Red Tide Algal Bloom Monitoring

Red Tide Algal Bloom Monitoring & Early Warning Skill

Skill Overview

This skill transforms Claude into a domain-expert for Harmful Algal Bloom (HAB) Monitoring & Aquaculture Safety. It delivers structured, evidence-backed outputs by combining real-time data aggregation, recognized domain methods, and academic research into a single orchestrated workflow with explicit risk disclosure.

Core Capabilities

• Bloom Detection: Satellite (Sentinel-3 OLCI, MODIS) + in-situ sensor analysis
• Species Identification: Karenia, Alexandrium, Dinophysis, Pseudo-nitzschia, cyanobacteria
• Toxin Risk Assessment: Paralytic, diarrhetic, amnesic, neurotoxic shellfish poisoning
• Aquaculture Impact: Shellfish vulnerability, harvest closure timing, economic risk
• Environmental Triggers: Temperature, nutrients (N/P/Si), stratification, upwelling
• Early Warning: Alert levels, response protocols, mitigation strategies

Evidence-Based Framework

All outputs cite ≥3 sources with ≥1 academic/authoritative reference, explicit evidence hierarchy (Tier 1-4), and mandatory risk/limitation disclosure. The skill continuously improves through automated knowledge crawling from academic databases and domain authorities.

---

Harness Architecture

Skill Registry Pattern

The skill implements a flexible agent & skill architecture using a modular pattern:

/skill activation
│
├─ Language Detection (pre-flight)
│   ├─ Vietnamese → translation + bilingual output
│   ├─ English → direct processing
│   └─ Other → English processing + translation offer
│
├─ Step 1: sub-gather-requirements
│   └─ Input: User query
│   └─ Output: Structured requirements (object, scope, timeframe, inputs, audience, language)
│
├─ Step 2: sub-evidence-collector
│   ├─ Fetch: Current satellite data (Copernicus, NOAA)
│   ├─ Fetch: In-situ sensor data (fluorometer, CTD)
│   ├─ Fetch: Authoritative documents (IOC-UNESCO, WOAH)
│   └─ Output: Evidence bundle with sources + dates
│
├─ Step 3: sub-core-analysis
│   ├─ Detect: Satellite chl-a + SST analysis
│   ├─ Detect: In-situ cell counts + species ID
│   ├─ Analyze: Environmental triggers (T, nutrients, stratification)
│   ├─ Assess: Toxin risk (type, concentration, regulatory limits)
│   └─ Alert: Aquaculture impact + response levels
│
├─ Step 4: sub-knowledge-updater
│   ├─ Query: SECOND-KNOWLEDGE-BRAIN.md
│   ├─ Surface: Academic citations (with Tier labels)
│   └─ Flag: Knowledge gaps for crawl pipeline
│
├─ Step 5: sub-advisor
│   ├─ Synthesize: All prior analysis
│   ├─ Conclude: Risk category (Low/Monitor/Critical)
│   ├─ Recommend: Specific actions with evidence chain
│   └─ Disclose: Limitations + uncertainty
│
└─ Step 6: main quality gate
    ├─ Verify: Evidence hierarchy compliance
    ├─ Verify: Source citations (≥3 sources, ≥1 authoritative)
    ├─ Verify: Risk disclosure present
    ├─ Verify: Output template completeness
    └─ Auto-fix: Up to 2 retries for missing elements

Agent Registration & Resolution

Skill Registration

Skills are registered in /skills/*.md with mandatory frontmatter:

---
name: sub-gather-requirements
description: Clarify the object of analysis, constraints, timeframe, available inputs, target audience, and language before any data fetching.
---

Registration Requirements:

• name: Unique identifier (kebab-case)
• description: One-line summary (mandatory, used for routing)
• Sections: Role & Persona, Workflow, Tools, Output Format, Quality Gates

Skill Resolution

The harness uses semantic routing to resolve the appropriate sub-skill:

1. Input Analysis: Extract task type from user query
2. Skill Matching: Compare against skill descriptions
3. Execution Order: Follow sequential harness flow
4. Fallback Chain: On failure → knowledge base → simplified analysis → explicit limitation flag

Skill Execution Model

Each sub-skill follows the execution lifecycle:

class SubSkillExecution:
    def execute(self, context: ExecutionContext) -> SkillResult:
        # 1. Input validation
        self._validate_inputs(context)
        
        # 2. Tool execution (with retries)
        result = self._execute_tools(context)
        
        # 3. Quality gate validation
        self._validate_quality_gates(result)
        
        # 4. Error handling (graceful degradation)
        if result.failed:
            return self._handle_degradation(context)
        
        # 5. Output formatting
        return self._format_output(result)

---

Input/Output JSON Schemas

Input Schema (User Query)

