Consolidate skills

scientific-helpers/scientific-context-initialization/SKILL.md

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----
-name: context-initialization
-description: "Always Auto-invoked skill that creates/updates workspace AGENTS.md to instruct the agent to always search for existing skills before attempting any scientific task."
----
-
-# Context Initialization
-
-## Overview
-
-This skill automatically creates or updates an `AGENTS.md` file in the workspace root that instructs the agent to use existing skills before attempting to solve scientific tasks. This ensures the agent uses documented patterns, authentication methods, working examples, and best practices from the repository's skills rather than inventing solutions from scratch.
-
-## When to Use This Skill
-
-This skill is automatically invoked when:
-- 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
-
-**No manual invocation required** - this skill runs automatically.
-
-## What This Skill Does
-
-Creates or updates `AGENTS.md` in the workspace root with instructions for the agent to:
-
-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
-
-**Important**: If `AGENTS.md` already exists in the workspace, this skill will update it intelligently rather than overwriting it. This preserves any custom instructions or modifications while ensuring the essential skill-search directives are present.
-
-## Skill Categories
-
-This unified context initialization covers four major 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
-
-When invoked, this skill manages the workspace `AGENTS.md` file as follows:
-
-- **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
-
-The file includes sections instructing the agent to search for and use existing skills across all scientific task categories.
-
-The complete reference template is available in `references/AGENTS.md`.
-
-## Benefits
-
-By centralizing context initialization, this skill ensures:
-- **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
-

scientific-helpers/scientific-context-initialization/references/AGENTS.md

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-# Reference: Complete Context Initialization Template
-
-This is the complete reference template for what gets added to the workspace root `AGENTS.md` file.
-
----
-
-# Agent Scientific Skills - Working Instructions
-
-## IMPORTANT: Use Available Skills First
-
-Before attempting any scientific task, use available skills.
-
----
-
-## Database Access Tasks
-
-**Before writing any database access code, use available 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 use available database skills before writing custom database access code.
-
----
-
-## Scientific Package Usage
-
-**Before writing analysis code with scientific packages, use available 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 use available package skills before writing custom analysis code.
-
----
-
-## Laboratory Platform Integration
-
-**Before writing any platform integration code, use available 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 use available integration skills before writing custom platform code.
-
----
-
-## Scientific Analysis & Research Methods
-
-**Before attempting any analysis, writing, or research task, use available 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 use available methodology skills before attempting scientific analysis or writing tasks.
-
----
-
-*This file is auto-generated by context-initialization skills. It ensures the agent uses available skills before attempting to solve scientific tasks from scratch.*
-
-