381,784 Collected SKILL.md files

Explore AI Agent Skills & Claude Prompts

Discover open-source agent skills for Claude Code, Codex, ChatGPT, and any tool that uses SKILL.md.

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biochemists and biophysicists
Showing 12 of 1,011 skills
aiming-lab

scientific-writing

by aiming-lab
star 13.4k

Academic manuscript writing with IMRAD structure, citation formatting, and reporting guidelines. Use when drafting or revising research papers.

navigation main article SKILL.md
schedule Updated 2 months ago
Galaxy-Dawn

publication-chart-skill

by Galaxy-Dawn
star 4.3k

This skill should be used when the user asks for a publication-quality scientific figure or table, wants help choosing the right chart for results, needs a paper-ready pubfig or pubtab workflow, wants a figure + companion table for a results section, wants an Excel sheet turned into publication-ready LaTeX, or wants an existing scientific figure/table reviewed and upgraded.

navigation main article SKILL.md
schedule Updated 1 month ago
Galaxy-Dawn

results-report

by Galaxy-Dawn
star 4.3k

This skill should be used when the user asks to "write an experiment report", "summarize experimental results", "do experiment retrospection", "write a results report", "写实验总结报告", "写实验复盘", or mentions turning completed experiment artifacts into a structured, decision-oriented research report. It assumes strict analysis should come from `results-analysis` first.

navigation main article SKILL.md
schedule Updated 1 month ago
openai

rcsb-pdb-skill

by openai
star 3.1k

Submit compact RCSB PDB requests for core metadata, Search API queries, and FASTA downloads. Use when a user wants concise RCSB summaries; save raw JSON or FASTA only on request.

navigation main article SKILL.md
schedule Updated 2 months ago
ResearAI

paper-plot

by ResearAI
star 3.1k

Use when structured numeric data, arrays, or CSV-like measurements should be turned into a publication-quality figure by adapting a bundled paper-style plotting template instead of improvising a new chart from scratch.

navigation main article SKILL.md
schedule Updated 2 months ago
HKUSTDial

tech-paper-template

by HKUSTDial
star 2.8k

Structures a technical paper's full logical skeleton using a thinking-template table (research background, limitations, key idea or goal, challenges, methodology modules, contributions), positions the paper as Technique or New Problem/Setting, and runs a four-point self-consistency check. Use when the user is brainstorming a paper, discussing progress with an advisor, or planning the paper before drafting. Also use for 'paper skeleton', 'paper logic chain', 'thinking template', 'paper-structure planning'.

navigation main article SKILL.md
schedule Updated 2 months ago
FreedomIntelligence

tooluniverse-metabolomics

by FreedomIntelligence
star 2.7k

Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (220k+ metabolites), MetaboLights, Metabolomics Workbench, and PubChem. Use when asked to identify or annotate metabolites (HMDB IDs, chemical properties, pathways), retrieve metabolomics study information from MetaboLights (MTBLS*) or Metabolomics Workbench (ST*), search for studies by keywords or disease, or generate comprehensive metabolomics research reports.

navigation main article SKILL.md
schedule Updated 3 months ago
FreedomIntelligence

tooluniverse-protein-structure-retrieval

by FreedomIntelligence
star 2.7k

Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles. Creates detailed structure reports with experimental metadata, ligand information, and download links. Use when users need protein structures, 3D models, crystallography data, or mention PDB IDs (4-character codes like 1ABC) or UniProt accessions.

navigation main article SKILL.md
schedule Updated 3 months ago
FreedomIntelligence

binding-characterization

by FreedomIntelligence
star 2.7k

Guidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting kinetic data artifacts, (4) Choosing between SPR vs BLI platforms.

navigation main article SKILL.md
schedule Updated 3 months ago
foryourhealth111-pixel

matchms

by foryourhealth111-pixel
star 2.3k

Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.

navigation main article SKILL.md
schedule Updated 1 month ago
foryourhealth111-pixel

scientific-critical-thinking

by foryourhealth111-pixel
star 2.3k

Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review.

navigation main article SKILL.md
schedule Updated 3 months ago
K-Dense-AI

scientific-critical-thinking

by K-Dense-AI
star 1.9k

Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence quality (GRADE, Cochrane ROB), for critical analysis of scientific claims.

navigation main article SKILL.md
schedule Updated 7 months ago
Page 1 of 85

Browse Agent Skills by Occupation

23 major groups · 867 SOC occupations

Browse by Category

Explore agent skills organized by their primary use case

SKILLMD / CREATORS AND OCCUPATION CATEGORIES

Explore the agent skills ecosystem by occupation and creator

SkillMD is not just a keyword search box. It is an open map that organizes public skills by occupation, creator, and repository, helping you see which workflows, judgment criteria, and domain habits people are writing for AI agents.

