Repository Structure

geneinsight-platform/
├── 🌐 Frontend (Next.js)
│   ├── app/                    # Next.js 13+ App Router
│   │   ├── page.tsx           # Landing page
│   │   ├── dashboard/         # SaaS dashboard
│   │   ├── ai-chat/          # LangChain AI chat interface
│   │   ├── docking/          # Molecular docking with 3D viewer
│   │   └── api/              # Next.js API routes
│   ├── components/           # React components
│   │   ├── langchain-chat.tsx # AI chat component
│   │   └── simple-3d-viewer.tsx # 3D molecular viewer
│   └── lib/                  # Utilities and client-side analysis
│
├── 🧠 ML Service (Python + LangChain)
│   ├── langchain_service/    # LangChain integration
│   │   └── molecular_chain.py # Conversational AI chains
│   ├── docking_service/      # Molecular docking algorithms
│   ├── models/              # ML models and utilities
│   ├── requirements.txt     # Python dependencies
│   └── app.py              # Flask application
│
├── ☕ Backend (Java Spring Boot)
│   ├── src/main/java/       # Java source code
│   │   └── com/geneinsight/ # Application packages
│   ├── src/main/resources/  # Configuration files
│   └── pom.xml             # Maven dependencies
│
├── 🐳 Deployment
│   ├── docker-compose.yml   # Multi-service Docker setup
│   ├── Dockerfile          # Main application container
│   ├── Dockerfile.apillon   # Apillon-optimized container
│   ├── apillon.json        # Apillon deployment config
│   ├── deploy-apillon.sh   # Automated Apillon deployment
│   └── vercel.json         # Vercel configuration
│
└── 📚 Documentation
    ├── README.md           # This file
    ├── DEPLOYMENT.md       # Deployment instructions
    └── APILLON_DEPLOYMENT.md # Apillon-specific guide

🏗️ Technical Architecture

🔗 LangChain AI Integration

Frontend (Next.js) → ML Service (Flask) → LangChain → DialoGPT-small
                                      ↓
                              Rule-based Analysis + LLM Enhancement

🧠 AI Components:

LangChain Framework: Conversational AI with memory and context
Model: microsoft/DialoGPT-small (351MB, CPU optimized)
Analysis Chains: 2 specialized chains (sequence analysis, docking analysis)
Output Parser: Custom molecular analysis result parser
Memory Management: Conversation context preservation
Hybrid Approach: Rule-based analysis enhanced with LLM insights

🚀 Multi-Technology Stack:

Frontend: Next.js 15.2.4 with TypeScript and Tailwind CSS
Backend: Java Spring Boot 3.2.0 with PostgreSQL
ML Service: Python Flask with LangChain integration
AI Models: LangChain + DialoGPT-small for conversational AI
3D Visualization: Canvas-based molecular viewer
Deployment: Apillon (Web3) + Vercel (Frontend) + Docker (Full Stack)

📊 System Capabilities:

Real-time AI Chat: Conversational molecular analysis
Automatic Sequence Detection: 50+ characters, 85% amino acid threshold
Context Awareness: AI remembers conversation history
COVID-19 Expertise: Specialized viral protein analysis
3D + AI Integration: Interactive visualization with AI insights
Production Ready: Scalable architecture with monitoring

🚀 Quick Start Guide

🌐 Option 1: Apillon (Web3 + Full LangChain) ⭐ RECOMMENDED

# 1. Clone repository
git clone https://github.com/saurabhhhcodes/geneinsight-platform.git
cd geneinsight-platform

# 2. Install Apillon CLI and deploy
npm install -g @apillon/cli
apillon auth login
chmod +x deploy-apillon.sh
./deploy-apillon.sh

# 3. Access full LangChain features on Web3
# Frontend: https://geneinsight.apillon.io
# AI Chat: https://geneinsight.apillon.io/ai-chat

🌐 Option 2: Vercel (Enhanced with Edge Functions)

# 1. Clone the repository
git clone https://github.com/saurabhhhcodes/geneinsight-platform.git
cd geneinsight-platform

# 2. Install dependencies
npm install

# 3. Deploy to Vercel
npm i -g vercel
vercel --prod

🐳 Option 3: Docker (Full Stack) - One Command Setup

# 1. Clone the repository
git clone https://github.com/saurabhhhcodes/geneinsight-platform.git
cd geneinsight-platform

# 2. Start all services
docker-compose up -d

# Access: Frontend (3000), Backend (8080), ML Service (5000)

🚂 Option 4: Railway.app (Full LangChain)

