diff --git a/claude.md b/claude.md
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+# Claude Scientific Skills - Working Instructions
+
+## IMPORTANT: Search for Skills First
+
+Before attempting any scientific task, search for relevant skills in this repository.
+
+---
+
+## Database Access Tasks
+
+**Before writing any database access code, search for relevant skills in this repository.**
+
+This repository contains skills for 24+ scientific databases. Each skill includes:
+- API endpoints and authentication patterns
+- Working code examples
+- Best practices and rate limits
+- Example scripts
+
+Always search for and use existing database skills before writing custom database access code.
+
+---
+
+## Scientific Package Usage
+
+**Before writing analysis code with scientific packages, search for relevant skills in this repository.**
+
+This repository contains skills for 40+ scientific Python packages. Each skill includes:
+- Installation instructions
+- Complete API usage examples
+- Best practices and common patterns
+- Working scripts and reference documentation
+
+Always search for and use existing package skills before writing custom analysis code.
+
+---
+
+## Laboratory Platform Integration
+
+**Before writing any platform integration code, search for relevant skills in this repository.**
+
+This repository contains skills for 6+ laboratory platforms and cloud services. Each skill includes:
+- Authentication and setup instructions
+- API access patterns
+- Working integration examples
+- Platform-specific best practices
+
+Always search for and use existing integration skills before writing custom platform code.
+
+---
+
+## Scientific Analysis & Research Methods
+
+**Before attempting any analysis, writing, or research task, search for relevant methodology skills in this repository.**
+
+This repository contains skills for scientific methodologies including:
+- Data analysis frameworks (EDA, statistical analysis)
+- Research methodologies (hypothesis generation, brainstorming, critical thinking)
+- Communication skills (scientific writing, visualization, peer review)
+- Document processing (DOCX, PDF, PPTX, XLSX)
+
+Always search for and use existing methodology skills before attempting scientific analysis or writing tasks.
+
+---
+
+*This file is auto-generated by context-initialization skills. It ensures Claude searches for and uses existing skills before attempting to solve scientific tasks from scratch.*
+
diff --git a/scientific-databases/context-initialization/SKILL.md b/scientific-databases/context-initialization/SKILL.md
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+---
+name: context-initialization
+description: "Always Auto-invoked skill that creates/updates workspace claude.md to instruct Claude to always search for existing database skills before attempting any database access task."
+---
+
+# Database Context Initialization
+
+## Overview
+
+This skill automatically creates or updates a `claude.md` file in the workspace root that instructs Claude to search for existing database skills before attempting to write database access code. This ensures Claude uses documented API patterns, authentication methods, and best practices from the repository's database skills rather than inventing solutions from scratch.
+
+## When to Use This Skill
+
+This skill is automatically invoked when:
+- Claude Code initializes in this workspace
+- User begins any database-related task
+- User mentions database access, queries, or API interactions
+- Any scientific data retrieval task is started
+
+**No manual invocation required** - this skill runs automatically.
+
+## What This Skill Does
+
+Creates or updates `claude.md` in the workspace root with instructions for Claude to:
+
+1. **Search first**: Look for relevant database skills in `scientific-databases/` before writing code
+2. **Use existing patterns**: Apply documented API access patterns and examples
+3. **Follow best practices**: Use rate limits, authentication, and error handling from skills
+4. **Adapt examples**: Leverage working code examples from `scripts/` folders
+
+## Implementation
+
+When invoked, this skill creates/updates the workspace `claude.md` file with a section instructing Claude to search for and use existing database skills for any database access tasks.
+
+The reference template is available in `references/claude.md`.
+
+## Integration
+
+Works alongside other context-initialization skills:
+- `scientific-packages/context-initialization` - for Python package usage
+- `scientific-integrations/context-initialization` - for lab platform integration
+- `scientific-thinking/context-initialization` - for analysis methodologies
+
+Together, these ensure Claude always leverages existing expertise before attempting scientific tasks.
diff --git a/scientific-databases/context-initialization/references/claude.md b/scientific-databases/context-initialization/references/claude.md
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+# Reference: Database Context Section
+
+This is the reference template for what gets added to the workspace root `claude.md` file.
+
+---
+
+## Database Access Tasks
+
+**Before writing any database access code, search for relevant skills in this repository.**
+
+This repository contains skills for 24+ scientific databases. Each skill includes:
+- API endpoints and authentication patterns
+- Working code examples
+- Best practices and rate limits
+- Example scripts
+
+Always search for and use existing database skills before writing custom database access code.
