mirror of
https://github.com/K-Dense-AI/claude-scientific-skills.git
synced 2026-01-26 16:58:56 +08:00
Use Agent.md
This commit is contained in:
Timothy Kassis
@@ -7,7 +7,7 @@
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},
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"metadata": {
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"description": "Claude scientific skills from K-Dense Inc",
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"version": "1.40.0"
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"version": "1.50.0"
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},
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"plugins": [
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{
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@@ -124,6 +124,12 @@
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"./scientific-integrations/omero-integration",
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"./scientific-integrations/opentrons-integration"
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]
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},
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{
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"name": "scientific-context-initialization",
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"description": "Always Auto-invoked skill that creates/updates workspace AGENT.md to instruct the agent to always search for existing skills before attempting any scientific task",
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"source": "./scientific-helpers/scientific-context-initialization",
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"strict": false
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}
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]
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}
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11
README.md
11
README.md
@@ -2,7 +2,7 @@
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[](LICENSE.md)
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[](https://github.com/K-Dense-AI/claude-scientific-skills)
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[](#what-s-included)
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[](#what-s-included)
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[](#what-s-included)
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A comprehensive collection of ready-to-use scientific skills for Claude, curated by the K-Dense team.
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@@ -47,6 +47,7 @@ These skills enable Claude to work with specialized scientific libraries and dat
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| 📊 **Scientific Databases** | 24 | PubMed, PubChem, UniProt, ChEMBL, COSMIC, AlphaFold DB, and more |
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| 🔬 **Scientific Packages** | 41 | BioPython, RDKit, PyTorch, Scanpy, and specialized tools |
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| 🔌 **Scientific Integrations** | 6 | Benchling, DNAnexus, Opentrons, LabArchives, LatchBio, OMERO |
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| 🎯 **Context Initialization** | 1 | Auto-invoked skill to ensure Claude uses existing skills effectively |
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| 📚 **Documented Workflows** | 122 | Ready-to-use examples and reference materials |
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---
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@@ -80,10 +81,13 @@ Then, to install a specific set of skills:
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- `scientific-packages` - 40 specialized Python packages
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- `scientific-thinking` - Analysis tools and document processing
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- `scientific-integrations` - Lab automation and platform integrations
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- `scientific-context-initialization` - Ensures Claude searches for and uses existing skills
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4. Select **Install now**
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After installation, simply mention the skill or describe your task - Claude Code will automatically use the appropriate skills!
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> 💡 **Tip**: If you find that Claude isn't utilizing the installed skills as much as you'd like, install the `scientific-context-initialization` skill. It automatically creates/updates an `AGENT.md` file in your workspace that instructs Claude to always search for and use existing skills before attempting any scientific task. This ensures Claude leverages documented patterns, authentication methods, working examples, and best practices from the repository.
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### Any MCP Client (including ChatGPT, Cursor, Google ADK, OpenAI Agent SDK, etc.)
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Use our newly released MCP server that allows you to use any Claude Skill in any client!
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@@ -361,6 +365,11 @@ Your contributions help make scientific computing more accessible and enable res
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### Common Issues
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**Problem: Claude not using installed skills**
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- Solution: Install the `scientific-context-initialization` skill
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- This creates an `AGENT.md` file that instructs Claude to search for and use existing skills before attempting tasks
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- After installation, Claude will automatically leverage documented patterns, examples, and best practices
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**Problem: Skills not loading in Claude Code**
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- Solution: Ensure you've installed the latest version of Claude Code
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- Try reinstalling the plugin: `/plugin marketplace add K-Dense-AI/claude-scientific-skills`
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@@ -1,44 +0,0 @@
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---
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name: context-initialization
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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."
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---
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# Database Context Initialization
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## Overview
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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.
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## When to Use This Skill
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This skill is automatically invoked when:
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- Claude Code initializes in this workspace
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- User begins any database-related task
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- User mentions database access, queries, or API interactions
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- Any scientific data retrieval task is started
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**No manual invocation required** - this skill runs automatically.
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## What This Skill Does
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Creates or updates `claude.md` in the workspace root with instructions for Claude to:
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1. **Search first**: Look for relevant database skills in `scientific-databases/` before writing code
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2. **Use existing patterns**: Apply documented API access patterns and examples
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3. **Follow best practices**: Use rate limits, authentication, and error handling from skills
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4. **Adapt examples**: Leverage working code examples from `scripts/` folders
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## Implementation
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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.
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The reference template is available in `references/claude.md`.
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## Integration
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Works alongside other context-initialization skills:
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- `scientific-packages/context-initialization` - for Python package usage
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- `scientific-integrations/context-initialization` - for lab platform integration
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- `scientific-thinking/context-initialization` - for analysis methodologies
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Together, these ensure Claude always leverages existing expertise before attempting scientific tasks.
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@@ -1,19 +0,0 @@
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# Reference: Database Context Section
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This is the reference template for what gets added to the workspace root `claude.md` file.
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---
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## Database Access Tasks
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**Before writing any database access code, search for relevant skills in this repository.**
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This repository contains skills for 24+ scientific databases. Each skill includes:
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- API endpoints and authentication patterns
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- Working code examples
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- Best practices and rate limits
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- Example scripts
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Always search for and use existing database skills before writing custom database access code.
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---
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@@ -0,0 +1,80 @@
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---
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name: context-initialization
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description: "Always Auto-invoked skill that creates/updates workspace AGENT.md to instruct the agent to always search for existing skills before attempting any scientific task."
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---
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# Context Initialization
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## Overview
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This skill automatically creates or updates an `AGENT.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.
