Bio-OS Navigen Agent

The Bio-OS Navigen Agent is a specialized, intelligent assistant designed to operate on the Bio-OS platform. It empowers users to perform complex biomedical big data analysis through natural language interaction, bridging the gap between scientific intent and computational execution.

Project Status

Important

Current Phase: V1 Release (Agent SKILLs Edition)

Bio-OS Navigen has evolved into a fully modular, plug-and-play 3-Tier Agent Capability Architecture.

Tier	Abstraction Layer	Core SKILLs
Tier 1	Atomic Capabilities Focused, script-backed tools (Data fetching, environment building).	bioos_data_fetcher, bioos_docker_builder, bioos_wdl_scripter, bioos_workspace_parser, bioos_platform_operator
Tier 2	Core Workflows Orchestrators for building pipelines or complex sub-routines.	bioos_pipeline_developer
Tier 3	Business Modes / SOPs High-level intent handlers that orchestrate Tiers 1 and 2.	bioos_paper2workspace, bioos_workspace2paper

Core Features

• Tripartite Expertise: Acts as a Bioinformatics Scientist, Automation Engineer, and Bio-OS Platform Specialist.
• Standards-Compliant: Strictly adheres to unified standards for Dockerfiles, WDL scripts, log formats, and error handling.
• Agentic Workflow: Autonomous planning, execution, and verification of tasks across different modes.

Development

The system prompt is maintained in a modular format under system_prompt/ and compiled into a single file GEMINI.md for deployment.

Deployment Options

To use Bio-OS Navigen, configure your preferred agent (e.g., Cline, Cursor, Google Antigravity) with the bioos-mcp-server.

Then, provide the Navigen instructions to your agent using one of the following methods:

1. Agent SKILLs (Recommended): Copy the entire skills/ directory into your agent's designated workspace or .agent/skills folder. This leverages the new modular 3-Tier architecture.
2. Single File GEMINI.md: For agents supporting only a single system prompt, use the compiled monolithic file.
3. Modular system_prompt/: For general agents supporting multiple prompt imports.

Contact

For feedback or issues during the trial phase, please contact the development team.