Context Initialization

Overview

AGENTS.md

When to Use This Skill

• The agent initializes in this workspace
• User begins any scientific task (database access, package usage, platform integration, or methodology)
• User mentions specific databases, packages, platforms, or research methods
• Any scientific data retrieval, analysis, or research task is started

What This Skill Does

AGENTS.md

1. Search first: Look for relevant skills across all skill categories before writing code
2. Use existing patterns: Apply documented API access patterns, workflows, and examples
3. Follow best practices: Use rate limits, authentication, configurations, and established methodologies
4. Adapt examples: Leverage working code examples from

   scripts/

   folders and reference documentation

AGENTS.md

Skill Categories

Database Access Tasks

• Search

  scientific-databases/

  for 24+ database skills
• Use documented API endpoints and authentication patterns
• Apply working code examples and best practices
• Follow rate limits and error handling patterns

Scientific Package Usage

• Search

  scientific-packages/

  for 40+ Python package skills
• Use installation instructions and API usage examples
• Apply best practices and common patterns
• Leverage working scripts and reference documentation

Laboratory Platform Integration

• Search

  scientific-integrations/

  for 6+ platform integration skills
• Use authentication and setup instructions
• Apply API access patterns and platform-specific best practices
• Leverage working integration examples

Scientific Analysis & Research Methods

• Search

  scientific-thinking/

  for methodology skills
• Use established data analysis frameworks (EDA, statistical analysis)
• Apply research methodologies (hypothesis generation, brainstorming, critical thinking)
• Leverage communication skills (scientific writing, visualization, peer review)
• Use document processing skills (DOCX, PDF, PPTX, XLSX)

Implementation

AGENTS.md

• If

  AGENTS.md

  does not exist: Creates a new file using the complete template from

  references/AGENTS.md

• If

  AGENTS.md

  already exists: Updates the file to ensure the essential skill-search directives are present, while preserving any existing custom content or modifications

references/AGENTS.md

Benefits

• Consistency: The agent always uses the same approach across all skill types
• Efficiency: One initialization covers all scientific tasks
• Maintainability: Updates to the initialization strategy occur in one place
• Completeness: The agent is reminded to search across all available skill categories