{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "title": "RedTideSkillInput",
  "type": "object",
  "required": ["query"],
  "properties": {
    "query": {
      "type": "string",
      "description": "User's natural language query about HAB monitoring or aquaculture safety",
      "minLength": 1,
      "examples": [
        "Analyze red tide risk for oyster farms in Apalachicola Bay",
        "What's the current bloom status off the coast of Maine?",
        "Assess toxin risk for shellfish harvest in Puget Sound"
      ]
    },
    "context": {
      "type": "object",
      "properties": {
        "region": {"type": "string", "description": "Geographic region of interest"},
        "timeframe": {"type": "string", "description": "Analysis timeframe (e.g., 'current', 'next 7 days')"},
        "target_audience": {"type": "string", "enum": ["aquaculture", "public_health", "researcher", "general"]},
        "language": {"type": "string", "enum": ["en", "vi", "es", "fr", "ja", "zh"], "default": "en"}
      }
    },
    "options": {
      "type": "object",
      "properties": {
        "include_recommendations": {"type": "boolean", "default": true},
        "include_scenarios": {"type": "boolean", "default": true},
        "detail_level": {"type": "string", "enum": ["brief", "standard", "comprehensive"], "default": "standard"}
      }
    }
  }
}

Output Schema (Skill Result)

{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "title": "RedTideSkillOutput",
  "type": "object",
  "required": ["metadata", "analysis", "evidence_chain", "conclusion", "disclosure"],
  "properties": {
    "metadata": {
      "type": "object",
      "required": ["skill_version", "timestamp", "language", "processing_time_ms"],
      "properties": {
        "skill_version": {"type": "string", "pattern": "^\\d+\\.\\d+\\.\\d+$"},
        "timestamp": {"type": "string", "format": "date-time"},
        "language": {"type": "string"},
        "processing_time_ms": {"type": "number"},
        "degradation_level": {"type": "integer", "minimum": 0, "maximum": 4}
      }
    },
    "requirements": {
      "type": "object",
      "properties": {
        "object_of_analysis": {"type": "string"},
        "scope": {"type": "string"},
        "timeframe": {"type": "string"},
        "available_inputs": {"type": "array", "items": {"type": "string"}},
        "target_audience": {"type": "string"},
        "language": {"type": "string"},
        "analysis_type": {"type": "string"}
      }
    },
    "evidence_bundle": {
      "type": "object",
      "properties": {
        "current_data": {
          "type": "object",
          "properties": {
            "satellite_chl_a": {"type": "object"},
            "sst": {"type": "object"},
            "in_situ_counts": {"type": "object"},
            "toxin_levels": {"type": "object"}
          }
        },
        "authoritative_docs": {
          "type": "array",
          "items": {
            "type": "object",
            "properties": {
              "source": {"type": "string"},
              "url": {"type": "string"},
              "date": {"type": "string"},
              "tier": {"type": "integer", "minimum": 1, "maximum": 4}
            }
          }
        },
        "recent_news": {"type": "array", "items": {"type": "object"}},
        "reference_benchmarks": {"type": "object"}
      }
    },
    "analysis": {
      "type": "object",
      "properties": {
        "detection": {
          "type": "object",
          "properties": {
            "bloom_status": {"type": "string"},
            "cell_concentration": {"type": "string"},
            "species_identified": {"type": "array", "items": {"type": "string"}},
            "confidence": {"type": "string"}
          }
        },
        "triggers": {
          "type": "object",
          "properties": {
            "temperature": {"type": "object"},
            "nutrients": {"type": "object"},
            "stratification": {"type": "string"},
            "upwelling": {"type": "string"}
          }
        },
        "toxin_risk": {
          "type": "object",
          "properties": {
            "toxin_type": {"type": "array", "items": {"type": "string"}},
            "risk_level": {"type": "string"},
            "regulatory_limit_exceeded": {"type": "boolean"}
          }
        },
        "aquaculture_impact": {
          "type": "object",
          "properties": {
            "species_affected": {"type": "array", "items": {"type": "string"}},
            "vulnerability_level": {"type": "string"},
            "economic_risk": {"type": "string"}
          }
        }
      }
    },
    "knowledge_base": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "citation": {"type": "string"},
          "tier": {"type": "integer", "minimum": 1, "maximum": 4},
          "relevance": {"type": "string"}
        }
      }
    },
    "evidence_chain": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "claim": {"type": "string"},
          "evidence": {"type": "array", "items": {"type": "string"}},
          "confidence": {"type": "string"}
        }
      }
    },
    "conclusion": {
      "type": "object",
      "required": ["category"],
      "properties": {
        "category": {
          "type": "string",
          "enum": [
            "Low Risk",
            "Normal",
            "Monitor (elevated)",
            "Critical Bloom Alert",
            "Inconclusive"
          ]
        },
        "summary": {"type": "string"},
        "confidence": {"type": "string"},
        "key_factors": {"type": "array", "items": {"type": "string"}}
      }
    },
    "recommendations": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "action": {"type": "string"},
          "priority": {"type": "string"},
          "evidence": {"type": "array", "items": {"type": "string"}}
        }
      }
    },
    "scenarios": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "name": {"type": "string"},
          "probability": {"type": "string"},
          "impact": {"type": "string"},
          "mitigation": {"type": "array", "items": {"type": "string"}}
        }
      }
    },
    "disclosure": {
      "type": "object",
      "required": ["limitations", "uncertainties", "data_quality"],
      "properties": {
        "limitations": {"type": "array", "items": {"type": "string"}},
        "uncertainties": {"type": "array", "items": {"type": "string"}},
        "data_quality": {"type": "string"},
        "assumptions": {"type": "array", "items": {"type": "string"}}
      }
    }
  }
}