# 1. Clone repository
git clone https://github.com/saurabhhhcodes/geneinsight-platform.git
cd geneinsight-platform

# 2. Install Railway CLI
npm install -g @railway/cli

# 3. Deploy to Railway
railway login
railway init
railway up --dockerfile Dockerfile.railway

# 4. Access full LangChain features
# Frontend: https://your-app.railway.app
# AI Chat: https://your-app.railway.app/ai-chat

🎨 Option 4: Render.com (FREE Alternative)

# 1. Fork repository on GitHub
# 2. Connect to Render.com
# 3. Use render.yaml configuration
# 4. Auto-deploys on git push
# Features: Full LangChain + PostgreSQL

✈️ Option 5: Fly.io (FREE with Docker)

# 1. Clone repository
git clone https://github.com/saurabhhhcodes/geneinsight-platform.git
cd geneinsight-platform

# 2. Install Fly CLI
curl -L https://fly.io/install.sh | sh

# 3. Deploy to Fly.io
flyctl auth login
flyctl launch
flyctl deploy

🧠 Option 6: Local Development (Full Features)

# 1. Clone and setup
git clone https://github.com/saurabhhhcodes/geneinsight-platform.git
cd geneinsight-platform

# 2. Install LangChain dependencies
pip install transformers torch langchain-community

# 3. Start ML service with LangChain
cd ml_service
python app.py

# 4. Start frontend
npm install && npm run dev

# 5. Access AI Chat: http://localhost:3001/ai-chat

🎯 Testing LangChain Features:

# Test COVID-19 analysis
curl -X POST http://localhost:5000/langchain/chat \
  -H "Content-Type: application/json" \
  -d '{"message": "covid 19"}'

# Test sequence analysis
curl -X POST http://localhost:5000/langchain/chat \
  -H "Content-Type: application/json" \
  -d '{"message": "SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ"}'

📊 Deployment Platform Comparison

Platform	Free Tier	LangChain Support	Database	Auto-Deploy	Best For
🌐 Apillon	Free tier available	✅ Full Support	✅ PostgreSQL	✅ GitHub	Web3 Production
🚂 Railway	$5 credit/month	✅ Full Support	✅ PostgreSQL	✅ GitHub	Production
🎨 Render	✅ Unlimited	✅ Full Support	✅ PostgreSQL	✅ GitHub	Development
✈️ Fly.io	3 VMs free	✅ Docker Support	✅ PostgreSQL	✅ GitHub	Global Edge
🌐 Vercel	✅ Unlimited	✅ Edge Functions	❌ External	✅ GitHub	Enhanced Demo
🐳 Local	✅ Free	✅ Full Support	✅ PostgreSQL	❌ Manual	Development

🎯 Recommendations:

🌐 Apillon: Best for Web3 deployment with full LangChain features and decentralized hosting
🚂 Railway: Great for production deployment with complete AI functionality
🎨 Render: Excellent for development and testing with unlimited free tier
✈️ Fly.io: Perfect for global deployment with edge computing
🌐 Vercel: Enhanced with Edge Functions for AI simulation and client-side analysis
🐳 Local: Ideal for development and testing all features

🌐 Apillon Web3 Deployment

Why Apillon?

✅ Full Backend Support: Deploy Python + LangChain on Web3
✅ Decentralized Hosting: Censorship-resistant infrastructure
✅ Real LLM: Complete conversational AI functionality
✅ Auto-Scaling: Handles traffic automatically
✅ Database Support: PostgreSQL included
✅ Cost-Effective: Pay for what you use

Quick Apillon Deploy:

# Install Apillon CLI
npm install -g @apillon/cli

# Login and deploy
apillon auth login
chmod +x deploy-apillon.sh
./deploy-apillon.sh

# Your live URLs:
# https://geneinsight.apillon.io
# https://api.geneinsight.apillon.io

Apillon Features:

🧬 Complete AI Platform: All LangChain features working
🦠 COVID-19 Analysis: Expert viral protein insights
🎯 Molecular Docking: Protein-ligand simulations
🔬 3D Visualization: Interactive molecular viewer
📊 Dashboard: SaaS features with subscription management
🌐 Web3 Infrastructure: Decentralized, global distribution

