@seosiri/biopharma-mcp

📖 Official Architecture & Documentation: SEOSiri Biopharma Technical Guide | Developer Portal & Graph Explorer | Central MCP Directory

An open-source, local-first Model Context Protocol (MCP) server written in TypeScript for Biopharma Software Infrastructure, FDA 21 CFR Part 11 GxP Audit Trailing, CDISC SDTM/Allotrope Data Exports, 4PL Dose-Response Curve Fitting, and HIPAA PII/PHI Redaction.

🛡️ Enterprise Compliance & Regulatory Clauses

1. FDA 21 CFR Part 11 Audit Trail Clause

All operational tool executions generate an immutable SHA-256 cryptographic digest written directly to the stderr stream (generate_gxp_audit_log). This preserves audit trail integrity, operator identification, and timestamp sequence rules without altering the standard JSON-RPC data payload.

2. HIPAA PII/PHI Privacy Redaction Clause

Every data payload passed through memory is automatically processed by a zero-latency privacy cleaning loop (redactPatientPii). Common sensitive patient identifiers—including Social Security Numbers (SSN), email addresses, Date of Birth (DOB) strings, and telephone patterns—are redacted prior to memory serialization or cloud database pooling.

3. Data-at-Rest AES-256-GCM Encryption Clause

Database connection parameters and sensitive data fields stored in cloud instances are encrypted using AES-256-GCM blocks with random 12-byte initialization vectors (IVs) and authentication tags (encryptRestData / decryptRestData).

🚀 10 Zod-Validated Production Tools

1. calculate_4pl_curve: Fits 4-Parameter Logistic non-linear regression sigmoidal dose-response curves.
2. assess_parallelism: Computes shared slope and asymptotes consistency via F-Test and TOST equivalence metrics.
3. calculate_z_factor: Validates microplate high-throughput screening (HTS) quality from positive and negative control series.
4. parse_large_plate_stream: Memory-safe stream parser for 96-well or 384-well microplate layout string rows.
5. resolve_biological_entity_safe: Fault-tolerant Circuit Breaker container for ChEBI and PubChem compound queries.
6. detect_assay_outliers: Grubbs and IQR mathematical filtering boundaries to detect and drop anomalous microplate artifacts.
7. calculate_lod_loq: Calculates Limit of Detection (LOD) and Limit of Quantitation (LOQ) from background blank deviations.
8. normalize_dilution_potency: Scales observed target calculations dynamically across complex serial dilution ratios.
9. export_cdisc_sdtm: Converts internal JSON records into CDISC SDTM v1.7 / Allotrope Data Model compliant structural models.
10. generate_gxp_audit_log: Records immutably hashed operation logs to maintain compliance with FDA 21 CFR Part 11.

📦 Installation & Setup Guide

1. Install via NPM / NPX

# Global installation
npm install -g @seosiri/biopharma-mcp

# Local project installation
npm install @seosiri/biopharma-mcp

2. Build and Test Locally

# Compile TypeScript to ESM (dist/index.js)
npm run build

# Run unit test suite
npm test

🔌 AI Host Client Integrations

Claude Desktop Setup

Add this to your claude_desktop_config.json file:

{
  "mcpServers": {
    "seosiri-biopharma": {
      "command": "node",
      "args": [
        "D:/biopharma-mcp/dist/index.js"
      ]
    }
  }
}

Cursor IDE Setup

Add this to your mcp.json file or configure it directly in the IDE settings:

{
  "mcpServers": {
    "seosiri-biopharma": {
      "command": "npx",
      "args": [
        "-y",
        "@seosiri/biopharma-mcp"
      ]
    }
  }
}

💖 Sponsorship, B2B Custom Solutions & Attribution

Lead Architect

Designed and engineered by Momenul Ahmad, Lead Architect and Founder of SEOSiri.

Enterprise B2B Custom Development

SEOSiri provides high-ticket systems architecture, custom biopharma MCP tool engineering, and Cloudflare Zero Trust gateway integration for corporate clients in the United States, United Kingdom, Canada, Germany, and Japan.

• Official Portal: developers.seosiri.com
• Corporate Support Email: [email protected]
• GitHub Sponsors: Sponsor SEOSiri-Official on GitHub

License

Distributed under the MIT License.