MCP Servers

External tool integrations

Claude Code / Advanced / MCP Servers

Advanced 10 min read Phase 4: Advanced

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MCP (Model Context Protocol) servers connect Claude to external tools, databases, and services.

What Are MCP Servers?

MCP servers provide Claude with: - Access to databases (PubMed, UniProt, etc.) - Integration with lab systems - Specialized scientific tools - Data visualization capabilities

Recommended Plugins

The lab recommends these plugins (which include MCP servers):

scientific-skills

Scientific databases and analysis tools:

claude plugins install scientific-skills@claude-scientific-skills

Provides access to: - Databases: PubMed, UniProt, KEGG, ChEMBL, ClinicalTrials.gov - Analysis: Statistical methods, visualization - Data formats: FASTA, PDB, CSV, Excel

superpowers

Development workflow tools:

claude plugins install superpowers@superpowers-marketplace

Provides: - Code review agents - TDD workflows - Debugging tools - Git worktree management

github

GitHub CLI integration:

claude plugins install github@claude-plugins-official

Provides: - Issue management - Pull request workflows - Repository operations

Using MCP-Provided Tools

Database Queries

With scientific-skills installed:

> Search PubMed for recent papers on TREM2 and Alzheimer's

> Get the protein sequence for human TP53 from UniProt

> What clinical trials are recruiting for glioblastoma?

Data Analysis

> Perform a power analysis for a two-sample t-test

> Create a volcano plot from this differential expression data

> Run a survival analysis on the patient data

File Operations

> Read the Excel file and summarize the data

> Convert this FASTA to a table format

> Parse the PDB file and extract chain A coordinates

Configuration

MCP servers are configured through plugins. Check your configuration:

# List installed plugins
claude plugins list

# Check what tools are available
claude tools list

Lab-Specific Integrations

Accessing Lab Data

For projects that need lab-specific integrations:

{
  "mcp": {
    "servers": {
      "lab-data": {
        "command": "python",
        "args": ["scripts/lab_data_server.py"],
        "description": "Access to /proj/rashidlab/ data"
      }
    }
  }
}

Custom Scientific Tools

For specialized analysis:

{
  "mcp": {
    "servers": {
      "simulation-tools": {
        "command": "Rscript",
        "args": ["scripts/simulation_server.R"],
        "description": "Run simulations with lab parameters"
      }
    }
  }
}

Available Skills from Plugins

scientific-skills Database Tools

Tool	Description
pubmed-database	Search PubMed literature
uniprot-database	Query protein sequences
pdb-database	Access protein structures
kegg-database	Query pathway data
chembl-database	Search compound data
clinicaltrials-database	Find clinical trials

scientific-skills Analysis Tools

Tool	Description
statistical-analysis	Statistical tests
exploratory-data-analysis	EDA workflows
scientific-visualization	Create figures
hypothesis-generation	Research planning

superpowers Development Tools

Tool	Description
code-review	Review code changes
test-driven-development	TDD workflows
systematic-debugging	Debug issues
brainstorming	Design discussions

Example Workflows

Literature Search

> Search PubMed for papers on Bayesian adaptive trials
> published in the last 2 years

Claude uses pubmed-database to query and summarize results.

Protein Analysis

> Get the TP53 sequence from UniProt and identify
> functional domains

Claude fetches data and analyzes the protein.

Statistical Analysis

> Run a power analysis for detecting a 0.5 effect size
> with alpha=0.05

Claude uses statistical tools to compute power.

Troubleshooting

Tool not found

# Reinstall the plugin
claude plugins uninstall scientific-skills@claude-scientific-skills
claude plugins install scientific-skills@claude-scientific-skills

Server connection failed

# Check plugin status
claude plugins list

# Check for updates
claude plugins update

Tool runs slowly

Large database queries may take time. For complex queries, consider: - Breaking into smaller queries - Using more specific search terms - Caching results locally

Security Notes

• MCP servers can access external resources
• Be cautious with sensitive data
• Lab data should stay on approved systems
• Don’t expose credentials in MCP configurations