bio-orchestrator

What This Skill Does

The bio-orchestrator acts as the central intelligence layer within the OpenClaw ecosystem for all bioinformatics tasks. It serves as a meta-agent designed to streamline complex computational biology workflows by automatically identifying input data formats, determining the optimal analysis path, and coordinating between specialized sub-skills. Whether you are dealing with genomics (VCF/FASTQ/BAM), proteomics (PDB), or single-cell transcriptomics (h5ad), the bio-orchestrator handles the heavy lifting of dependency verification, tool execution planning, and output synthesis. By maintaining an audit log and generating structured markdown reports complete with reproducibility metadata, it ensures that your scientific results are not only accurate but also traceable and verifiable.

Installation

To integrate the bio-orchestrator into your OpenClaw environment, use the primary package manager: clawhub install openclaw/skills/skills/manuelcorpas/clawbio-orchestrator. Ensure that your environment has sufficient permissions to write to your working directory, as the orchestrator generates logs and reports automatically during its runtime.

Use Cases

• Genomic Variant Analysis: Automatically route VCF files to the equity-scorer for population diversity metrics or the vcf-annotator for biological impact assessments.
• Multi-step Pipeline Execution: Chain operations such as aligning FASTQ reads via seq-wrangler followed by structure prediction on a resulting protein sequence via struct-predictor.
• Scientific Reproducibility: Generate full analysis summaries that include software versions, command histories, and data checksums for publication or internal auditing.
• Literature Integration: Contextualize your findings by cross-referencing analysis outputs with relevant research papers using the integrated lit-synthesizer.

Example Prompts

1. "I have a folder containing a patient's BAM files and a VCF. Please perform quality control, annotate the variants for clinical significance, and generate a final reproducibility report."
2. "Perform a structure prediction on the BRCA1 protein sequence stored in this PDB file and compare the output to the existing AlphaFold database entries."
3. "Summarize the recent literature regarding single-cell clustering methods for my h5ad object and suggest the best workflow to identify marker genes."

Tips & Limitations

• Tip: Always place your data files in a consistent directory structure to allow the orchestrator to resolve paths reliably.
• Tip: Use the 'Make reproducible' trigger if you need to export your current workflow into a containerized format like Nextflow or Singularity for high-performance computing clusters.
• Limitation: The orchestrator relies on the availability of downstream skills; if a required tool (e.g., samtools) is not installed on your system path, the orchestrator will prompt you to install dependencies before it can proceed with execution.