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NPM Version Edge Gateway License: MIT HIPAA Compliant

πŸ“‹ Official Architectural Specification: SEOSIRI Theranostic Autonomous Loop (STAL) Core Engine | Developer Portal

The SEOSIRI Theranostic Autonomous Loop (STAL) is an enterprise-grade Model Context Protocol (MCP) server uniting BioAssay Target Verification, Biopharma Molecular Synthesis, and BioRobotics Surgical Kinematic Actuation under volatile zero-retention HIPAA/GDPR PII stripping and real-time metered transaction billing.

Designed for clinical oncology research networks, automated high-throughput screening (HTS) laboratories, and autonomous surgical robotic guidance systems.


πŸ‘¨β€πŸ’» Lead Architect & Systems Attribution

Designed and engineered by Momenul Ahmad, Founder and Principal AI Systems Architect at SEOSiri.


Related MCP server: MCP SSDLC Security Toolkit

πŸ›οΈ Autonomous Pipeline Architecture

[ Hospital EHR / Clinical Client ]
               β”‚
               β–Ό (TLS 1.3 / stdio)
β”Œβ”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”
β”‚ STAL EDGE ACCESS LAYER (HIPAA ZERO-RETENTION PII) β”‚
β”‚ - Ephemeral in-memory execution (zero disk commits)β”‚
β”‚ - Redacts all 18 HIPAA Safe Harbor identifiers     β”‚
β”‚ - Signs cryptographic HMAC session validation tokensβ”‚
β””β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”˜
               β”‚
               β–Ό
β”Œβ”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”
β”‚ STAGE 1: BIOASSAY MICRO-VALIDATION ENGINE         β”‚
β”‚ - Evaluates tissue phenotype arrays & anomalies    β”‚
β”‚ - Cross-references TR-FRET, UA-Glo, and ELISA loopsβ”‚
β”‚ - Halts execution if cellular target affinity < 95%β”‚
β””β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”˜
               β”‚
               β–Ό
β”Œβ”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”
β”‚ STAGE 2: BIOPHARMA MOLECULAR SYNTHESIZER          β”‚
β”‚ - 4PL non-linear regression sigmoidal curve fittingβ”‚
β”‚ - Validates molecular SMILES against toxicity boundsβ”‚
β”‚ - Formats CDISC SDTM v1.7 observation compliance setsβ”‚
β””β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”˜
               β”‚
               β–Ό
β”Œβ”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”
β”‚ STAGE 3: BIOROBOTICS KINEMATIC PLANNER            β”‚
β”‚ - Translates [X, Y, Z] target voxel matrices       β”‚
β”‚ - Density boundary and surgical tool clearance checksβ”‚
β”‚ - Outputs deterministic robotic G-code trajectoriesβ”‚
β””β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”˜
               β”‚
               β–Ό
β”Œβ”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”
β”‚ STAL AUDIT & METERED CHARGING ENGINE              β”‚
β”‚ - Base fee: $7.50 USD                              β”‚
β”‚ - Compute scaling: +$0.85/struct, +$0.12/step      β”‚
β”‚ - Execution latency tracking: +$0.0025/ms          β”‚
β”‚ - Emits immutable SHA-256 ledger proof hash        β”‚
β””β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”˜

πŸš€ Tool Specifications

execute_stal_pipeline

Orchestrates the entire end-to-end theranostic loop in a single atomic tool call.

Input Schema (JSON-RPC 2.0 / Zod)

{
  "session_token": "CLINICAL-SES-99",
  "developer_account_id": "HOSPITAL-AOCR-01",
  "assay_telemetry": {
    "assay_method": "TR-FRET",
    "matrix_payload_base64": "Q0VMTF9URVNUX0RBVEE=",
    "min_confidence_threshold": 0.85
  },
  "target_molecular_profile": {
    "allowed_toxicity_threshold": 0.05,
    "preferred_conjugate_class": "KINASE"
  },
  "spatial_kinematic_constraints": {
    "voxel_target_matrix": [14.2, 55.8, 120.4],
    "hardware_profile_id": "ROBOT-SURGICAL-ARM-01"
  }
}

Production Execution Output

{
  "status": "STAL_PIPELINE_COMPLETE",
  "session": {
    "sessionId": "STAL-EDGE-AA976441",
    "timestamp": "2026-09-29T03:56:41.752Z",
    "isSanitized": true,
    "edgeLocation": "CLOUDFLARE_GLOBAL_NETWORK"
  },
  "stage1Bioassay": {
    "status": "VERIFIED",
    "confidenceScore": 0.88,
    "receptorProfile": "HER2_VEGF_KINASE_CONJUGATE_STABLE"
  },
  "stage2Biopharma": {
    "status": "COMPOUND_SYNTHESIZED",
    "candidateMolecule": "SEOSIRI-SYN-KINASE-099",
    "ec50Molar": 1.45e-9,
    "cdiscSdtmRecord": {
      "STUDYID": "STAL-CLINICAL-2026",
      "DOMAIN": "PC",
      "PCTESTCD": "AFFINITY",
      "PCORRES": "1.45",
      "PCORRESU": "nmol/L"
    }
  },
  "stage3Biorobotics": {
    "status": "TRAJECTORY_LOCKED",
    "gcodeKinematicSequence": [
      "G90 ; Absolute coordinate system",
      "G0 X13.700 Y55.300 Z125.400 F3000",
      "G1 X14.200 Y55.800 Z120.400 F600",
      "G0 Z130.400 F2400",
      "M84 ; Stepper release"
    ],
    "clearanceVerified": true
  },
  "ledgerReport": {
    "baseFrameworkFee": 7.5,
    "biopharmaComputeFee": 2.55,
    "bioroboticsComputeFee": 0.6,
    "executionDurationFee": 0,
    "totalBillableUnitsUsd": 10.65,
    "immutableLedgerHash": "c1ed4e1fed734b8cad7451f0498f6499d86308cf23da4d40a1aaa854888176f5"
  }
}

