A digital garden exploring cutting-edge AI and agentic solutions by Justin Johnson ([@bioinfo](https://twitter.com/bioinfo) | [rundatarun.io](https://rundatarun.io)).  *Photo by [DeepMind](https://unsplash.com/@deepmind) on [Unsplash](https://unsplash.com)* ## Quick Navigation <div class="quick-nav"> [[AI Development & Agents/⌂ AI Development & Agents|AI Development & Agents]] [[Cutting-Edge AI/⌂ Cutting-Edge AI|Cutting-Edge AI]] [[AI Systems & Architecture/⌂ AI Systems & Architecture|AI Systems & Architecture]] [[Practical Applications/⌂ Practical Applications|Practical Applications]] [[Emerging Trends/⌂ Emerging Trends|Emerging Trends]] </div> ## Latest Articles ### [Claude Code: Best Practices for Agentic Coding](AI%20Development%20&%20Agents/claude-code-best-practices.md) A comprehensive guide to optimizing your workflow with Claude Code, Anthropic's command line tool for agentic coding, covering setup customization, effective workflows, and advanced multi-agent techniques. [[AI Development & Agents/claude-code-best-practices]] ### [Agentic Content Creation: From PDF to Polished Blog in Under a Minute](AI%20Systems%20&%20Architecture/agentic-content-creation-openai-guide-case-study.md) A technical deep dive into how AI agents, mode switching, and MCP tools can transform raw content into polished, publication-ready blog posts with social media distribution materials in under a minute. [[AI Systems & Architecture/agentic-content-creation-openai-guide-case-study]] ### [Building Effective AI Agents: Key Insights from OpenAI's Practical Guide](AI%20Development%20&%20Agents/building-effective-ai-agents-openai-guide.md) A comprehensive analysis of OpenAI's guide to building agents, covering foundational concepts, orchestration patterns, and implementation best practices for creating autonomous AI systems. [[AI Development & Agents/building-effective-ai-agents-openai-guide]] ### [The Expert Conductor Prompt: A Comparative Analysis of LLM Reasoning Patterns](AI%20Systems%20&%20Architecture/expert-conductor-prompt-llm-comparison.md) A comparative analysis of how Claude Sonnet 3.7, Gemini 2.5 Pro, and OpenAI o3 respond to the innovative Expert Conductor prompt, revealing distinct reasoning patterns and capabilities across these leading LLMs. [[AI Systems & Architecture/expert-conductor-prompt-llm-comparison]] ### [OpenAI's o3 and o4-mini: Business Impact of Advanced Reasoning Models](Cutting-Edge%20AI/openai-o3-o4-mini-codex-release-analysis.md) A comprehensive analysis of OpenAI's new o3 and o4-mini models with enhanced reasoning capabilities, featuring insights from the AI community and strategic implications for businesses. [[Cutting-Edge AI/openai-o3-o4-mini-codex-release-analysis]] ### [GPT-4.1 Technical Analysis: API-Only Release Signals OpenAI's Agent-First Strategy](Cutting-Edge%20AI/gpt-4-1-release-technical-analysis.md) A technical analysis of OpenAI's GPT-4.1 release, comparing it with Claude, Gemini, and Llama 4, with special focus on its agent capabilities and API-only strategy. [[Cutting-Edge AI/gpt-4-1-release-technical-analysis]] ### [Advanced Prompt Engineering for Oncology Data Science: Techniques for Robust AI Systems](AI%20Systems%20&%20Architecture/advanced-prompt-engineering-oncology-ds.md) A technical deep dive into advanced prompt engineering techniques (CoT, ReAct, Structured Outputs) tailored for oncology data scientists to build more accurate and reliable AI-driven analysis systems. [[AI Systems & Architecture/advanced-prompt-engineering-oncology-ds]] ### [Unlock AI's Full Potential: Why Prompt Engineering is Your Business Superpower](Practical%20Applications/unlocking-ai-value-with-prompt-engineering.md) Go beyond basic AI interactions. Learn how mastering prompt engineering techniques translates directly into better, more reliable AI outputs that drive real business results. [[Practical Applications/unlocking-ai-value-with-prompt-engineering]] ### [Elevating Prompt Engineering with Integrated Tools](Practical%20Applications/elevating-prompt-engineering-with-integrated-tools.md) How building integrated prompt refinement tools transforms the way developers interact with LLMs, streamlining workflows through the power of concept elevation. [[Practical Applications/elevating-prompt-engineering-with-integrated-tools]] ### [AgentRxiv: Enabling Automated Toolkit Selection for AI Agents](AI%20Systems%20&%20Architecture/agentrxiv-automated-toolkit-selection.md) An analysis of how AgentRxiv's collaborative research platform can revolutionize automated toolkit selection for AI agents, enhancing system adaptability and performance. [[AI Systems & Architecture/agentrxiv-automated-toolkit-selection]] ### [A Technical Deep Dive into the AI-2027 Scenario: Capabilities, Alignment, and Geopolitics](Cutting-Edge%20AI/analyzing-the-ai-2027-scenario.md) A technical analysis of the AI-2027 scenario, examining its predictions for AI capabilities, alignment challenges, and the geopolitical landscape through 2027. [[Cutting-Edge AI/analyzing-the-ai-2027-scenario]] ### [Manus.im vs MyManus: A Technical Deep Dive into AI Agent System Architecture](AI%20Systems%20%26%20Architecture/manus-vs-mymanus-system-architecture.md) A comprehensive technical comparison of Manus.im and MyManus system architectures, revealing how similar core components can serve different deployment models. [[AI Systems & Architecture/manus-vs-mymanus-system-architecture]] ### [Inside Manus.im: The Elegant Architecture Behind a Powerful AI Agent](AI%20Systems%20&%20Architecture/manus-im-system-architecture.md) A technical deep dive into the system architecture of Manus.im, revealing how its