+
+---
diff --git a/scientific-integrations/context-initialization/SKILL.md b/scientific-integrations/context-initialization/SKILL.md
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+++ b/scientific-integrations/context-initialization/SKILL.md
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+---
+name: context-initialization
+description: "Auto-invoked skill that creates/updates workspace claude.md to instruct Claude to always search for existing integration skills before attempting any laboratory platform or cloud service integration task."
+---
+
+# Integration Context Initialization
+
+## Overview
+
+This skill automatically creates or updates a `claude.md` file in the workspace root that instructs Claude to search for existing integration skills before attempting to write platform integration code. This ensures Claude uses documented authentication patterns, API access methods, and platform-specific best practices from the repository's integration skills rather than inventing integration code from scratch.
+
+## When to Use This Skill
+
+This skill is automatically invoked when:
+- Claude Code initializes in this workspace
+- User begins any laboratory platform or cloud service integration task
+- User mentions platform names, LIMS, ELN, automation, or workflows
+- Any task involving scientific platforms is started
+
+**No manual invocation required** - this skill runs automatically.
+
+## What This Skill Does
+
+Creates or updates `claude.md` in the workspace root with instructions for Claude to:
+
+1. **Search first**: Look for relevant integration skills in `scientific-integrations/` before writing platform code
+2. **Use existing patterns**: Apply documented authentication and API access patterns
+3. **Follow best practices**: Use platform-specific conventions and workflows
+4. **Adapt examples**: Leverage working integration examples from `scripts/` folders
+
+## Implementation
+
+When invoked, this skill creates/updates the workspace `claude.md` file with a section instructing Claude to search for and use existing integration skills for any platform integration tasks.
+
+The reference template is available in `references/claude.md`.
+
+## Integration
+
+Works alongside other context-initialization skills:
+- `scientific-databases/context-initialization` - for database access
+- `scientific-packages/context-initialization` - for Python package usage
+- `scientific-thinking/context-initialization` - for analysis methodologies
+
+Together, these ensure Claude always leverages existing expertise before attempting scientific tasks.
diff --git a/scientific-integrations/context-initialization/references/claude.md b/scientific-integrations/context-initialization/references/claude.md
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+++ b/scientific-integrations/context-initialization/references/claude.md
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+# Reference: Integration Context Section
+
+This is the reference template for what gets added to the workspace root `claude.md` file.
+
+---
+
+## Laboratory Platform Integration
+
+**Before writing any platform integration code, search for relevant skills in this repository.**
+
+This repository contains skills for 6+ laboratory platforms and cloud services. Each skill includes:
+- Authentication and setup instructions
+- API access patterns
+- Working integration examples
+- Platform-specific best practices
+
+Always search for and use existing integration skills before writing custom platform code.
+
+---
diff --git a/scientific-packages/context-initialization/SKILL.md b/scientific-packages/context-initialization/SKILL.md
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+---
+name: context-initialization
+description: "Auto-invoked skill that creates/updates workspace claude.md to instruct Claude to always search for existing package skills before attempting any data analysis or scientific computing task."
+---
+
+# Package Context Initialization
+
+## Overview
+
+This skill automatically creates or updates a `claude.md` file in the workspace root that instructs Claude to search for existing package skills before attempting to write analysis code. This ensures Claude uses documented workflows, best practices, and working examples from the repository's package skills rather than writing generic code from scratch.
+
+## When to Use This Skill
+
+This skill is automatically invoked when:
+- Claude Code initializes in this workspace
+- User begins any data analysis or scientific computing task
+- User mentions package names or analysis workflows
+- Any task involving scientific Python packages is started
+
+**No manual invocation required** - this skill runs automatically.
+
+## What This Skill Does
+
+Creates or updates `claude.md` in the workspace root with instructions for Claude to:
+
+1. **Search first**: Look for relevant package skills in `scientific-packages/` before writing analysis code
+2. **Use existing workflows**: Apply documented analysis patterns and pipelines
+3. **Follow best practices**: Use proper installation, configuration, and API usage patterns
+4. **Adapt examples**: Leverage working code examples from `scripts/` folders
+
+## Implementation
+
+When invoked, this skill creates/updates the workspace `claude.md` file with a section instructing Claude to search for and use existing package skills for any analysis tasks.
