bio-orchestrator

What problem does it solve?

The Bio Orchestrator routes diverse bioinformatics requests to specialised sub-skills, removing the burden of manual skill selection, file-format detection, and multi-step workflow assembly so users can focus on scientific questions instead of tooling logistics.

Core Features & Use Cases

• File Type Detection & Routing: Detects common bioinformatics file types (VCF, FASTQ, BAM, PDB, h5ad, CSV) and routes them to the appropriate specialised skill.
• Multi-Step Analysis Planning: Plans and chains multiple skills for complex workflows (e.g., annotate VCF then compute diversity metrics) with dependency checks and human checkpoints.
• Report Generation & Reproducibility: Produces structured markdown reports with methods, results, figures, citations, reproducibility bundles (conda environment, commands, checksums), and an audit log.
• Safety & Governance: Enforces local-first policies, explicit consent for uploads, path validation, and audit logging to prevent accidental data exfiltration or destructive actions.

Quick Start

Route sample.vcf for annotation and diversity scoring and produce a reproducible markdown report.