HeLa MCP Ecosystem

A modular, immortal cellular AI tooling ecosystem built on the Model Context Protocol (MCP), engineered by Azzar to equip AI agents with full-spectrum autonomous capabilities across reasoning, persistent memory, workspace management, system execution, research, design, device automation, and 3D modeling.

New to MCP or non-technical? Read the Beginner's Step-by-Step Guide for a 3-minute, zero-code onboarding walkthrough.

Respectful Attribution & Metaphor

The HeLa MCP Ecosystem is named in respectful recognition of Henrietta Lacks (1920–1951) and the immortal scientific legacy of HeLa cells, which transformed global biomedical research. In this software architecture, HeLa serves as a cellular biology metaphor:

Cellular Modularity: Just as biological cells contain specialized organelles coordinated by the nucleus and genome, the HeLa MCP Ecosystem deploys specialized tool servers coordinated by a dual backbone.
Continuous Replicability & Immortality: Environments can be snapshot-pinned, reproduced deterministically on any machine, and restored cleanly without state degradation.
Component Independence: Underlying repositories, technical package names, and Git commit histories remain autonomous and unaltered while functioning as a harmonious organism.

Dual-Backbone Architecture

Every profile in the HeLa ecosystem is anchored by two core backbone servers:

flowchart TB
    Agent["Agent / LLM Orchestrator"]

    Mitosis["HeLa Mitosis<br/>(Orchestrator)<br/>- Dynamic Routing<br/>- Step Reasoning<br/>- Tool Planning"]
    Genome["HeLa Genome<br/>(State & Memory)<br/>- Knowledge Graph<br/>- Entities / Relations<br/>- Observations"]

    Membrane["HeLa Membrane<br/>Workspace FS"]
    Nucleus["HeLa Nucleus<br/>Command Exec"]
    Ribosome["HeLa Ribosome<br/>PTY Harness"]
    Enzyme["HeLa Enzyme<br/>Research / Wiki"]
    Cytosol["HeLa Cytosol<br/>Browser DOM"]

    Agent -- "stdio JSON-RPC" --> Mitosis
    Agent -- "stdio JSON-RPC" --> Genome
    Mitosis <-->|"Shared Context"| Genome
    Mitosis --> Membrane & Nucleus & Ribosome & Enzyme & Cytosol
    Genome --> Membrane & Nucleus & Ribosome & Enzyme & Cytosol

HeLa Mitosis (hela-mitosis): Cellular division and orchestration backbone. Handles dynamic tool routing, prompt decomposition, step-by-step reasoning (sequentialthinking), and multi-tool planning.
HeLa Genome (hela-genome): Cellular memory and state backbone. Maintains the persistent SQLite knowledge graph (memory.db), entity-relation tracking, session restoration, and project milestones.

10-MCP Component Taxonomy

Canonical Identity	Machine ID (`id`)	Technical Source Repo	Scope	Cellular Metaphor & Role
HeLa Mitosis	`hela-mitosis`	`chaining-mcp-server`	Core	Orchestrator: Dynamic routing, sequential reasoning, 42 bundled prompt templates
HeLa Genome	`hela-genome`	`Project-Guardian-mcp-server`	Core	State Backbone: Entity-relation knowledge graph, milestone tracking, memory persistence
HeLa Membrane	`hela-membrane`	`filesystem-mcp-server`	Core	Workspace: Sandboxed filesystem operations, recursive search, archive extraction
HeLa Nucleus	`hela-nucleus`	`terminal-mcp-server`	Core	Execution: Command execution, subshell isolation, RTK token-optimized execution
HeLa Ribosome	`hela-ribosome`	`menager-mcp-server`	Core	Process Harness: Interactive PTY multiplexing, Regex hooks, lifecycle management
HeLa Enzyme	`hela-enzyme`	`research-assistant-mcp-server`	Core	Knowledge: Unified Google Custom Search + cached Wikipedia synthesis and fact-checking
HeLa Cytosol	`hela-cytosol`	`Browser-Agent`	Core	Interaction: Playwright browser automation, accessibility trees, DOM perception
HeLa Phenotype	`hela-phenotype`	`the-designer`	Specialized	Design: UI/UX design tokens, OKLCH color palettes, Tailwind and component synthesis
HeLa Receptor	`hela-receptor`	`scrcpy-mcp`	Specialized	Mobile: Android device automation, ADB bridge, XML view hierarchy inspection
HeLa Plastid	`hela-plastid`	`ll3m-agent`	Specialized	3D Modeling: Autonomous Blender procedural modeling, materials, and render pipeline