---

Tool Definitions & Schemas

Tool Registry

The skill defines rich tool definitions with schemas and execution handlers:

Satellite Data Fetch Tool

{
  "tool_name": "fetch_satellite_data",
  "description": "Fetch current satellite chlorophyll-a and sea surface temperature data for specified region",
  "parameters": {
    "region": {
      "type": "string",
      "description": "Geographic region (bounding box or named region)",
      "required": true
    },
    "date_range": {
      "type": "string",
      "description": "Date range for data retrieval (ISO 8601 format)",
      "required": false,
      "default": "last_7_days"
    },
    "resolution": {
      "type": "string",
      "enum": ["1km", "4km", "9km"],
      "default": "4km"
    }
  },
  "response_schema": {
    "chl_a": {
      "mean": "float",
      "max": "float",
      "anomaly": "float",
      "data_url": "string"
    },
    "sst": {
      "mean": "float",
      "min": "float",
      "max": "float",
      "anomaly": "float",
      "data_url": "string"
    },
    "metadata": {
      "satellite": "string",
      "processing_date": "string",
      "coverage": "float"
    }
  },
  "execution_handler": "sub-evidence-collector",
  "timeout": 30,
  "retry": 3
}

In-Situ Sensor Query Tool

{
  "tool_name": "query_in_situ_sensors",
  "description": "Query in-situ monitoring stations for cell counts and environmental parameters",
  "parameters": {
    "region": {"type": "string", "required": true},
    "sensor_types": {
      "type": "array",
      "items": {"enum": ["fluorometer", "ctd", "spectrometer"]},
      "default": ["fluorometer"]
    },
    "timeframe": {"type": "string", "default": "last_7_days"}
  },
  "response_schema": {
    "stations": [
      {
        "station_id": "string",
        "location": {"lat": "float", "lon": "float"},
        "measurements": {
          "cell_count": {"value": "int", "units": "cells/L"},
          "chlorophyll": {"value": "float", "units": "mg/m³"},
          "temperature": {"value": "float", "units": "°C"},
          "salinity": {"value": "float", "units": "PSU"}
        },
        "timestamp": "string"
      }
    ],
    "metadata": {
      "station_count": "int",
      "data_quality": "string"
    }
  },
  "execution_handler": "sub-evidence-collector",
  "timeout": 20,
  "retry": 2
}

Authoritative Document Fetch Tool

{
  "tool_name": "fetch_authoritative_docs",
  "description": "Fetch current guidance and standards from authoritative HAB monitoring sources",
  "parameters": {
    "sources": {
      "type": "array",
      "items": {"enum": ["IOC-UNESCO", "NOAA", "Copernicus", "WOAH"]},
      "default": ["IOC-UNESCO", "NOAA"]
    },
    "topic": {"type": "string", "required": true},
    "document_types": {
      "type": "array",
      "items": {"enum": ["guidelines", "standards", "reports", "alerts"]},
      "default": ["guidelines", "alerts"]
    }
  },
  "response_schema": {
    "documents": [
      {
        "source": "string",
        "title": "string",
        "url": "string",
        "publication_date": "string",
        "tier": "int",
        "summary": "string",
        "key_points": ["string"]
      }
    ],
    "metadata": {
      "document_count": "int",
      "source_coverage": "string"
    }
  },
  "execution_handler": "sub-evidence-collector",
  "timeout": 45,
  "retry": 3
}

Knowledge Base Query Tool

{
  "tool_name": "query_knowledge_base",
  "description": "Query SECOND-KNOWLEDGE-BRAIN.md for academic and professional evidence",
  "parameters": {
    "keywords": {
      "type": "array",
      "items": {"type": "string"},
      "required": true
    },
    "max_results": {"type": "integer", "default": 5, "maximum": 10},
    "min_tier": {"type": "integer", "enum": [1, 2, 3, 4], "default": 2}
  },
  "response_schema": {
    "results": [
      {
        "citation": "string",
        "tier": "int",
        "relevance_score": "float",
        "year": "int",
        "venue": "string",
        "doi": "string",
        "key_findings": ["string"]
      }
    ],
    "coverage": {
      "total_entries": "int",
      "matched_entries": "int",
      "gap_areas": ["string"]
    }
  },
  "execution_handler": "sub-knowledge-updater",
  "timeout": 10,
  "retry": 1
}

---

Hooks & Lifecycle Management

Hook Types

The skill implements clean, reusable hooks for lifecycle events:

Pre-Execution Hooks

class PreExecutionHooks:
    """Hooks invoked before skill execution"""
    
    @h

…

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [dungnotnull](https://github.com/dungnotnull)
- **Source:** [dungnotnull/red-tide-algal-bloom-monitoring-agent-skill](https://github.com/dungnotnull/red-tide-algal-bloom-monitoring-agent-skill)
- **License:** MIT

Install and usage instructions live in the source repository linked above.