Everything I have built, and what each thing is.

Context Layer for Input/Output. The agentic-science ecosystem built through IOWarp: a tiered context store, a scientific tool kit, science agents, a remote-execution relay, a terminal front end, and the coding agent.

Components ship at their own pace. Core and Kit are released and maintained; Agent is beta; Coder is experimental; Researcher and Bench are private.

• iowarp/clio-core Tiered context and data runtime; led by the GRC core team.
• iowarp/clio-kit MCP servers for scientific computing; team-built, with my contributions.
• iowarp/clio-agent The science agent; team-built, with my contributions.
• iowarp/clio-relay
• iowarp/gact-tui
• iowarp/clio-agent-marketplace
• iowarp/clio-web-search
• iowarp/clio-schemas
• iowarp/docs
• clio-researcher private Local-first auto-researcher for I/O systems and science data lifecycles; alpha.
• clio-bench private The CLIO agentic benchmark suite.

A terminal coding agent for scientific and HPC software. Local models are the design target, the model never gets a raw shell by default, work goes to bounded workers across a cluster, and every run seals a receipt.

v0.3.7 on npm as @iowarp/clio-coder; experimental, interfaces may change before 1.0.

• iowarp/clio-coder

The NSF-funded platform for context orchestration in scientific computing. Its runtime, transfer and assimilation engines, and tool kit are the ground CLIO stands on.

Active 2024–2029; PI Xian-He Sun; I am a co-PI and the architect of the CLIO layer.

Label-based I/O. A request carries its intent, so the storage system can schedule and transform it.

Public 2.1.0-rc.1 branch for development and evaluation; patent US11630834B2.

Multi-tier distributed I/O buffering that became versioned middleware under The HDF Group.

Complete since 2024; final public release v1.2.1.

A distributed, tiered log store that orders data by time.

Active; public v3.0.0.

Task-based I/O that turns traditional operations into distributed, schedulable work.

Complete; prerelease tagged for SSDBM 2025.

I/O for deep-learning workloads. DLIO, the benchmark, now generates MLPerf Storage workloads.

DLIO v2.0.1 maintained by the Argonne team and collaborators.

Metadata-aware I/O adapters for in-situ scientific workflows.

Institutional record marks the project complete; v0.1 prerelease.

A unified I/O layer over POSIX files and object stores, from my doctoral work.

Complete since 2023.

A small MCP server that lets an agent read, search, and take part in Zulip conversations.

v0.7.2 on PyPI.

A staged research-writing workflow for coding agents. Spec, outline, section plans, isolated drafts, review.

v0.5.0 on npm. A material-science variant, wtf-ms, lives in the IOWarp organization.

Gives agents native access to academic paper search and metadata.

Public prototype.

A shared, searchable clipboard for a person and their coding agent.

Public prototype.

Converts scientific paper PDFs into Markdown an agent can read.

Public prototype.

A single-file agent that answers natural-language questions about HDF5 files.

Public prototype from early 2025; the idea carried into CLIO Kit's HDF5 server.

A runtime for autonomous multi-agent workflows where each agent runs in its own bounded context.

Private prototype.

A lightweight, developer-first agent orchestration framework.

Private prototype.

A multi-agent deliberation runtime.

Private prototype; preparing for public release.

Speculative dispatch for multi-agent orchestration: a cheap prediction runs beside an expensive optimization, and alignment improves over time.

Public research code.

A probe that watches what an agent does through vision-model analysis of its screen.

Private prototype; preparing for public release.

A context-removal agent that keeps long-running coding agents from drowning in their own history.

Private prototype; preparing for public release.

Generates compact context bundles so an agent can pick up a task without rereading everything.

Private prototype; preparing for public release.

Structured interviews with AI agents on any topic, with typed outputs.

Private prototype; preparing for public release.

A claim genealogy system for tracking how a piece of knowledge evolves.

Private prototype; preparing for public release.

An LLM-powered Obsidian note processor that labels, tags, annotates, and links notes.

Private prototype; preparing for public release.

A multi-agent system that looks for hidden methodology breaks in official statistics.

Public research code.

The earlier MCP toolkit that turned a general agent into a science partner. Superseded by CLIO Kit.

Archived precursor; the private repository is kept for history.

• iowarp-mcp private
• hdf5-mcp-server private An HDF5 MCP proxy for remote files; folded into the toolkit line.

Scientific-computing extensions for two coding assistants, built on the IOWarp toolkit.

Public, from 2025; CLIO Kit is the maintained path now.

• akougkas/claude-code-4-science
• akougkas/gemini-4-science

The 2025 CLI companion for IOWarp, a fork I experimented with before Clio Coder existed.

Archived; Clio Coder is the successor.

Co-founding and directing the Gnosis Research Center.

Active since 2023.

This site. Jekyll, validated content contracts, static redirects, and a dependency-free browser layer.

Relaunched August 2026.