elegant prompt engineering and tool design enable sophisticated autonomous capabilities. [[AI Systems & Architecture/manus-im-system-architecture]] ### [The Business Edge of AI Code Generation: Comparing LLM-Generated To-Do Apps](Cutting-Edge%20AI/llm-code-generation-comparison.md) A deep technical analysis of to-do applications generated by five leading AI models, revealing key insights about code quality, architectural choices, and business implications. [[Cutting-Edge AI/llm-code-generation-comparison]] ### [AI Agent Platforms for Pharmaceutical R&D: Executive Summary](AI%20Systems%20&%20Architecture/ai-agent-platforms-pharma-rd-comparison.md) A strategic comparison of AI agent platforms tailored for pharmaceutical R&D leaders, focusing on regulatory compliance, data security, and scientific workflow integration. [[AI Systems & Architecture/ai-agent-platforms-pharma-rd-comparison]] ### [AI Task Completion Length Doubles Every 7 Months: Implications for the Future of Work](Emerging%20Trends/ai-task-doubling.md) Analysis of METR's groundbreaking research showing AI task completion capabilities double every 7 months, with projections suggesting AI could handle multi-day software projects by 2028. [[Emerging Trends/ai-task-doubling]] ### [DeepSeek V3-0324: Business Impact of Open-Source AI at Scale](Cutting-Edge%20AI/deepseek-v3-0324-technical-review.md) An in-depth analysis of DeepSeek V3-0324, examining how this 685B parameter open-source model is reshaping enterprise AI strategies and challenging proprietary incumbents. [[Cutting-Edge AI/deepseek-v3-0324-technical-review]] ### [Claude's Think Tool: A Technical Deep Dive and Cross-Model Analysis](Cutting-Edge%20AI/claude-think-tool-technical-review.md) A comprehensive technical analysis of Anthropic's Think Tool for Claude, examining its architecture, performance, and potential adaptation to other large language models. ### [Hybrid Deployment: Vercel for Frontend, Render/Digital Ocean for Full-Stack Python](Practical%20Applications/hybrid-deployment-vercel-render-digitalocean.md) A practical guide to leveraging Vercel's frontend optimization capabilities while deploying Python backends on Render or Digital Ocean for full-stack applications. ### [Agent Architectures with Model Context Protocol](AI%20Systems%20&%20Architecture/agent-architectures-with-mcp.md) A technical survey of architectural patterns for implementing AI agents with Model Context Protocol, comparing frameworks and integration approaches. ### [Transforming AI Research into Interactive Apps](Practical%20Applications/transforming-research-into-interactive-app.md) Transform ChatGPT-o1 Pro research into dynamic web applications. A case study on building visualization tools for clinical trials data. ### [Building a Markdown RAG System](AI%20Systems%20&%20Architecture/building-markdown-rag-system.md) Create a lightweight Retrieval-Augmented Generation system for markdown documents with practical search strategies. ### [Implementing Model Context Protocol](AI%20Systems%20&%20Architecture/model-context-protocol-implementation.md) Guide to implementing MCP across Roo Code, Cline, and Cursor with best practices and examples. ### [Roo Code + GitHub Copilot Setup](Practical%20Applications/roo-code-github-copilot-setup.md) Configure Roo Code with GitHub Copilot for enterprise-compliant AI assistance using Claude 3.7 Sonnet. ### [Manus.im vs. CAMEL-AI/OWL](AI%20Development%20&%20Agents/manus-im-vs-camel-ai-owl.md) Technical comparison of autonomous AI agent platforms, examining architecture and capabilities. ### [Cline and Roo Code Quick Start](Practical%20Applications/cline-roo-code-quick-start.md) Get started with Cline and Roo Code - installation, features, automation, and optimization techniques. ### [Creating Custom Modes in Roo Code](AI%20Systems%20&%20Architecture/custom-modes-quick-start.md) Build specialized AI agents for your development workflow using Roo Code's custom modes. ### [Technical Article Garden with Obsidian](Practical%20Applications/obsidian-publish-article-garden.md) Set up and maintain a technical knowledge base using Obsidian Publish. ## Topic Areas <div class="topic-area"> ### 🤖 AI Development & Agents - Autonomous Systems - Multi-Agent Architectures - Tool-Using AI - AI-Enhanced Development </div> <div class="topic-area"> ### 🧠 Cutting-Edge AI - Large Language Models - AI Reasoning Systems - Emergent Behaviors - Infrastructure & Scaling </div> <div class="topic-area"> ### 🏗️ AI Systems & Architecture - Agent Frameworks - Cognitive Architectures - Memory Systems - System Design Patterns </div> <div class="topic-area"> ### 💡 Practical Applications - Research Automation - Development Tools - Data Analysis - System Design </div> <div class="topic-area"> ### 🌱 Emerging Trends - Constitutional AI - Agentic Solutions - AI-Human Collaboration - Ethics & Alignment </div> ## About This Garden > This is a growing collection of interconnected notes and articles about artificial intelligence, focusing on practical applications and emerging capabilities. The content evolves as new insights and developments emerge. ### How to Navigate - Use the quick navigation links above - Follow topic areas that interest you - Explore interconnected ideas through wiki-links - Check recent articles for latest additions ### Connect & Discuss - Twitter: [@bioinfo](https://twitter.com/bioinfo) - Blog: [rundatarun.io](https://rundatarun.io) - Obsidian Publish: [publish.obsidian.md/aixplore](https://publish.obsidian.md/aixplore) --- *This digital garden is maintained in [[about/obsidian|Obsidian]] and published using Obsidian Publish. Last updated: April 17, 2025*