+
+The reference template is available in `references/claude.md`.
+
+## Integration
+
+Works alongside other context-initialization skills:
+- `scientific-databases/context-initialization` - for database access
+- `scientific-integrations/context-initialization` - for lab platform integration
+- `scientific-thinking/context-initialization` - for analysis methodologies
+
+Together, these ensure Claude always leverages existing expertise before attempting scientific tasks.
diff --git a/scientific-packages/context-initialization/references/claude.md b/scientific-packages/context-initialization/references/claude.md
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index 0000000..a822710
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+++ b/scientific-packages/context-initialization/references/claude.md
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+# Reference: Package Context Section
+
+This is the reference template for what gets added to the workspace root `claude.md` file.
+
+---
+
+## Scientific Package Usage
+
+**Before writing analysis code with scientific packages, search for relevant skills in this repository.**
+
+This repository contains skills for 40+ scientific Python packages. Each skill includes:
+- Installation instructions
+- Complete API usage examples
+- Best practices and common patterns
+- Working scripts and reference documentation
+
+Always search for and use existing package skills before writing custom analysis code.
+
+---
diff --git a/scientific-thinking/context-initialization/SKILL.md b/scientific-thinking/context-initialization/SKILL.md
new file mode 100644
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+++ b/scientific-thinking/context-initialization/SKILL.md
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+---
+name: context-initialization
+description: "Auto-invoked skill that creates/updates workspace claude.md to instruct Claude to always search for existing methodology skills before attempting any scientific analysis, writing, visualization, or research methodology task."
+---
+
+# Scientific Thinking Context Initialization
+
+## Overview
+
+This skill automatically creates or updates a `claude.md` file in the workspace root that instructs Claude to search for existing methodology skills before attempting to perform scientific analysis, writing, or research tasks. This ensures Claude uses established frameworks, best practices, and structured approaches from the repository's methodology skills rather than inventing ad-hoc methods.
+
+## When to Use This Skill
+
+This skill is automatically invoked when:
+- Claude Code initializes in this workspace
+- User begins any data analysis, visualization, or scientific writing task
+- User mentions analysis methods, statistics, hypothesis generation, or peer review
+- Any research methodology task is started
+
+**No manual invocation required** - this skill runs automatically.
+
+## What This Skill Does
+
+Creates or updates `claude.md` in the workspace root with instructions for Claude to:
+
+1. **Search first**: Look for relevant methodology skills in `scientific-thinking/` before attempting analysis or writing tasks
+2. **Use established frameworks**: Apply documented analysis workflows, writing structures, and visualization templates
+3. **Follow best practices**: Use scientific standards, reporting guidelines, and community conventions
+4. **Adapt examples**: Leverage templates, scripts, and style files from methodology folders
+
+## Implementation
+
+When invoked, this skill creates/updates the workspace `claude.md` file with a section instructing Claude to search for and use existing methodology skills for any research tasks.
+
+The reference template is available in `references/claude.md`.
+
+## Integration
+
+Works alongside other context-initialization skills:
+- `scientific-databases/context-initialization` - for database access
+- `scientific-packages/context-initialization` - for Python package usage
+- `scientific-integrations/context-initialization` - for lab platform integration
+
+Together, these ensure Claude always leverages existing expertise before attempting scientific tasks.
diff --git a/scientific-thinking/context-initialization/references/claude.md b/scientific-thinking/context-initialization/references/claude.md
new file mode 100644
index 0000000..34db655
--- /dev/null
+++ b/scientific-thinking/context-initialization/references/claude.md
@@ -0,0 +1,19 @@
+# Reference: Scientific Thinking Context Section
+
+This is the reference template for what gets added to the workspace root `claude.md` file.
+
+---
+
+## Scientific Analysis & Research Methods
+
+**Before attempting any analysis, writing, or research task, search for relevant methodology skills in this repository.**
+
+This repository contains skills for scientific methodologies including:
+- Data analysis frameworks (EDA, statistical analysis)
+- Research methodologies (hypothesis generation, brainstorming, critical thinking)
+- Communication skills (scientific writing, visualization, peer review)
+- Document processing (DOCX, PDF, PPTX, XLSX)
+
+Always search for and use existing methodology skills before attempting scientific analysis or writing tasks.
+
+---