bioskills

What This Skill Does

The bioSkills meta-skill is a comprehensive suite designed to transform an OpenClaw agent into a high-powered bioinformatics workstation. It serves as an umbrella installer for 425 specialized skills organized across 62 distinct categories. Instead of installing individual bioinformatics tools manually, bioSkills handles the deployment of the entire ecosystem required for complex biological data analysis. It covers the full spectrum of modern omics research, ranging from foundational sequence alignment and read processing to advanced, cutting-edge fields like single-cell transcriptomics, structural biology, spatial genomics, and multi-omics integration. By installing this package, your agent gains the ability to interpret raw sequencing data, manage complex biological databases, perform statistical differential expression analysis, and execute end-to-end bioinformatics workflows.

Installation

To deploy the full suite, execute the following command in your terminal:

bash scripts/install-bioskills.sh

For users who prefer a modular approach to save storage or focus on specific pipelines, you can install selected categories by providing a comma-separated list:

bash scripts/install-bioskills.sh --categories "single-cell,variant-calling,differential-expression"

Alternatively, you can install directly via the OpenClaw hub: clawhub install openclaw/skills/skills/djemec/bioskills.

Use Cases

bioSkills is designed for researchers, bioinformaticians, and lab managers who need to automate data-heavy pipelines. Use this when you are performing primary analysis on FASTQ files, secondary analysis such as differential expression or variant calling, or tertiary analysis involving pathway mapping and systems biology. It is particularly effective for high-throughput screen analysis, such as CRISPR-Cas9 libraries or single-cell experiments where standard desktop software lacks the computational integration required for large-scale datasets.

Example Prompts

1. "I have RNA-seq counts from treated vs control samples. Please perform a differential expression analysis and generate a volcano plot."
2. "Cluster my single-cell RNA-seq data from the provided h5ad file and identify marker genes for each cluster."
3. "Predict the 3D structure of this protein sequence and identify potential binding pockets for small molecule docking."

Tips & Limitations

• Resource Allocation: Because bioSkills covers 425 distinct tools, initial installation may take considerable time depending on your internet connection and local build environment.
• Dependency Management: Ensure your environment has sufficient disk space, as some metagenomics and structural biology databases (like AlphaFold weights) can be large.
• Task Context: While the skill handles execution, always provide the specific file formats (BAM, FASTQ, VCF, etc.) needed for your analysis to ensure the agent selects the correct sub-skill.
• Security: Since this skill installs and executes external bioinformatics packages, ensure you are pulling from trusted repositories to prevent supply-chain vulnerabilities.