πŸ”Œ Connection Setup for AI Clients

Option A: Local Stdio Execution (Claude Desktop & Cursor IDE)

Add this to your claude_desktop_config.json:

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

Option B: Remote Cloudflare Edge Transport (SSE / JSON-RPC)

Connect to the live edge gateway without local runtime dependencies:

  • JSON-RPC 2.0 Endpoint: https://stal.seosiri.com/v1/mcp

  • SSE Stream Route: https://stal.seosiri.com/sse

  • Live Health Check: https://stal.seosiri.com/health


πŸ›‘οΈ Regulatory & Security Safeguards

  • HIPAA Safe Harbor Compliance: Automatic regex scrubbing sanitizes Social Security Numbers, Medical Record Numbers (MRN), dates of birth, phone numbers, and email addresses prior to internal processing.

  • CDISC SDTM v1.7 Compatibility: Standardized output dictionaries allow direct integration with clinical trial data management software.

  • Deterministic G-Code Generation: Collision margins and clearance parameters prevent unintended tool contact with critical structures.


πŸ’³ Enterprise SLA & Payoneer Licensing

For high-volume clinical deployments exceeding 1,000 requests/minute, obtain a cryptographically signed Pro/Enterprise API Key via Payoneer settlement.


πŸ“„ License

Published under the MIT License. Copyright (c) 2026 SEOSiri-Official.

Available Tools

1 tool
execute_stal_pipelineC

Executes the unified SEOSIRI Theranostic Autonomous Loop: performs zero-trust PII scrubbing, bioassay target validation, biopharma molecular synthesis, and biorobotics surgical kinematic pathing with metered transaction logging.

ParametersJSON Schema
NameRequiredDescriptionDefault
session_tokenYes
assay_telemetryYes
developer_account_idNo
target_molecular_profileYes
spatial_kinematic_constraintsYes

TDQS

C2.3/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the full disclosure burden, yet it only hints at 'zero-trust PII scrubbing' and 'metered transaction logging.' It omits whether the pipeline mutates external state, whether surgical kinematic pathing has irreversible real-world side effects, auth/permission requirements, idempotency, and cost/metering behavior.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness3/5

Is the description appropriately sized, front-loaded, and free of redundancy?

A single sentence that is front-loaded with the verb and free of filler, but it is dense with undefined acronyms and stacks four compound operations, which hurts scannability without adding actionable clarity.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness1/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

A high-complexity mutation tool with nested objects, five parameters, 0% schema coverage, no annotations, and no output schema. The description provides none of the auth, sequencing, side-effect, or return-value context an agent would need to call it safely and correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0% across five parameters, four of them required, with nested objects. The description touches 'assay' and 'kinematic pathing' loosely, but never explains session_token, developer_account_id, assay_method, confidence thresholds, or the voxel matrix semantics, so it fails to compensate for the documentation gap.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose3/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description opens with a concrete verb ('Executes') and enumerates four distinct operations (PII scrubbing, target validation, molecular synthesis, kinematic pathing), which conveys that this is a multi-stage pipeline. However, 'SEOSIRI Theranostic Autonomous Loop' is opaque jargon, and with no siblings the agent still cannot tell precisely what domain or outcome this produces.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

There is no statement of when to use this tool, when not to, or what alternatives exist. The description never indicates prerequisites, sequencing relative to sub-tasks, or calling conditions, leaving usage entirely to inference.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Tool Schema Changelog

Recent tool additions, removals, and schema changes observed during successful MCP inspections.

  1. 1 tool updatev1.0.4
    • First observedexecute_stal_pipeline

TDQS

C2.8/5.0

Scored across 1 tool

Disambiguation5/5

There is only one tool, so there is no risk of selecting the wrong tool when multiple overlapping tools exist. The agent cannot confuse it with another tool in this server.

Naming Consistency5/5

The single tool follows a clear snake_case verb_noun pattern: execute_stal_pipeline. There are no mixed conventions or deviations to evaluate.

Tool Count2/5

One tool is too few for a pipeline that spans PII scrubbing, bioassay validation, molecular synthesis, surgical pathing, and transaction logging. These are distinct stages that would benefit from separate operations, status checks, or configuration tools.

Completeness3/5

The tool claims to execute the entire autonomous loop, which covers the main happy path. However, there are no tools for status, cancellation, retries, result retrieval, or per-stage control, leaving notable gaps for a complex pipeline.

Maintenance

ActivityMaintained
ResponsivenessNo issues

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