🎓 Intranet

Claude Code with MCP Tools

8 min read

Extend Claude Code with MCP (Model Context Protocol) tools to directly interact with your email, calendar, documents, and web - turning it into a powerful AI assistant for research workflow automation.

Prerequisites

  • claude-code - Basic Claude Code installation required
  • Node.js 18+ for MCP server installation
  • API access for Google services if using Gmail/Calendar tools

🚀 Quick Start: MCP Setup

Install Essential MCP Tools

# Core productivity tools
npm install -g @modelcontextprotocol/server-gmail
npm install -g @modelcontextprotocol/server-google-calendar
npm install -g @modelcontextprotocol/server-filesystem
npm install -g @modelcontextprotocol/server-pdf
npm install -g @modelcontextprotocol/server-puppeteer

Configure Claude Code

Create or edit ~/.config/claude/claude_desktop_config.json:

{
  "mcpServers": {
    "gmail": {
      "command": "npx",
      "args": ["@modelcontextprotocol/server-gmail"]
    },
    "calendar": {
      "command": "npx",
      "args": ["@modelcontextprotocol/server-google-calendar"]
    },
    "filesystem": {
      "command": "npx",
      "args": ["@modelcontextprotocol/server-filesystem", "/Users/yourname/Documents"]
    },
    "pdf": {
      "command": "npx",
      "args": ["@modelcontextprotocol/server-pdf"]
    },
    "browser": {
      "command": "npx",
      "args": ["@modelcontextprotocol/server-puppeteer"]
    }
  }
}

First Test

After configuration, test with simple commands like:

claude "List the files in my Documents folder"

📧 Research Email Management

Process Student Applications

# Extract application information
claude "Find all emails with subject 'PhD Application' in my Gmail, extract applicant names, emails, and research interests into a CSV file called applicant_database.csv"
 
# Organize by research area
claude "Read the applicant_database.csv and create separate folders for each research interest, then email the relevant professors with summarized candidate information"

Literature Review Email Workflow

# Monitor for new papers
claude "Check my Gmail for emails with subject containing 'new publication' or 'paper alert', extract the paper information, and add to my literature review spreadsheet"
 
# Request paper copies
claude "For emails about interesting papers, draft polite requests to authors asking for PDF copies"

Conference and Collaboration Management

# Track conference deadlines
claude "Find all conference-related emails, extract deadlines and requirements, create a calendar event for each deadline"
 
# Follow up on collaborations
claude "Find emails from potential collaborators from the last 2 weeks that haven't received replies and draft follow-up messages"

📅 Academic Calendar Management

Research Meeting Coordination

# Schedule group meetings
claude "Find available 1-hour slots next week when all my PhD students are free, schedule a weekly research sync, and send calendar invitations with agenda"
 
# Meeting preparation
claude "For my meeting tomorrow with Prof. Chen about solar cell research, find related emails, recent papers, and create a meeting agenda document"

Conference and Travel Planning

# Conference scheduling
claude "Check the materials science conference schedule, find sessions related to perovskite solar cells, and add them to my calendar with notes"
 
# Travel coordination
claude "I'm attending a conference in Singapore next month. Check my calendar for conflicts, find flights, and create a travel itinerary"

Deadline Management

# Grant and paper deadlines
claude "Extract all deadlines from my emails and calendar, create a comprehensive deadline tracker with reminders 2 weeks before each deadline"
 
# Weekly planning
claude "Every Monday morning, review my calendar for the week, identify urgent tasks, and create a prioritized todo list"

📄 Document and Literature Management

Research Paper Processing

# Literature review automation
claude "Read all PDFs in my Downloads/papers folder, extract titles, authors, abstracts, and create a literature review matrix in literature_review.xlsx"
 
# Paper categorization
claude "Organize research papers by methodology (experimental, computational, theoretical) and move them to appropriate subfolders with standardized naming"

Grant Proposal Management

# Proposal analysis
claude "Compare our current grant proposal with 3 successful similar proposals I have saved, identify strengths and weaknesses, and suggest improvements"
 
# Supporting document preparation
claude "Extract all relevant publications from my CV and create formatted publication lists for the grant proposal"

Data Extraction and Processing

# Experimental data extraction
claude "Extract all numerical data tables from these experimental PDFs and compile into a single analysis spreadsheet"
 
# Reference management
claude "Extract all citations from this review paper, find the full papers online, download PDFs, and organize by topic with proper naming"

