CodeXomics¶
The AI-native genome browser
Talk to your genome — AI agents drive the view and run the analysis.
CodeXomics is an AI-native genome browser — a cross-platform Electron workspace where conversational AI agents drive the visualization and run real biological analyses, with plugin development, benchmark testing, and Model Context Protocol (MCP) integration.
The current release is v0.722. Download installers from GitHub Releases, or build from source for the latest changes.
- Get Started
Install CodeXomics, configure an AI provider, and load your first genome.
- User Guide
Learn the genome browser, ChatBox, plugins, BLAST, and benchmark workflows.
- MCP Server
Connect CodeXomics tools to MCP-compatible clients in tools or agent mode.
- Developer Guide
Understand the codebase, tool registry, agents, plugins, and tests.
Current System Snapshot¶
| Area | Current state |
|---|---|
| Application version | 0.722.0 (v0.722 display) |
| Runtime baseline | Node.js 20/22 for source builds; Electron 41.7.1 |
| Tool registry | 179 YAML schemas across 18 active categories |
| Built-in ChatBox tools | 143 mapped local tools |
| MCP tools mode | 96 tools exposed |
| MCP agent mode | codexomics_chat, list_genome_windows, switch_active_window |
| Runtime agents | Coordinator, Analysis, Data, Navigation, External, Plugin, DeepResearch |
| UI styling | Vanilla CSS with default, professional, minimal, pastel, amy, red, elegant, and midnight presets |
Core Capabilities¶
Production-readiness release
Version 0.722.0 adds secure credential storage, hardened renderer boundaries, structured logging and crash capture, auto-update support, stronger CI gates, and an Electron smoke-test harness. See the v0.722.0 release notes.
Genome Visualization¶
- Load FASTA, GenBank, GFF/GTF, BED, VCF, SAM/BAM, WIG, KGML, and
.prj.GAIprojects. - Explore genes, sequence, GC content/skew, variants, reads, protein data, pathway views, and custom annotation tracks.
- Use SVG and Canvas renderers for responsive browsing across dense genomic datasets.
AI-Assisted Analysis¶
- Configure OpenAI, Anthropic, Google, DeepSeek, SiliconFlow, OpenRouter, or local LLM-compatible endpoints.
- Ask the ChatBox to navigate, search, analyze sequence content, design primers, run BLAST workflows, retrieve protein structures, and manage tasks.
- Use multi-agent routing for complex workflows that need decomposition and tool coordination.
Extensibility¶
- Build plugins with the VS Code-inspired extension host and Plugin API
2.0.0. - Expose plugin functions to AI tool calling.
- Serve and test marketplace plugins through
packages/marketplace-server/.
MCP Integration¶
- Run CodeXomics as a standalone MCP server.
- Use tools mode for direct tool calls.
- Use agent mode when an external client should delegate natural-language prompts to the in-app AI pipeline.
Screenshots¶
Genome browser¶
Feature track, GC content and skew, multi-track WIG data, the gene details sidebar, and the protein/sequence view.
Read alignment and references¶
Coverage and base-resolution sequencing-read tracks alongside gene references and operons in the side panel.
Base-level read pileup over a selected gene:
Protein structures¶
AlphaFold structure lookup and an interactive 3D protein viewer, driven from the AI ChatBox.
Primer design¶
Designed primers rendered directly on the sequence view.
Documentation Map¶
| Section | Start here |
|---|---|
| New users | Getting Started |
| Daily usage | User Guide |
| MCP clients | MCP Server Guide |
| Plugin users | Plugin Marketplace Guide |
| Developers | Developer Guide |
| AI coding assistants | AI Assistant Guidelines |
| Architecture | Multi-Agent System |
| BLAST | BLAST Guide |
| Benchmarks | Benchmark Methods |
| Current release | v0.722.0 Release Notes |