MAGELLAN: A 15-Agent Autonomous Scientific Discovery System Built on Claude Code

System Architecture and Implementation

MAGELLAN is built entirely on Claude Code with 15 custom agents defined in .claude/agents/, coordinated by an orchestrator. The system uses model pinning: each agent has model: opus or model: sonnet in frontmatter to guarantee effort levels regardless of session settings.

Opus handles deep cross-domain reasoning through four agents: Scout, Generator, Critic, and Quality Gate. Sonnet handles structured tasks through three agents: Literature Scout, Ranker, and Computational Validator.

Workflow and Patterns

The orchestrator (Opus with 200-turn circuit breaker) dispatches to sub-agents and never executes phases inline. The system implements reflection loops via agent prompts: SELF-CRITIQUE (Generator), META-CRITIQUE (Critic), and TARGET QUALITY CHECK (Scout).

Adaptive cycles adjust based on results: early completion if top-3 hypotheses score >= 7.0, extension to cycle 3 if survival rate is < 30%. After the pipeline, cross-model validation occurs via bash scripts calling GPT-5.4 and Gemini 3.1 APIs for independent review.

Results and Availability

After 19 sessions, the system has proposed approximately 260 hypotheses, with about 60% killed by the adversarial pipeline. All results are available on the project website with full methodology.

The system is open source under Apache 2.0 license. The Claude Code pipeline details, discoveries, and contribution information are available through the project links.