Anndata Workshop

BioContextAI - Registry Tests Documentation

A very interesting piece of code

Getting started

Please refer to the documentation, in particular, the API documentation.

You can also find the project on BioContextAI, the community-hub for biomedical MCP servers: anndata-mcp-workshop on BioContextAI.

Installation

You need to have Python 3.10 or newer installed on your system. If you don't have Python installed, we recommend installing uv.

There are several alternative options to install anndata-mcp-workshop:

1. Use uvx to run it immediately

After publication to PyPI:

uvx anndata_mcp_workshop

Or from a Git repository:

uvx git+https://github.com/dschaub95/anndata-mcp-workshop.git@main

2. Include it in one of various clients that supports the mcp.json standard

If your MCP server is published to PyPI, use the following configuration:

{
  "mcpServers": {
    "anndata-mcp-workshop": {
      "command": "uvx",
      "args": ["anndata_mcp_workshop"]
    }
  }
}

In case the MCP server is not yet published to PyPI, use this configuration:

{
  "mcpServers": {
    "anndata-mcp-workshop": {
      "command": "uvx",
      "args": ["git+https://github.com/dschaub95/anndata-mcp-workshop.git@main"]
    }
  }
}

For purely local development (e.g., in Cursor or VS Code), use the following configuration:

{
  "mcpServers": {
    "anndata-mcp-workshop": {
      "command": "uvx",
      "args": [
        "--refresh",
        "--from",
        "path/to/repository",
        "anndata_mcp_workshop"
      ]
    }
  }
}

If you want to reuse and existing environment for local development, use the following configuration:

{
  "mcpServers": {
    "anndata-mcp-workshop": {
      "command": "uv",
      "args": ["run", "--directory", "path/to/repository", "anndata_mcp_workshop"]
    }
  }
}

3. Install it through pip:

pip install --user anndata_mcp_workshop

4. Install the latest development version:

pip install git+https://github.com/dschaub95/anndata-mcp-workshop.git@main

Contact

If you found a bug, please use the issue tracker.

Citation

t.b.a