BaseCamp --- An Agentic AI Framework for Automating DNA Sequencing Data Pipelines

arXiv:2609.28557 · cs.AI, q-bio.GN · Submitted 2026-09-23 · Read on arXiv

cs.AI, q-bio.GN

Submitted: 2026-09-23

Updated: 2026-09-23

Terminology

• Alignment — 57× in this paper · explained in 1 episode
• Agentic AI — 45× in this paper · explained in 1 episode
• Fine-Tuning — 22× in this paper · explained in 5 episodes
• AI Agents — 13× in this paper · explained in 2 episodes
• Trace — 10× in this paper · explained in 2 episodes
• Agentic AI Framework — 9× in this paper · explained in 1 episode
• Agentic AI systems — 7× in this paper · explained in 1 episode
• Human-in-the-Loop — 7× in this paper · explained in 3 episodes
• Model Context Protocol — 7× in this paper
• Accuracy — 6× in this paper · explained in 1 episode
• Core — 6× in this paper · explained in 2 episodes
• Model Context Protocol (MCP) — 5× in this paper · explained in 8 episodes
• Provenance — 4× in this paper · explained in 4 episodes
• Agentic Reasoning — 3× in this paper · explained in 1 episode
• Agentic Workflows — 3× in this paper · explained in 1 episode
• Accountability — 2× in this paper · explained in 2 episodes
• Adaptation — 2× in this paper · explained in 1 episode
• Agentic AI Workflows — 2× in this paper · explained in 1 episode
• Benchmark — 2× in this paper · explained in 2 episodes
• Consistency — 2× in this paper · explained in 3 episodes
• Explainability — 2× in this paper · explained in 3 episodes
• Explainable AI (XAI) — 2× in this paper · explained in 7 episodes
• Generative AI — 2× in this paper · explained in 2 episodes
• Reasoning Traces — 2× in this paper · explained in 3 episodes
• Ablation — 1× in this paper · explained in 1 episode
• Actionability — 1× in this paper · explained in 3 episodes
• Adam — 1× in this paper · explained in 2 episodes
• Agent Interactions — 1× in this paper · explained in 1 episode
• Agentic System — 1× in this paper · explained in 2 episodes
• Alignment Problem — 1× in this paper · explained in 1 episode
• Contextual Awareness — 1× in this paper · explained in 2 episodes
• Downstream Tasks — 1× in this paper · explained in 2 episodes
• Hallucination — 1× in this paper · explained in 4 episodes
• Interpretability — 1× in this paper · explained in 15 episodes
• LLM Integration — 1× in this paper · explained in 2 episodes
• Large Language Models (LLMs) — 1× in this paper · explained in 6 episodes
• Modularity — 1× in this paper · explained in 9 episodes
• Multi-Agent System — 1× in this paper · explained in 6 episodes
• Scaffolding — 1× in this paper · explained in 3 episodes
• Transformer — 1× in this paper · explained in 2 episodes
• Verifiability — 1× in this paper · explained in 2 episodes
• Verification — 1× in this paper · explained in 2 episodes

Sources

• AI Agents vs. Agentic AI: A Conceptual Taxonomy, Applications and Challenges
• Survey on Evaluation of LLM-based Agents
• A Practical Guide to Agentic AI Transition in Organizations
• A Practical Guide for Designing, Developing, and Deploying Production-Grade Agentic AI Workflows
• Towards Responsible and Explainable AI Agents with Consensus-Driven Reasoning
• Model Context Protocol (MCP): Landscape, Security Threats, and Future Research Directions
• Model Context Protocol (MCP) at First Glance: Studying the Security and Maintainability of MCP Servers
• Model Context Contracts - MCP-Enabled Framework to Integrate LLMs With Blockchain Smart Contracts
• LLM as a Mastermind: A Survey of Strategic Reasoning with Large Language Models
• gpt-oss-120b & gpt-oss-20b Model Card
• Language Models Enable Simple Systems for Generating Structured Views of Heterogeneous Data Lakes
• A New Era in LLM Security: Exploring Security Concerns in Real-World LLM-based Systems
• Understanding the planning of LLM agents: A survey
• A Tutorial on LLM Reasoning: Relevant Methods behind ChatGPT o1
• The Llama 3 Herd of Models
• Qwen2-VL: Enhancing Vision-Language Model's Perception of the World at Any Resolution
• Agentsway -- Software Development Methodology for AI Agents-based Teams
• The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery
• Train the Trainers -- An Agentic AI Framework for Peer-Based Mental Health Support in Battlefield Environments
• VTutor: An Open-Source SDK for Generative AI-Powered Animated Pedagogical Agents with Multi-Media Output

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