---
name: skills-hub-675dc1305450
description: Browse and install community skills from the BioClaw Skills Hub. Use when a user's task is not covered by built-in skills, or when the user asks about available skills, advanced workflows, or specialized analysis pipelines. Triggers on "skills hub", "more skills", "install skill", "community skills", "find a skill for".
---

# Skills Hub Browser

Search, browse, and install community-contributed skills from the [BioClaw Skills Hub](https://github.com/zongtingwei/Bioclaw_Skills_Hub).

The Hub contains 70+ specialized bioinformatics skills organized into domains. Skills downloaded from the Hub are cached locally so they persist for the rest of the session.

## When to Use

- User requests an analysis not covered by the built-in skills listed in your system prompt
- User asks "what other skills are available" or "do you have a skill for X"
- User needs a specialized pipeline (e.g., protein design, EHR analysis, spatial transcriptomics workflows beyond the built-in)

## Hub Structure

The Hub organizes skills into these domains:

| Domain | Examples |
|--------|----------|
| `core-bioinformatics` | alignment-and-mapping, read-qc, sequence-io, database-access |
| `transcriptomics` | bulk-rna-expression, differential-expression |
| `single-cell-and-spatial` | scrna-preprocessing, spatial-transcriptomics, cell-annotation |
| `epigenomics-and-regulation` | atac-seq, chip-seq, dna-methylation |
| `genomics-and-variation` | variant-calling, genome-assembly, long-read-genomics |
| `metagenomics-and-microbiome` | metagenomics, phylogenetics, microbial-community |
| `proteomics-and-metabolomics` | mass-spec, metabolomics |
| `multi-omics-and-systems` | multi-omics-integration, pathway-analysis |
| `protein-design` | alphafold2-multimer, proteinmpnn, rfdiffusion, boltzgen |
| `ehr-analysis` | electronic health record analysis |

## How to Execute

### Step 1: Fetch the taxonomy (skill index)

```bash
curl -sL "https://raw.githubusercontent.com/zongtingwei/Bioclaw_Skills_Hub/main/catalog/taxonomy.yaml"
```

This returns the full skill catalog organized by domain. Use it to find the skill name that matches the user's need.

### Step 2: List skills in a specific domain

```bash
curl -sL "https://api.github.com/repos/zongtingwei/Bioclaw_Skills_Hub/contents/skills/<domain>" | python3 -c "
import json, sys
for item in json.load(sys.stdin):
    if item['type'] == 'dir':
        print(item['name'])
"
```

Replace `<domain>` with a domain name from the table above.

### Step 3: Download and read a skill

```bash
# Download the SKILL.md
DOMAIN="<domain>"
SKILL="<skill-name>"
CACHE_DIR="/workspace/group/.hub-skills/${SKILL}"
mkdir -p "${CACHE_DIR}"
curl -sL "https://raw.githubusercontent.com/zongtingwei/Bioclaw_Skills_Hub/main/skills/${DOMAIN}/${SKILL}/SKILL.md" \
  -o "${CACHE_DIR}/SKILL.md"
```

Then read the downloaded skill:
```
read_file({ file_path: "/workspace/group/.hub-skills/<skill-name>/SKILL.md" })
```

### Step 4: Install dependencies (if needed)

Some Hub skills require extra Python packages. Check the SKILL.md for a "Preferred Tools" or "Dependencies" section. Install with:

```bash
pip install <package> --quiet 2>/dev/null
```

### Step 5: Execute the skill

Follow the workflow described in the downloaded SKILL.md, just like any built-in skill.

## Important Notes

- Always check built-in skills first before fetching from the Hub
- Downloaded skills are cached in `/workspace/group/.hub-skills/` for the session
- The Hub is a community resource — skills may reference tools not installed in the container; install them with pip/apt as needed
- If GitHub is unreachable, inform the user and suggest using built-in skills instead


---
Source attribution: Runchuan-BU
Original project: https://github.com/Runchuan-BU/BioClaw
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

MIT License

Copyright (c) 2026 Gabriel Moreira

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: Runchuan-BU
Original project: https://github.com/Runchuan-BU/BioClaw
Attribution basis: Upstream repository explicitly recorded in package mirror path

Fields of work: Data & Analytics, Development & Engineering, Education & Research, Product Management
Roles: Data Scientist, Growth Product Manager, ML / AI Engineer, Product Manager, Researcher
Specialties: API
Tools: GitHub, Python
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: ee6dd46443959e55796b57fdd6044256644f519c100a2154e9adde5b05b15425