🌐 Academic Web Research

Literature Discovery

# Automated literature search
claude "Search for recent papers (last 6 months) on 'lead-free perovskite solar cells' with efficiency >20%, download PDFs, and add to my literature database"
 
# Competitor monitoring
claude "Set up weekly alerts to check for new publications from top 5 materials science groups and summarize key findings"

Funding Opportunity Research

# Grant discovery
claude "Find upcoming grant deadlines for renewable energy research in Singapore, extract requirements, and create deadline calendar events"
 
# Collaboration opportunities
claude "Search for recent papers on computational materials science at NUS and NTU, identify potential collaborators, and create contact list"

Research Tool and Software Updates

# Software updates
claude "Monitor websites for VASP, Quantum ESPRESSO, and materials simulation tools for updates and new features relevant to my research"
 
# Tutorial and resource collection
claude "Find the latest tutorials on machine learning for materials discovery and organize by difficulty level"

🔬 Research Workflow Integration

Complete Manuscript Preparation

# Multi-step workflow
claude "1. Find related papers in my reference database
2. Extract relevant literature for introduction
3. Create figures from data in my results folder
4. Draft manuscript sections following target journal format
5. Extract citations and format bibliography"

Student Supervision Automation

# Progress tracking
claude "Check recent emails from my students, identify progress updates and issues, create a summary document for our next group meeting"
 
# Resource recommendation
claude "Based on my students' research topics, find relevant recent papers and tutorials, and email personalized recommendations"

Lab Management

# Equipment scheduling
claude "Check equipment booking calendars, identify scheduling conflicts, and email affected users with alternative times"
 
# Safety and compliance
claude "Review recent lab safety emails, extract important updates, and create summary for lab meeting"

🔧 Advanced MCP Combinations

Cross-Tool Workflows

# Email → Calendar → Documents
claude "When I receive conference acceptance emails, automatically: check my calendar, add the conference dates, create a folder for that conference, and search for related papers"
 
# Web → PDF → Research
claude "Find the latest review paper on metal halide perovskites, download it, extract key references, and download those papers too"
 
# Calendar → Email → Preparation
claude "Every Friday, check my calendar for next week's meetings, find related emails and documents, and create a weekend prep package"

Custom Automation Scripts

# Weekly research report
claude "Create a weekly automation that:
1. Checks calendar for meetings attended
2. Reviews emails for action items
3. Searches for new papers in my field
4. Creates progress summary for my supervisor
5. Emails me the report every Friday at 5pm"

💡 Best Practices for Research Use

Privacy and Security

  • Use institutional accounts for Gmail and Calendar to maintain data ownership
  • Limit filesystem access to research folders only
  • Regular permission reviews to maintain security

Effective Research Prompts

  • Be specific about journals, conferences, research areas
  • Include context about your current projects and goals
  • Request sources for web searches to verify accuracy

Integration with Existing Tools

🛠️ Troubleshooting

Common Issues

MCP servers not found:

# Reinstall with global flag
npm install -g @modelcontextprotocol/server-gmail

Permission errors:

  • Check folder paths in configuration
  • Ensure Google API access is enabled

Google API authentication:

  1. Visit Google Cloud Console
  2. Enable Gmail and Calendar APIs
  3. Create OAuth credentials
  4. Add to MCP server configuration

Performance Optimization

  • Limit search scopes to specific folders/date ranges
  • Use batch operations for processing multiple files
  • Schedule heavy tasks for off-peak hours

📚 Related Tools and Resources

Core Tools

  • claude-code - Basic Claude Code setup and configuration
  • python - Custom scripting for specialized tasks
  • git - Version control for research workflows

Research Integration

HPC Integration

  • slurm - Job scheduling for computational work
  • conda - Environment management for research software
  • docker - Reproducible research environments

🔗 Quick Reference Commands

Email Management

claude "Find unread emails from professors about grant deadlines"
claude "Extract all PDF attachments from student applications"
claude "Create template for responding to paper reviewer comments"

Calendar Management

claude "Schedule weekly lab meetings for Tuesdays at 2pm"
claude "Check for conflicts with conference travel dates"
claude "Set reminder for grant submission deadline"

Document Processing

claude "Extract experimental data from these PDF papers"
claude "Organize research papers by methodology type"
claude "Create literature review matrix from PDFs in folder"

Web Research

claude "Find recent papers on perovskite stability improvements"
claude "Search for funding opportunities in Singapore for materials research"
claude "Monitor competitor publications for new techniques"

With MCP tools, Claude Code becomes an indispensable research assistant that can handle the administrative burden of academic work, letting you focus on the science and discovery!

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