Audit History

Most markdown and reference-link detections are false positives, but the skill has real operational risk. It handles API credentials, writes local setup files, and documents Biomni workflows that can execute LLM-generated code with broad local privileges.

Most markdown and reference-link detections are false positives, but the skill has real operational risk. It handles API credentials, writes local setup files, and documents Biomni workflows that can execute LLM-generated code with broad local privileges.

Static analysis produced many hits, and most Markdown backtick, weak-crypto, C2, and hardcoded-URL detections are false positives from documentation examples. However, the skill intentionally supports autonomous LLM-generated code execution, external MCP tools, local file writes, and API key storage, so it should not be published without strong warnings and sandbox guidance.

The static analysis flagged 415 patterns, but 95% are FALSE POSITIVES from markdown documentation. The backtick patterns are markdown code delimiters, not shell execution. The API key patterns show example environment variable names in documentation, not actual secrets. The skill is a legitimate Stanford SNAP lab biomedical research framework. The code execution + network + credential combination is the intended design for an AI agent that generates bioinformatics analysis code. Proper security warnings are documented recommending sandboxed execution.

The static analysis flagged 415 patterns, but 95% are FALSE POSITIVES from markdown documentation. The backtick patterns are markdown code delimiters, not shell execution. The API key patterns show example environment variable names in documentation, not actual secrets. The skill is a legitimate Stanford SNAP lab biomedical research framework. The code execution + network + credential combination is the intended design for an AI agent that generates bioinformatics analysis code. Proper security warnings are documented recommending sandboxed execution.

Biomni is a legitimate biomedical research framework from Stanford that requires code execution capabilities for its core functionality. While static analysis flags many security patterns, these are necessary for an AI agent that generates and executes analysis code. The skill includes proper security warnings and recommends sandboxed execution.

This skill provides documentation and helper scripts for the biomni biomedical AI framework. The setup script runs external commands (conda) and writes API keys to .env files, which are legitimate setup operations but expand the attack surface. No evidence of obfuscation, credential theft, or malicious network calls.