Then follow creators and GitHub repositories back to the source: compare the skills a team maintains, whether the repo is active, and how the README frames the work before you open, install, or reuse anything.

Use it three ways: learn an unfamiliar field by occupation, study how creators organize skills, then use source context to decide what is worth opening or reusing.

01 Map a field

Browse 23 occupation groups and 867 SOC roles to learn what skills exist in adjacent domains and how they break down real work.

02 Follow creators

Use creator and repository pages to inspect maintained skill collections, recent updates, and source context before trusting a result.

03 Search with sources

Search 1.7M+ collected skills, then use occupation tags, creators, and GitHub source context to decide what is worth opening.

Start with the occupation map, then follow creators and repositories back to real code. SkillMD helps explain why a skill is worth opening, not only what it is named.

SEO KNOWLEDGE HUB & TECHNICAL OVERVIEW

Standardizing Agent Capabilities with SKILL.md and Model Context Protocol (MCP)

In the rapidly evolving landscape of artificial intelligence, LLM agents (Large Language Model agents) have transitioned from simple text predictors to autonomous problem solvers. To orchestrate complex, multi-step agentic workflows, developers require a standardized format to specify agent capabilities, prompt instructions, system rules, and database bindings. This is where SKILL.md and the Model Context Protocol (MCP) have emerged as standard developer paradigms. SkillMD serves as the central directory for indexing, exploring, and sharing these critical agent configurations.

Our open-source registry currently tracks over 1.7 million collected SKILL.md configurations and system prompts. By compiling agent configurations from active developers on GitHub, we bridge the gap between prompt engineering research and production execution. Whether you are building agents with Anthropic's Claude Code, OpenAI's GPT-4, Google's Gemini, or local models using Ollama and LlamaIndex, standardized skill definitions ensure your agents behave predictably across different runtime environments.

What is the Model Context Protocol (MCP)?

The Model Context Protocol (MCP) is an open-source standard designed to connect LLMs to data sources, developer tools, and external environments. MCP establishes a bidirectional communication channel between client applications (like Cursor, Claude Desktop, or custom agent systems) and servers hosting data or capabilities. Standardizing instructions via SKILL.md enables LLMs to query databases, read local files, execute terminal commands, and integrate third-party APIs. SkillMD allows you to find ready-to-run MCP servers and prompt instructions for various occupations and technical tasks.

The Structure of a Professional SKILL.md File

A valid SKILL.md configuration is designed to be easily read by humans and parsed by LLMs. It contains precise system instructions, trigger conditions, required parameters, and execution examples. Below is the typical architectural blueprint of a professional agent skill:

  • Metadata & Core Scope: Declares the name of the skill, author details, target models, and a description of the capability.
  • Triggers & Intent Detection: Details semantic triggers that help the agent decide when to invoke this skill.
  • System Prompts: Explicit system-level instructions that direct the agent's behavior, personality, safety guardrails, and formatting preferences.
  • Capabilities & Tools: Lists the files, databases, or APIs the agent must access to complete the tasks.
  • Few-Shot Examples: Demonstrates real inputs and outputs, helping the model generalize behavior through in-context learning.

Optimizing Agent Workflows for Modern LLMs

Writing effective agent skills requires deep knowledge of prompt engineering. With the release of advanced reasoning models like Claude 3.5 Sonnet, ChatGPT o1, and DeepSeek-V3, prompt templates must focus on structured thinking. Developers are encouraged to use XML tags (e.g., <thought>, <context>, and <rules>) to isolate execution boundaries. Standardized prompts prevent agents from suffering from context drift, ensuring that long-running tasks remain aligned with the initial system parameters.

Exploring by SOC Occupations and Creator Profiles

What makes SkillMD unique is its taxonomy. Instead of simple text search, we parse and organize files according to the Standard Occupational Classification (SOC) system. This means you can discover skills written for Computer and Mathematical roles, Business and Financial operations, Legal, Design, and and Educational Instruction fields. By tracking creator profiles, developers can study how different teams organize their custom instructions, compare version updates, and fork public configs for specialized enterprise use cases.

SkillMD operates as a high-performance index running on a fast Go backend and a highly responsive Astro SSR frontend. All search queries execute in milliseconds, featuring smart debouncing to prevent multiple API requests while keeping user data secure. Join our community of developers to standardize your AI agent instructions and optimize your LLM prompting workflows today.

8 QUESTIONS

Frequently Asked Questions

A practical guide to agent skills: what they are, how to inspect them, and how SkillMD helps you explore the ecosystem.