deepseek-aix

English | 中文

deepseek-aix is an AI research assistant for scholarly literature: describe a research topic in conversation, and the agent collects relevant papers through built-in multi-source search (PubMed, arXiv, Semantic Scholar, Crossref, and more), presenting the results as collapsible, bookmarkable paper cards.

Built as a fork of DeepSeek Harness, deepseek-aix keeps the full agent infrastructure — sessions, tools, subagents, workflows, sandboxed code execution, and the Web GUI — and adds a literature capability on top: a multi-source literature-search service, a durable favorites collection with category folders, and a Web UI that renders search results and bookmarks as first-class cards.

Features

Literature Search

• Conversational research-topic description: new sessions start in the deepseek-aix research-assistant mode; describe a topic in natural language (Chinese or English) and the agent searches, deduplicates, and ranks papers.
• Multi-source search: simultaneously searches PubMed, Europe PMC, bioRxiv/medRxiv, Crossref, OpenAlex, Semantic Scholar, and arXiv via a built-in MCP service.
• Automatic deduplication: cross-round merging of results.
• Paper cards in chat: every search result renders as a card with authors, year, venue, abstract, and DOI/PMID/arXiv identifiers.
• Full-text retrieval: open-access subset available for detailed reading.
• Right-side literature panel: auto-expands after each conversation round to show all collected papers from the current session.

Literature Favorites

• Bookmark with folders: star papers to save them in a durable, per-user collection organized into category folders.
• Cross-session persistence: favorites are stored server-side ($DSH_HOME/storages/literature_favorites.json) and survive across sessions and browsers.
• Folder management: create, rename, delete folders; move papers between folders.
• Agent tools: agent can also read/write favorites via literature_favorites_add/remove/list/folder_create/folder_rename/folder_delete/move tools.

Skin Center

• Multiple themes: choose from a variety of UI skins including blue-fantasy, dragon-heir, harbor, miku, minecraft, qq98, ths, trading, whale-song, xp, and the classic home skin.
• Live preview: try on skins before applying; instant theme switching.
• Skin management: new skins can be installed as plugins.

Aionui Panel (Right-Side Panel)

• File explorer: browse the workspace directory tree with search.
• Multi-tab preview: preview files (markdown, images, code) in multiple tabs.
• Drag-and-drop: drag files from the explorer directly into the conversation input.
• Workspace-gated: respects the current workspace root.

File @-mentions

• File references: type @ in the input bar to reference files from the workspace.
• Inline file chips: selected files appear as chips in the input area.

Underlying Harness Capabilities

• Workspace and file management: full file system access with sandboxing.
• Sandboxed code execution: bash and PowerShell with permission controls.
• Subagents and parallel research: spawn background agents for multi-task research.
• Goal auto-continuation: autonomous progress toward defined goals.
• Plan mode and task breakdown: structured planning and execution.
• Durable sessions, replay, and multi-model configuration: persistent conversation history and flexible model selection.
• Plugin architecture: everything is a plugin, powered by Cordis.

Quick Start

Prerequisites

• Node.js ≥ 22
• pnpm
• DeepSeek API Key (configured in ~/.dsh/.credentials.yaml)

Run from source

git clone https://github.com/PHoenixs57/AixLab.git aixlab
cd aixlab
pnpm install
pnpm run build:lib
pnpm run build:web
pnpm dsh web --patch dev.cordis.yml

Open http://127.0.0.1:3090, create a new session, and try:

"Find me the latest papers on IL-6 signaling in rheumatoid arthritis, 3 papers."

Development

For hot-reload of client plugins:

pnpm run dev:web
pnpm dsh web --patch dev.cordis.yml

Architecture

aixlab/
├── apps/cli/config/agent-presets/aixlab/   # Production "deepseek-aix" preset
│   ├── preset.yml
│   ├── agent.cordis.yml
│   └── skills/literature-search/
├── presets/aixlab/                         # Same content for customization
├── mcp/literature-search-mcp/              # Multi-source literature search MCP (stdio)
├── packages/
│   ├── literature/literature-favorites/    # Host plugin: favorites tools + panel
│   ├── literature/literature-attachments/  # Full-text retrieval service
│   ├── client/ui-literature/               # Client plugin: paper cards + favorites panel
│   ├── client/ui-aionui-panel/             # Right-side panel: explorer + preview + drag
│   ├── client/ui-skin-center/              # Skin management center
│   ├── client/ui-skin-*/                   # Individual theme skins
│   └── client/ui-sidebar/                  # Modified: sidebar.favorites slot
├── packages/api/remotes/                   # literatureFavorites Remote registration
├── packages/bundle/web-app/                # Web app bundle with all integrations
└── dev.cordis.yml                          # Development overlay (port 3090)

Modes & Features

Feature	Literature Search mode	Research mode
Conversational research-topic description (Chinese / English)	✓	✓
Multi-source literature search (PubMed, Europe PMC, bioRxiv/medRxiv, Crossref, OpenAlex, Semantic Scholar, arXiv)	✓	—
Automatic deduplication and cross-round merging	✓	—
Paper cards (authors, year, venue, abstract, DOI/PMID/arXiv, open-access badge)	✓	—
Favorites with category folders (durable across sessions)	✓	—
Full-text retrieval (open-access subset)	✓	—
Skin center with multiple themes	✓	✓
Right-side panel (file explorer, preview, drag-to-input)	✓	✓
File @-mentions in input	✓	✓
Workspace and file management	✓	✓
Sandboxed code execution (bash / PowerShell)	✓	✓
Subagents and parallel research	✓	✓
Goal auto-continuation	✓	✓
Plan mode and task breakdown	✓	✓
Durable sessions, replay, and multi-model configuration	✓	✓

Configuration

• MCP server location: defaults to mcp/literature-search-mcp/dist/server.js; override with AIXLAB_MCP_SERVER environment variable.
• MCP working directory: override with AIXLAB_MCP_DIR.
• Default preset: agent-presets.default: aixlab in packages/bundle/web-app/cordis.patch.yml; can be changed to standard in settings.
• Port: dev.cordis.yml uses port 3090; change if needed.

Testing

# Literature favorites service
pnpm exec vitest run packages/literature/literature-favorites/tests/literature-favorites.spec.ts

# Paper card model (client)
pnpm exec vitest run packages/client/ui-literature/tests/paper-model.client.spec.ts

# GUI end-to-end smoke test (requires running server on 3090; playwright chromium)
node scripts/e2e-smoke.mjs

To run from a repository checkout:

git clone https://github.com/PHoenixs57/deepseek-aix.git
cd deepseek-aix
pnpm install
pnpm run build
pnpm dsh web

Community and support

• Feel free to submit feedback or bug reports through GitHub Discussions.
• Join DeepSeek Harness Discord community.

Contributing

See CONTRIBUTING.md.

Development

Start with the development guide and architecture documentation.

For agents, follow AGENTS.md.

License

MIT

Third-party dependencies and their licenses are disclosed in THIRD_PARTY_NOTICES.md.