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## When to Use This Skill
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This skill is automatically invoked when:
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- The agent initializes in this workspace
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- User begins any scientific task (database access, package usage, platform integration, or methodology)
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- User mentions specific databases, packages, platforms, or research methods
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- Any scientific data retrieval, analysis, or research task is started
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**No manual invocation required** - this skill runs automatically.
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## What This Skill Does
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Creates or updates `AGENT.md` in the workspace root with instructions for the agent to:
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1. **Search first**: Look for relevant skills across all skill categories before writing code
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2. **Use existing patterns**: Apply documented API access patterns, workflows, and examples
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3. **Follow best practices**: Use rate limits, authentication, configurations, and established methodologies
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4. **Adapt examples**: Leverage working code examples from `scripts/` folders and reference documentation
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**Important**: If `AGENT.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.
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## Skill Categories
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This unified context initialization covers four major skill categories:
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### Database Access Tasks
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- Search `scientific-databases/` for 24+ database skills
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- Use documented API endpoints and authentication patterns
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- Apply working code examples and best practices
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||||
- Follow rate limits and error handling patterns
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||||
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### Scientific Package Usage
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||||
- Search `scientific-packages/` for 40+ Python package skills
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||||
- Use installation instructions and API usage examples
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- Apply best practices and common patterns
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- Leverage working scripts and reference documentation
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||||
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### Laboratory Platform Integration
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- Search `scientific-integrations/` for 6+ platform integration skills
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||||
- Use authentication and setup instructions
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||||
- Apply API access patterns and platform-specific best practices
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||||
- Leverage working integration examples
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||||
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||||
### Scientific Analysis & Research Methods
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- Search `scientific-thinking/` for methodology skills
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- Use established data analysis frameworks (EDA, statistical analysis)
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- Apply research methodologies (hypothesis generation, brainstorming, critical thinking)
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- Leverage communication skills (scientific writing, visualization, peer review)
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- Use document processing skills (DOCX, PDF, PPTX, XLSX)
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## Implementation
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When invoked, this skill manages the workspace `AGENT.md` file as follows:
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- **If `AGENT.md` does not exist**: Creates a new file using the complete template from `references/AGENT.md`
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- **If `AGENT.md` already exists**: Updates the file to ensure the essential skill-search directives are present, while preserving any existing custom content or modifications
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The file includes sections instructing the agent to search for and use existing skills across all scientific task categories.
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The complete reference template is available in `references/AGENT.md`.
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## Benefits
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By centralizing context initialization, this skill ensures:
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- **Consistency**: The agent always uses the same approach across all skill types
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- **Efficiency**: One initialization covers all scientific tasks
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- **Maintainability**: Updates to the initialization strategy occur in one place
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- **Completeness**: The agent is reminded to search across all available skill categories
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@@ -1,14 +1,20 @@
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# Claude Scientific Skills - Working Instructions
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# Reference: Complete Context Initialization Template
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## IMPORTANT: Search for Skills First
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This is the complete reference template for what gets added to the workspace root `AGENT.md` file.
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||||
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Before attempting any scientific task, search for relevant skills in this repository.
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---
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# Agent Scientific Skills - Working Instructions
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## IMPORTANT: Use Available Skills First
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Before attempting any scientific task, use available skills.
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|
||||
---
|
||||
|
||||
## Database Access Tasks
|
||||
|
||||
**Before writing any database access code, search for relevant skills in this repository.**
|
||||
**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
|
||||
@@ -16,13 +22,13 @@ This repository contains skills for 24+ scientific databases. Each skill include
|
||||
- Best practices and rate limits
|
||||
- Example scripts
|
||||
|
||||
Always search for and use existing database skills before writing custom database access code.
|
||||
Always use available 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.**
|
||||
**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
|
||||
@@ -30,13 +36,13 @@ This repository contains skills for 40+ scientific Python packages. Each skill i
|
||||
- Best practices and common patterns
|
||||
- Working scripts and reference documentation
|
||||
|
||||
Always search for and use existing package skills before writing custom analysis code.
|
||||
Always use available package skills before writing custom analysis code.
|
||||
|
||||
---
|
||||
|
||||
## Laboratory Platform Integration
|
||||
|
||||
**Before writing any platform integration code, search for relevant skills in this repository.**
|
||||
**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
|
||||
@@ -44,13 +50,13 @@ This repository contains skills for 6+ laboratory platforms and cloud services.
|
||||
- Working integration examples
|
||||
- Platform-specific best practices
|
||||
|
||||
Always search for and use existing integration skills before writing custom platform code.
|
||||
Always use available 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.**
|
||||
**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)
|
||||
@@ -58,9 +64,9 @@ This repository contains skills for scientific methodologies including:
|
||||
- Communication skills (scientific writing, visualization, peer review)
|
||||
- Document processing (DOCX, PDF, PPTX, XLSX)
|
||||
|
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Always search for and use existing methodology skills before attempting scientific analysis or writing tasks.
|
||||
Always use available methodology skills before attempting scientific analysis or writing tasks.
|
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---
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*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.*
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||||
*This file is auto-generated by context-initialization skills. It ensures the agent uses available skills before attempting to solve scientific tasks from scratch.*
|
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|
||||
@@ -1,44 +0,0 @@
|
||||
---
|
||||
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.
|
||||
@@ -1,19 +0,0 @@
|
||||
# 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.
|
||||
|
||||
---
|
||||
@@ -1,44 +0,0 @@
|
||||
---
|
||||
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.
|
||||
@@ -1,19 +0,0 @@
|
||||
# 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.
|
||||
|
||||
---
|
||||
@@ -1,44 +0,0 @@
|
||||
---
|
||||
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.
|
||||
@@ -1,19 +0,0 @@
|
||||
# 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.
|
||||
|
||||
---
|
||||
Reference in New Issue
Block a user