Medical Paper Assistant

🔬 A Guided & Exploratory Medical Paper Writing Tool
Powered by MCP + GitHub Copilot

📖 繁體中文版

🎯 Why This Tool?

Traditional paper writing tools require you to know exactly what you want before you start. But research is rarely that linear.

Medical Paper Assistant is different:

🔍 Explore First, Decide Later - Browse literature freely, save interesting papers, then decide your research direction
💬 Conversational Workflow - Chat naturally with AI to refine your ideas, not fight with forms
🧭 Guided Process - Step-by-step prompts guide you from concept to publication-ready manuscript
🔗 Native MCP + Copilot Integration - Works directly inside VS Code, no context switching

💡 What Makes Us Unique

Traditional Tools	Medical Paper Assistant
Fixed templates, rigid workflow	Flexible, exploratory approach
Separate apps for search/write/cite	All-in-one integrated experience
Manual reference management	Auto-save with rich metadata & citation formats
Export then format	Direct Word export with journal styles
Learn complex UI	Natural language conversation

🆕 Coming Soon: Artifact-Centric Architecture

📋 Design Document

We're redesigning to support truly non-linear workflows:

Today: Must create project first → then save references
Soon:  Save anything first → decide project later

Feature	Description
`_workspace/` Staging	Save references, PDFs, notes without a project
Three-Phase State	EMPTY → EXPLORATION → PROJECT
Link Artifacts	Connect saved items to projects when ready
Zero Friction Start	Just start searching, the rest follows

🌐 Our Ecosystem

flowchart LR
    subgraph IDE["VS Code"]
        Agent[Copilot Agent]
        Foam[Foam Plugin]
    end
    
    subgraph MCP["MCP Servers"]
        mdpaper[mdpaper<br/>Draft・Export・Validate]
        pubmed[pubmed-search<br/>Search・Metrics]
        cgu[CGU<br/>Deep Think]
    end
    
    subgraph Data["Project Data"]
        proj[("projects/{slug}/<br/>• .memory/<br/>• references/<br/>• drafts/")]
    end
    
    Agent <-->|MCP| mdpaper
    Agent <-->|MCP| pubmed
    Agent <-->|MCP| cgu
    mdpaper -->|HTTP API| pubmed
    Foam <-->|Wikilinks| proj
    mdpaper <--> proj

Component	Role	Key Feature
mdpaper	Paper writing, export	MCP-to-MCP verified data
pubmed-search	Literature search	HTTP API for cross-MCP
Foam	Knowledge graph	`[[citation_key]]` linking
CGU	Creative thinking	Deep analysis for concepts
Project Memory	Cross-session context	`.memory/` persistence

🚀 Quick Start: MCP Prompts

Just type these in Copilot Chat to get started:

Prompt	What It Does
`/mdpaper.search`	🔍 Start here! Explore literature freely, save interesting papers
`/mdpaper.concept`	📝 Develop research concept with novelty validation
`/mdpaper.strategy`	⚙️ Configure search strategy (date, exclusions, article types)
`/mdpaper.analysis`	📊 Analyze CSV data, generate figures & Table 1
`/mdpaper.draft`	✍️ Write manuscript draft with auto-citations
`/mdpaper.clarify`	🔄 Refine specific sections through conversation
`/mdpaper.format`	📄 Export to Word with journal formatting

💡 Recommended Workflow: /mdpaper.search → /mdpaper.concept → /mdpaper.draft → /mdpaper.format

🧠 Skill System + Project Memory

This is our core differentiator: We don't just provide tools—we provide guided workflows that know how to combine tools effectively, AND project memory that remembers your research journey.

What is a Skill?

Tool (工具) = Single capability (search, save, analyze...)
Skill (技能) = Complete knowledge (how

...

u9401066/med-paper-assistant

README