Quick Start

1. Prerequisites

Node.js: >= 18.0.0 (v20+ LTS recommended)
Git: >= 2.25.0
SQLite3: System CLI or built-in Node SQLite bindings

2. Run Diagnostics (`setup.sh doctor`)

Check your host environment, compiler readiness, external runtimes, and API key fallbacks:

git clone https://github.com/1999AZZAR/hela-mcp-ecosystem.git
cd hela-mcp-ecosystem
./setup.sh doctor

3. Interactive Installation & Profile Selection

./setup.sh

4. Non-Interactive One-Liners

Full Developer Desktop (Cursor IDE):

./setup.sh --profile dev-workspace --client cursor --non-interactive

Headless Linux Server (Claude Desktop / CLI):

./setup.sh --profile headless-server --client claude --non-interactive

Pinned Immutable Release Snapshot:

./setup.sh --profile dev-workspace --client cursor --snapshot v1.0.0 --non-interactive

Supported AI Clients & Output Formats

The HeLa MCP Ecosystem generates tailored, valid configuration formats across 10 client backends:

Client Platform	Output Config Location	Format
Cursor IDE	`~/.cursor/mcp.json`	JSON (`mcpServers`)
Claude Desktop / CLI	`~/.claude.json`	JSON (`mcpServers`)
Gemini CLI	`~/.gemini/antigravity-cli/mcp_config.json`	JSON (`mcpServers`)
Antigravity CLI	`~/.gemini/antigravity-cli/mcp_config.json`	JSON (`mcpServers`)
OpenCode	`~/.config/opencode/opencode.json`	JSON (`mcp`)
Kilo CLI	`~/.config/kilo/config.json`	JSON (`mcp`)
Zed Editor	`~/.config/zed/settings.json`	JSON (`context_servers`)
Codex / ChatGPT	`~/.codex/config.toml`	TOML (`[mcpServers.*]`)
Docker Compose	`config/docker-compose.generated.yml`	Docker Compose v3

Available Agent Profiles

Profile ID	Target System	Backbone Included	Servers Included	Focus Area
`dev-workspace`	Any (GUI recommended)	Mitosis + Genome	Membrane, Nucleus, Ribosome, Enzyme, Phenotype, Cytosol	Full-stack software engineering, testing, web UI
`headless-server`	Headless Linux	Mitosis + Genome	Membrane, Nucleus, Ribosome, Enzyme, Phenotype	Cloud server administration, CI/CD, headless dev
`research`	Headless or GUI	Mitosis + Genome	Enzyme, Membrane, Cytosol	Deep literature research, document synthesis, web crawling
`web-devops`	Headless or GUI	Mitosis + Genome	Membrane, Nucleus, Phenotype, Cytosol	Frontend development, Tailwind styling, DOM verification
`android-testing`	Device connected	Mitosis + Genome	Nucleus, Receptor, Enzyme	Mobile QA testing, ADB automation, APK validation
`3d-modeling`	GUI (Blender installed)	Mitosis + Genome	Plastid, Membrane, Nucleus	3D procedural modeling, materials, rendering
`all`	Full workstation	Mitosis + Genome	All 10 HeLa MCP servers	Complete full-spectrum AI agent capabilities

For complete persona guides and pipeline specifications, see Profiles Catalog.

