Clinical Research Coordinator: Multi-Server MCP Integration

Prerequisites

• Claude AI access (Claude 3.5 Sonnet or newer recommended)
• Node.js 18+ installed
• API keys for relevant services (arXiv, Notion, Google Sheets, Gmail, Memory Bank, Sequential Thinking, MongoDB)
• Basic understanding of clinical research workflows
• Familiarity with your research domain

Environment Preparation

1. API Keys and Accounts
   • arXiv: Get API key from https://arxiv.org/api/account
   • Notion: Set up integration at https://developers.notion.com
   • Google Sheets: Connect to Google Sheets API
   • Gmail: Enable API at Google Cloud Console, create OAuth credentials
   • Memory Bank: Configure storage location
   • Sequential Thinking: Set up research planning tool
   • MongoDB: Set up database for clinical data storage
2. MCP Server Installation

# Install all required MCP servers
npm install -g @arxiv/mcp-server
npm install -g @notion/mcp-server
npm install -g @google-sheets/mcp-server
npm install -g @gmail/mcp-server
npm install -g @memory-bank/mcp-server
npm install -g @sequential-thinking/mcp-server
npm install -g @mongodb/mcp-server
npm install -g @excel/mcp-server
npm install -g @slack/mcp-server

Claude Configuration

Add the following to your Claude MCP configuration:

{
  "servers": {
    "arxiv": {
      "command": "npx",
      "args": ["@arxiv/mcp-server"],
      "env": {}
    },
    "notion": {
      "command": "npx",
      "args": ["@notion/mcp-server"],
      "env": {
        "NOTION_API_KEY": "your_notion_api_key",
        "NOTION_DATABASE_ID": "your_research_database_id"
      }
    },
    "google-sheets": {
      "command": "npx",
      "args": ["@google-sheets/mcp-server"],
      "env": {
        "GOOGLE_SHEETS_API_KEY": "your_google_sheets_api_key"
      }
    },
    "gmail": {
      "command": "npx",
      "args": ["@gmail/mcp-server"],
      "env": {
        "GMAIL_CREDENTIALS": "/path/to/gmail/credentials.json",
        "GMAIL_TOKEN": "/path/to/gmail/token.json"
      }
    },
    "memory-bank": {
      "command": "npx",
      "args": ["@memory-bank/mcp-server"],
      "env": {
        "MEMORY_BANK_PATH": "/path/to/your/research/memory"
      }
    },
    "sequential-thinking": {
      "command": "npx",
      "args": ["@sequential-thinking/mcp-server"],
      "env": {}
    },
    "mongodb": {
      "command": "npx",
      "args": ["@mongodb/mcp-server"],
      "env": {
        "MONGODB_URI": "mongodb://username:password@host:port/database"
      }
    },
    "excel": {
      "command": "npx",
      "args": ["@excel/mcp-server"],
      "env": {
        "EXCEL_CLIENT_ID": "your_microsoft_client_id",
        "EXCEL_CLIENT_SECRET": "your_microsoft_secret",
        "EXCEL_TENANT_ID": "your_tenant_id"
      }
    },
    "slack": {
      "command": "npx",
      "args": ["@slack/mcp-server"],
      "env": {
        "SLACK_API_TOKEN": "your_slack_api_token"
      }
    }
  }
}

Step 1: Initial Setup and Testing

1. Verify All Servers Are Connected

"Please verify that all MCP servers are connected: arXiv, Notion, Google Sheets, Gmail, Memory Bank, Sequential Thinking, and MongoDB."

2. Test Each Server Individually
   • arXiv: “Search arXiv for a recent paper on clinical research”
   • Notion: “Create a research database in my Notion workspace”
   • Google Sheets: “Import my clinical trial data”
   • Gmail: “Send a test email to schedule a consultation”
   • Memory Bank: “Check data integration status”
   • Sequential Thinking: “Help me plan a new research project”
   • MongoDB: “Connect to my clinical data database”

Step 2: Literature Search and Analysis

Basic Paper Search:

"Search arXiv for papers on 'clinical trial design' published in the last 6 months.
Summarize the top 5 most relevant papers."

Advanced Search with Filtering:

"Find papers on arXiv that:
- Focus on randomized controlled trials
- Published by authors from top medical journals
- Have more than 10 citations
- Published between 2023-2024"

Cross-Reference Search:

"Search for papers by [Author Name] on clinical trial outcomes, then find any industry
applications mentioned in tech news using Perplexity."

