Week 25, 2025 (June 17 - June 23)

Weekly Research Progress Report

RNA Lab Navigator Platform Enhancement COMPLETED

Status: Successfully enhanced the RNA Lab Navigator with intelligent research capabilities, clean UI transformation, and production-ready features.

Component	Progress	Details
UI Transformation	100%	Complete overhaul from complex animated interface to clean ChatGPT/Claude-like design. Removed problematic 3D animations and particle effects causing performance issues. Implemented professional chat interface with session management and conversation memory. Added dark mode support and responsive design for all screen sizes. React 18 Tailwind CSS Vite Framer Motion
Enhanced RAG System	100%	Implemented production-ready Retrieval Augmented Generation with research intelligence. Built multi-hop reasoning capabilities for complex research queries. Integrated experiment suggestion system with protocol recommendations. Added context-aware answer validation and citation tracking. OpenAI GPT-4 Weaviate LangChain Redis Cache
Multi-Agent Intelligence	100%	Developed specialized agents for literature analysis, hypothesis generation, and protocol design. Literature Agent: Analyzes papers to extract methodologies and insights. Hypothesis Agent: Generates testable hypotheses based on research gaps. Protocol Agent: Suggests experimental approaches with step-by-step guidance. Critique Agent: Provides constructive feedback on experimental designs. Agent Architecture: User Query → Query Classifier → Appropriate Agent Selection Agent Processing → Cross-validation → Enhanced Response Response → Citation Addition → User Interface
Document Processing	100%	Built advanced PDF processor handling research papers, protocols, and theses. Implemented figure extraction with automatic caption association. Created intelligent chunking preserving section context and references. Added support for batch ingestion of entire document libraries. Successfully ingested: 20 papers, 10 protocols, 1 PhD thesis (Rhythm's).

Key Technical Achievements:

✅ Replaced problematic animated UI with clean, professional interface
✅ Implemented session-based chat with conversation memory
✅ Built comprehensive feedback system with analytics
✅ Added real-time WebSocket support for live updates
✅ Created modular agent system for specialized research tasks
✅ Optimized vector search with hybrid keyword + semantic matching

StickForStats Platform Deployment LIVE

Status: Successfully deployed StickForStats frontend to Vercel after resolving multiple build and runtime errors. Platform is now accessible for testing.

Component	Progress	Details
Frontend Deployment	100%	Successfully deployed React frontend to Vercel after fixing 20+ missing component errors. Resolved Material-UI v7 beta compatibility issues by downgrading to stable v5. Fixed React Context errors by adding missing functions (openSearch, closeSearch). Created placeholder components for missing enterprise features. Live URLs: https://stickforstats-19yh.vercel.app https://stickforstats.vercel.app (custom domain pending)
Error Resolution	100%	Fixed critical deployment blockers through systematic debugging: Missing Components: Created 15+ placeholder components including BrandedLogo, ThemeToggle, LanguageSelector, EnterpriseFormFields Package Issues: Installed missing dependencies (@react-three/fiber, @react-three/drei), fixed import mismatches Runtime Errors: Fixed "Cannot read properties of undefined (reading 'map')" by adding openSearch to SearchContext Build Optimization: Increased Node.js heap size, disabled source maps, optimized webpack configuration
Documentation	100%	Created comprehensive session context documentation for future deployments. Documented all fixes and workarounds for inherited codebase issues. Updated CLAUDE.md with deployment commands and common patterns. Prepared deployment checklist for backend and database setup.

Component

Progress

Details

Frontend Deployment

100%

Successfully deployed React frontend to Vercel after fixing 20+ missing component errors.

Resolved Material-UI v7 beta compatibility issues by downgrading to stable v5.

Fixed React Context errors by adding missing functions (openSearch, closeSearch).

Created placeholder components for missing enterprise features.

Live URLs:

https://stickforstats-19yh.vercel.app
https://stickforstats.vercel.app (custom domain pending)

Error Resolution

100%

Fixed critical deployment blockers through systematic debugging:

Missing Components: Created 15+ placeholder components including BrandedLogo, ThemeToggle, LanguageSelector, EnterpriseFormFields

Package Issues: Installed missing dependencies (@react-three/fiber, @react-three/drei), fixed import mismatches

Runtime Errors: Fixed "Cannot read properties of undefined (reading 'map')" by adding openSearch to SearchContext

Build Optimization: Increased Node.js heap size, disabled source maps, optimized webpack configuration

Documentation

100%

Created comprehensive session context documentation for future deployments.

Documented all fixes and workarounds for inherited codebase issues.

Updated CLAUDE.md with deployment commands and common patterns.

Prepared deployment checklist for backend and database setup.

Deployment Challenges Overcome:

✅ Resolved missing version control history by recreating components
✅ Fixed memory constraints during build process
✅ Handled environment variable misconfigurations
✅ Addressed Material-UI version incompatibilities
✅ Created systematic approach for incremental deployment

Technical Skills & Infrastructure

Skill Area	Application & Learning
Production Deployment	Mastered Vercel deployment with custom configurations and build optimizations. Learned systematic debugging of inherited codebases without documentation. Implemented CI/CD best practices with automated builds on git push.
AI/ML Integration	Built production-ready RAG system with multi-agent architecture. Implemented prompt engineering for specialized research tasks. Created context-aware answer validation and ranking systems.
Full-Stack Development	React 18 with modern hooks and context management. Django REST framework with WebSocket support. Vector databases (Weaviate) for semantic search. Redis for caching and session management.
DevOps & Infrastructure	Docker containerization for microservices architecture. NGINX configuration for reverse proxy and load balancing. Monitoring setup with Prometheus and Grafana.

Weekly Summary

This week marked significant achievements in both platform development and deployment. The RNA Lab Navigator transformation from a complex animated interface to a clean, professional research platform demonstrates the importance of user-centric design in scientific tools. The successful implementation of multi-agent AI systems for research assistance represents a cutting-edge approach to accelerating scientific discovery.

The StickForStats deployment journey highlighted the challenges of working with inherited codebases and the importance of systematic debugging. Through persistent problem-solving, we transformed a project with missing version control into a live, accessible platform. The deployment process involved fixing over 20 critical errors, from missing components to package compatibility issues.

Key innovations this week included:

Multi-agent architecture for specialized research tasks (literature analysis, hypothesis generation, protocol design)
Production-ready RAG system with context-aware answer validation
Clean UI transformation prioritizing functionality over aesthetics
Systematic approach to deploying inherited codebases
Comprehensive documentation ensuring knowledge transfer

Technical challenges addressed:

React 18 compatibility issues with Material-UI v7 beta
Memory optimization for large React applications
WebSocket integration for real-time features
Vector database optimization for semantic search
Cross-origin resource sharing in distributed architectures

Both platforms are now positioned for user testing and feedback. The RNA Lab Navigator provides researchers with an intelligent assistant for experimental design and literature analysis. StickForStats offers comprehensive statistical analysis tools with a modern web interface. Next steps include backend deployment for StickForStats, user testing for both platforms, and iterative improvements based on feedback.