🔌 SaaS API Endpoints

🏢 Organization Management

GET /api/organizations          // Get organization details
POST /api/organizations         // Create new organization
PUT /api/organizations          // Update organization settings

💳 Subscription & Billing

GET /api/subscriptions          // Get subscription status and usage
POST /api/subscriptions         // Upgrade subscription plan
GET /api/usage/track           // Get usage statistics
POST /api/usage/track          // Track usage (automatic)

🛠 Technology Stack

Frontend

Next.js 15 with TypeScript for type-safe, performant web application
Tailwind CSS for responsive, modern UI design
3DMol.js for hardware-accelerated 3D molecular rendering

Backend

Spring Boot 3.2 with Java 17 for enterprise-grade API services
MySQL 8.0 with Redis caching for optimal data management
JWT Authentication with multi-tenant support

ML Service

Python 3.11 with Flask for advanced bioinformatics algorithms
Scikit-learn for machine learning capabilities
NumPy & Pandas for data processing

SaaS Infrastructure

Multi-tenant database design with proper isolation
Stripe integration for subscription billing
Usage tracking and limits enforcement
Role-based access control with organization management

📖 Using the Application

🎯 Getting Started as a User

🏠 Homepage & Navigation
- Visit the application URL
- Navigate: Home, Analyze, Visualize, Pricing, Dashboard
🧬 Analyzing Sequences
- Go to /analyze page
- Input DNA, RNA, or protein sequences
- Supported formats: FASTA, PDB, plain text
- View comprehensive results with usage tracking
🧪 3D Molecular Visualization
- Go to /visualize page
- Load structures via PDB ID or file upload
- Interactive controls: rotate, zoom, pan, reset
- Multiple rendering styles and color schemes
📊 Managing Your Organization
- Access SaaS dashboard for usage analytics
- Manage team members and permissions
- Monitor billing and subscription status
- Upgrade plans as needed

💰 Business Benefits

🚀 For SaaS Entrepreneurs

Complete SaaS foundation with proven business model
Scalable technology built on modern, cloud-native stack
Market validation in the $4.2B bioinformatics market

🏢 For Organizations

Cost-effective with pay-as-you-scale pricing
Team collaboration with enterprise security
Professional support based on subscription tier

🔬 For Researchers

Instant access with no software installation
Collaborative analysis sharing with team members
Always updated with latest features and algorithms

🤝 Contributing

We welcome contributions! Check out our Contributing Guide and look for Good First Issues.

🛠️ Development Setup

# Clone and setup
git clone https://github.com/saurabhhhcodes/geneinsight-platform.git
cd geneinsight-platform
npm install
npm run dev

📜 License

This project is licensed under the MIT License - see the LICENSE file for details.

🙏 Acknowledgments

3DMol.js Team - For excellent 3D molecular visualization capabilities
Next.js & Vercel Team - For the amazing React framework and deployment platform
Open Source Community - For inspiration, feedback, and contributions
Bioinformatics Community - For domain expertise and scientific guidance

🧬 Built with ❤️ for the bioinformatics community

Ready to transform your bioinformatics workflow? 🚀 Get Started | 💰 View Pricing | 📖 Documentation

Name		Name	Last commit message	Last commit date
Latest commit History 99 Commits
.github		.github
.idea		.idea
.streamlit		.streamlit
.vscode		.vscode
components		components
database		database
hooks		hooks
lib		lib
ml_service		ml_service
public		public
src/main/java/com/geneinsight		src/main/java/com/geneinsight
streamlit_backend		streamlit_backend
streamlit_frontend		streamlit_frontend
.apillon.env		.apillon.env
.dockerignore		.dockerignore
.eslintrc.json		.eslintrc.json
.gitignore		.gitignore
.npmrc		.npmrc
.replit		.replit
CONTRIBUTING.md		CONTRIBUTING.md
Dockerfile		Dockerfile
LICENSE		LICENSE
README.md		README.md
components.json		components.json
docker-compose.yml		docker-compose.yml
improved_backend.py		improved_backend.py
next.config.mjs		next.config.mjs
package-lock.json		package-lock.json
package.json		package.json
pnpm-lock.yaml		pnpm-lock.yaml
postcss.config.mjs		postcss.config.mjs
tailwind.config.ts		tailwind.config.ts
tsconfig.json		tsconfig.json
vercel.json		vercel.json

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