Step 3: Organizing Research Findings

Create Research Database:

"Create a Notion database for my clinical research literature review with columns:
- Paper Title
- Authors
- Key Contributions
- Methodology
- Limitations
- Relevance to My Research
- Citation Count"

Populate Database:

"For each paper found on clinical research:
1. Extract key information
2. Add entry to Notion database
3. Store important insights in Memory Bank
4. Tag connections between papers"

Step 4: Building Knowledge Connections

Memory Bank Integration:

"Store these key insights in Memory Bank:
- Main breakthrough from [Paper Title]
- Connection to my previous research on [Topic]
- Potential applications identified
- Open questions for future investigation"

Creating Research Maps:

"Using my stored memories, create a concept map in Notion showing:
- Key research themes in clinical research
- Connections between different approaches
- Evolution of ideas over time
- Gaps in current research"

Step 5: Real-World Application Tracking

Industry Search:

"Using Perplexity, find:
- Companies working on clinical trial design
- Recent funding announcements in clinical research
- Patent applications related to clinical trial protocols
- Commercial medical device developments"

Academic-Industry Bridge:

"For each theoretical approach in my literature review, find:
- Industry implementations or attempts
- Technical challenges mentioned in news
- Timeline for practical applications
- Key players and their approaches"

Step 6: Complex Problem Analysis

Problem Decomposition:

"Using Sequential Thinking, help me understand:
'How do randomized controlled trials achieve statistical power?'

Break this down into:
- Fundamental concepts
- Mathematical framework
- Physical implementation
- Sample size calculations"

Research Question Development:

"Based on my literature review and stored insights, use Sequential Thinking to:
1. Identify gaps in current research
2. Formulate 3 specific research questions
3. Outline methodology for each question
4. Predict potential challenges"

Step 7: Comprehensive Research Workflow

Weekly Literature Update:

"Perform my weekly research update:
1. Search arXiv for new papers in my field (since last week)
2. Check Perplexity for industry developments
3. Update my Notion literature database
4. Store key findings in Memory Bank
5. Identify papers to read in detail"

Research Synthesis:

"Create a research synthesis:
1. Review all Memory Bank entries on [specific topic]
2. Identify common themes and contradictions
3. Create a synthesis document in Notion
4. Highlight areas needing further investigation
5. Generate questions for advisor meeting"

Advanced Workflows

Citation Network Analysis:

"For the paper [Title]:
1. Find all papers it cites on arXiv
2. Find papers that cite it
3. Create a citation network in Notion
4. Identify influential papers in the network
5. Store key relationships in Memory Bank"

Research Timeline Creation:

"Create a historical timeline of clinical research:
1. Search arXiv for seminal papers by year
2. Find industry milestones via Perplexity
3. Create timeline in Notion with key breakthroughs
4. Store evolution patterns in Memory Bank"

Collaborative Research Support:

"Prepare for research group meeting:
1. Summarize this week's findings from Memory Bank
2. Create presentation outline in Notion
3. Find recent news to discuss (Perplexity)
4. Prepare 3 discussion questions using Sequential Thinking"

Research Project Management

Thesis Chapter Organization:

"Help me organize my thesis chapter on [Topic]:
1. Review all relevant Memory Bank entries
2. Create chapter outline in Notion
3. Find supporting papers on arXiv for each section
4. Identify areas needing more research
5. Create writing timeline"

Progress Tracking:

"Create a research progress tracker:
1. List all research questions in Notion
2. Track papers read vs. to-read
3. Monitor Memory Bank growth by topic
4. Visualize research coverage gaps
5. Set weekly research goals"

Troubleshooting Common Issues

arXiv Search Problems:

• Try different keyword combinations
• Use author names or specific paper IDs
• Check category filters (quant-ph, cs.IT, etc.)

Memory Bank Organization:

• Regularly tag and categorize memories
• Create hierarchical memory structures
• Periodically review and consolidate similar memories

Notion Sync Issues:

• Verify API permissions
• Check database structure compatibility
• Ensure proper field mappings

Complex Analysis Challenges:

• Break problems into smaller components
• Use Sequential Thinking iteratively
• Combine with domain knowledge from arXiv

Best Practices

1. Daily Research Routine:
   • Morning: Check new arXiv submissions
   • Afternoon: Read and annotate papers
   • Evening: Update Notion and Memory Bank
2. Weekly Synthesis:
   • Review all Memory Bank entries
   • Update literature database
   • Identify research priorities
3. Monthly Deep Dives:
   • Comprehensive literature review update
   • Industry landscape analysis
   • Research direction reassessment
4. Citation Management:
   • Always store complete citation information
   • Track paper relationships
   • Maintain bibliography in Notion