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databricks-industry-solutions/vital-skills

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Health & Life Sciences agent skills for Databricks Genie Code: genomics, RWE cohorts, PHI de-identification, payer/provider measures, and skill evaluation

Overview

Each skill is a SKILL.md folder that teaches Genie Code following the Agent Skills standard) how to run domain workflows with libraries, tools and MCP servers. Site: https://databricks-industry-solutions.github.io/vital-skills/ Git clone this repo onto Databricks. Then open Genie Code and click on Customizations to add the cloned folder. It should point to the skills subfolder Run sync_skills_git2unity.py to sync the latest skills from the repo to Unity Catalog. They also show up on Unity Gateway under Skills. On Databricks, start Serverless or a cluster (>= 15.0 runtime) for compute. Then open the terminal (how-to-guide). It should already have the Databricks CLI installed. You can get the SQL warehouse id from the Databricks left menu bar: SQL Warehouses > select warehouse > Name. It should list the warehouse ID. More details here. Repo layout and skill templates are inspired by the patterns in SciAgent-Skills Licensed under the Databricks License. See LICENSE.md and NOTICE.

README

Vital Skills

Agent skills for Health & Life Sciences workflows.

Each skill is a SKILL.md folder that teaches Genie Code following the Agent Skills standard) how to run domain workflows with libraries, tools and MCP servers.

Site: https://databricks-industry-solutions.github.io/vital-skills/

Setup

Git clone this repo to Databricks

Git clone this repo onto Databricks. Then open Genie Code and click on Customizations to add the cloned folder. It should point to the skills subfolder

Available Skills

Skill Category What it does
bulk-rnaseq Bioinformatics Find top differentially expressed genes from bulk RNA-seq counts.
open-weight-models Bioinformatics Package, register, validate & deploy open-weight HLS models on Databricks, such as TEDDY and Geneformer.
pathway-enrichment-analysis Bioinformatics Pathway enrichment for RNA-seq (ORA or GSEA).
sc-rnaseq Bioinformatics Analyze single-cell RNA-seq data from .h5ad files.
cohort-builder Clinical Build a reproducible, feasibility-checked patient cohort from coded + free-text clinical data.
phi-deidentifier Clinical HIPAA Safe-Harbor de-identify a Unity Catalog table (k-anonymity + governed view).
rwe-cohortstudy Clinical Comparative effectiveness (cohort study) with propensity adjustment (matching, IPW).
semantic-builder Clinical Canonical payer+provider measure catalog mapped to Unity Catalog metric views.
accelerators Others Route imaging, biology-model and HL7v2 tasks to an HLS accelerator (Pixels, Genesis Workbench or funke-hl7v2) with the exact next step.
presentation-builder Others Turn a cohort, dataset, model, or analysis into a grounded, shareable HTML deck (PHI de-id delegated to phi-deidentifier).
report-builder Others LaTeX report generation and PDF compilation from analysis notebooks via Tectonic.
scientific-figures Others Publication-quality scientific and biopharma figures for notebooks, apps, and reports.
skill-eval Others Benchmark a skill: paired runs with/without it, MLflow genai.evaluate scoring, win/loss + failure taxonomy.

Repository Layout

vital-skills/
├── AGENTS.md                 # Skill authoring guide
├── CLAUDE.md                 # Compatibility shim → AGENTS.md
├── templates/                # Pipeline / toolkit / guide templates
└── skills/
    ├── bulk-rnaseq/
    ├── cohort-builder/
    └── …

Each skill:

skills//
├── SKILL.md          # Required
├── references/       # Optional — loaded on demand
├── assets/           # Optional
└── scripts/          # Optional

Creating a Skill

See CONTRIBUTING.md.

Repo layout and skill templates are inspired by the patterns in SciAgent-Skills

License

Licensed under the Databricks License. See LICENSE.md and NOTICE.md.

Disclaimer

This is an open source solution to provide agent skills to assist with healthcare and life sciences tasks. However, all compliance obligations remain with the user. This includes but is not limited to:

  • HIPAA: You are responsible for ensuring your deployment meets HIPAA requirements (encryption, access controls, audit logging, BAAs, etc.)
  • GDPR, CCPA, and other privacy regulations: Evaluate whether your use of this tool satisfies applicable data protection laws
  • Validation: You must verify that results are complete and accurate for your specific data and use case
  • Data Encryption: Enable encryption at rest and in transit in your Databricks workspace
  • Access Controls: Configure appropriate table/catalog permissions in Unity Catalog
  • Audit Logging: Enable workspace audit logs for compliance tracking

Databricks makes no guarantees that use of this solution alone is sufficient for regulatory compliance

Contributors

To add yourself, see CONTRIBUTING.md.

Acknowledgements

Thanks to Eli Swanson, Douglas Moore, Parastou Eslami and Khagay Nagdimov for their advice.

View the full README on GitHub

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Install

npx skillfish add databricks-industry-solutions/vital-skills
New to MCP? Start with the mcpskill.org guide →