Operational Workflows (Workflows A–F)

The ecosystem is built for structured multi-server agent workflows:

Workflow A: Autonomous Feature Engineering: Genome (restore) → Mitosis (decompose) → Membrane (code) → Nucleus (test) → Genome (persist).
Workflow B: Deep Research & Architecture Synthesis: Enzyme (search) → Cytosol (scrape) → Mitosis (synthesize) → Genome (record) → Membrane (write).
Workflow C: Web Feature with Design & Browser Verification: Phenotype (tokens) → Membrane (build) → Nucleus (serve) → Cytosol (DOM QA) → Genome (record).
Workflow D: Mobile App Test Automation: Genome (issue) → Nucleus (adb) → Receptor (drive UI) → Genome (record pass).
Workflow E: Autonomous 3D Asset Creation & Render Pipeline: Genome (spec) → Mitosis (plan) → Plastid (Blender) → Membrane (save) → Genome (record).
Workflow F: Long-Horizon Complex Refactor with PTY Harness: Ribosome (PTY) → Nucleus (exec) → Genome (persist).

For step-by-step tool invocation sequences, schemas, and diagrams, see Workflows & Integration Guide.

Project Health & Diagnostics

# Run system and server diagnostic health check
npm run doctor
# or
./setup.sh doctor

# Run 70-combination multi-client matrix test suite
npm run test:matrix

# Run master integration test suite (295 tools across all 10 servers)
npm test

Documentation Index

Beginner's Step-by-Step Guide: 3-minute, zero-code onboarding.
Keys & Secrets Guide: API key setup, sign-up URLs, and zero-key offline fallbacks.
Profiles Reference: Full persona reference and capability mappings.
Workflows & Integration Guide: Cross-MCP workflow pipelines (Workflows A–F).
Security & Reliability Audit: Threat model, sandboxing, and isolation standards.
Architecture Guide: In-depth cellular architecture and communication topologies.
Troubleshooting Guide: Common issues, diagnostic codes, and recovery procedures.

License & Attribution

Distributed under the MIT License. Underlying repositories remain independently copyrighted by their respective authors.

The HeLa project respectfully recognizes Henrietta Lacks and the enduring scientific legacy of HeLa cells.

Name		Name	Last commit message	Last commit date
.github/workflows		.github/workflows
assets		assets
conductor		conductor
config		config
docs		docs
scripts		scripts
.gitignore		.gitignore
.pre-commit-config.yaml		.pre-commit-config.yaml
CONTRIBUTING.md		CONTRIBUTING.md
LICENSE		LICENSE
README.md		README.md
RELEASE_NOTES.md		RELEASE_NOTES.md
package.json		package.json
setup.sh		setup.sh
update.sh		update.sh

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HeLa MCP Ecosystem

Respectful Attribution & Metaphor

Dual-Backbone Architecture

10-MCP Component Taxonomy

Quick Start

1. Prerequisites

2. Run Diagnostics (`setup.sh doctor`)

3. Interactive Installation & Profile Selection

4. Non-Interactive One-Liners

Supported AI Clients & Output Formats

Available Agent Profiles

Operational Workflows (Workflows A–F)

Project Health & Diagnostics

Documentation Index

License & Attribution

About

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Repository files navigation

HeLa MCP Ecosystem

Respectful Attribution & Metaphor

Dual-Backbone Architecture

10-MCP Component Taxonomy

Quick Start

1. Prerequisites

2. Run Diagnostics (setup.sh doctor)

3. Interactive Installation & Profile Selection

4. Non-Interactive One-Liners

Supported AI Clients & Output Formats

Available Agent Profiles

Operational Workflows (Workflows A–F)

Project Health & Diagnostics

Documentation Index

License & Attribution

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2. Run Diagnostics (`setup.sh doctor`)