CLIO Seismology

CLIO Kit

CLIO Kit is the IoWarp meta-marketplace for scientific computing. It brings together MCP servers, workflow skills, plugins, agent definitions, and community contributions—including plugins from external marketplaces—and enables AI agents to interact with HPC resources, scientific data formats, and research datasets.

Choose individual MCPs, skills, agents and hooks—or a plugin that bundles what your workflow needs. A plugin can include any of these components; it does not need all four.

Website | IOWarp

Documentation · For agents: read here.

Chat with us on Zulip or join us

Developed by Gnosis Research Center

---

❌ Without CLIO Kit

Working with scientific data and HPC resources requires manual scripting and tool-specific knowledge:

• ❌ Write custom scripts for every HDF5/Parquet file exploration
• ❌ Manually craft Slurm job submission scripts
• ❌ Switch between multiple tools for data analysis
• ❌ No AI assistance for scientific workflows
• ❌ Repetitive coding for common research tasks

✅ With CLIO Kit

Install workflow bundles, use skills to guide your agent, and discover community tools:

• ✅ "Analyze the temperature dataset in this HDF5 file" - HDF5 MCP does it
• ✅ "Submit this simulation to Slurm with 32 cores" - Slurm MCP handles it
• ✅ "Find papers on neural networks from ArXiv" - ArXiv MCP searches
• ✅ "Plot the results from this CSV file" - Plot MCP visualizes
• ✅ "Optimize memory usage for this pandas DataFrame" - Pandas MCP optimizes
• ✅ Workflow guidance - Skills explain tool sequences; optional agents help plan and review results
• ✅ Community contributions - Discover external plugins and marketplace collections

MCP servers · Skills · Plugins · Agents · Hooks · Community marketplaces

CLIO Kit is part of the IoWarp platform's tooling ecosystem for AI agents. Its meta-marketplace brings tools and reusable workflows together for scientific computing—from exploring HDF5 datasets and managing Slurm jobs to analyzing results and finding research papers. Built by researchers, for researchers, at Illinois Institute of Technology with NSF support.

Part of IoWarp Platform: CLIO Kit is the platform's meta-marketplace and tooling layer, bringing together MCP servers, skills, workflow plugins, agent definitions, and community marketplace collections.

One launcher for MCP servers. Individual components or workflow bundles. BSD-3-Clause licensed, with automated checks and real installation, MCP, and HPC workflow tests. See the validation guide for tested coverage and environment requirements.

🚀 Quick Installation

git clone https://github.com/iowarp/clio-kit.git

cd clio-kit

Recommended: Ask your agent:

Read setup.md and set up CLIO Kit for me.

Manual setup: Install this checkout's launcher, then choose an option below. For the no-clone release route (2.11.0 or newer), see selective installation.

uv tool install --force --reinstall --editable ".[verification]"

Claude Code

Install a workflow plugin (bundle) with its MCP servers and skills:

claude plugin marketplace add "$PWD"

claude plugin install clio-hpc@clio-kit claude mcp list

Restart Claude Code after installation and confirm the servers connect. First launches download dependencies; see startup recovery if a server exceeds the client's connection timeout.

Or install an individual MCP or a skill collection:

claude plugin install clio-hdf5@clio-kit                  # HDF5 server

claude plugin install clio-scientific-io-skills@clio-kit # Scientific I/O skills

Claude Code uses plugin install for component packages too. CLIO Kit lists those separately from workflow plugins; see components and plugins.

Codex and Other Agents

Install a workflow's skills and MCP configuration together:

clio-kit plugin install clio-scientific-io --client codex --project /path/to/project

Also supports opencode, cursor, antigravity, vscode and claude-code. This sets up project components; native agents and hooks need client-specific adapters. See client installation and limits.

Install a bundle or one skill into your project:

# Bundle

clio-kit skill install --bundle clio-scientific-io --target /path/to/project/.agents/skills

Individual skill

clio-kit skill install dataset-explore --target /path/to/project/.agents/skills

Configure the required MCP servers using setup.md. Use your agent’s supported skill directory.

Install Skills with npm

Requires Node.js 22.20.0+. From your working project:

# All skills

npx skills@1.5.25 add /path/to/clio-kit --skill '*' --agent codex --copy

Individual skill

npx skills@1.5.25 add /path/to/clio-kit --skill dataset-explore --agent codex --copy

Replace codex with claude-code or antigravity. MCP servers require separate configuration.

Choose either the Python or npm installer for each skill. See the skills CLI guide for selecting skills, updates and removal.

One Command for Any Server

# From the CLIO Kit checkout, install the CLI in a persistent tool environment

uv tool install --force --reinstall --editable .

If uv's executable directory is not on PATH:

uv tool update-shell

List all 22 available MCP servers

clio-kit mcp-servers

Run an individual server

clio-kit mcp-server hdf5 clio-kit mcp-server pandas clio-kit mcp-server slurm

Once 2.11.0 is published, install it with uv tool install 'clio-kit>=2.11.0' (2.11.0 or newer; earlier releases lack the skill, plugin and doctor commands). uv tool install creates a persistent, isolated environment; use uvx --from 'clio-kit>=2.11.0' clio-kit ... for a temporary, one-shot invocation.

The release separates the small launcher from component downloads: one MCP fetches only that server, one skill fetches only its files, and a workflow selects its components. Server dependencies stay isolated and locked. See selective installation for release, checkout and native plugin routes. The --branch option is for development, not an immutable release installation.

The wheel also includes machine-readable tool contracts for JARVIS, Slurm, Spack and Scientific Catalog, with SHA-256 digests for downstream verification:

clio-kit mcp-contracts

clio-kit mcp-contract clio-kit-jarvis-user-v3.7.2 clio-kit mcp-contract clio-kit-slurm-user-v3.1 clio-kit mcp-contract clio-kit-spack-user-v2.3 clio-kit mcp-contract clio-kit-scientific-catalog-user-v1.1

Workflow Bundles

These are broad workflow plugins. Each combines its MCP servers and skills.

Some servers require additional system software. See setup and prerequisites. See plugin composition for primary bundles and task plugins that combine components across them.

For a complete dataset-report workflow—HDF5, Pandas, Plot, a skill, evidence review and a verification hook:

claude plugin install clio-dataset-report@clio-kit

See dataset reports for inputs and verification limits.

Skills and Agents

Skills provide workflow instructions and guidance for interpreting results. Claude Code users can install skills or agent definitions separately:

claude plugin install clio-skills@clio-kit

claude plugin install clio-agents@clio-kit

The shared installer supports Codex, Claude Code, OpenCode, Cursor, Antigravity and VS Code. Codex, Claude Code and OpenCode also have adapters for the scientific agents and Dataset Report hooks. See client support.

Add the optional Clio Coder coding and research skills, including Materio procedures:

clio-kit skill install --bundle clio-coder --target .agents/skills

Or through Claude Code:

claude plugin install clio-coder-skills@clio-kit

Individual skills also work: clio-kit skill install clio-kit-scientific-debugging --target .agents/skills. Adapted Clio Coder skills use the clio-kit- prefix to distinguish them from upstream originals. See Clio Coder integration for upstream packages and native plugin support.

Agentic Search

clio-agentic-search is a standalone hybrid retrieval service in this repository, not an MCP server. It indexes documen