crazymsn/academic-skills

★ 14PythonAudience · researcherComplexity · 2/5LicenseSetup · easy

Mindmap

mindmap
  root((academic-skills))
    What it does
      AI agent skill library
      Scientific workflows
      139 skills included
    Fields covered
      Bioinformatics genomics
      Drug discovery modeling
      Geospatial science
      Materials science physics
      Literature review writing
    Supported agents
      Claude Code
      Codex OpenAI
      OpenCode
    Installation
      npx skills command
      All at once or by name
      Project or user level
    Security
      Shell command warnings
      Cisco AI scanner included
      Pre-run audit available

mindmap root((academic-skills)) What it does AI agent skill library Scientific workflows 139 skills included Fields covered Bioinformatics genomics Drug discovery modeling Geospatial science Materials science physics Literature review writing Supported agents Claude Code Codex OpenAI OpenCode Installation npx skills command All at once or by name Project or user level Security Shell command warnings Cisco AI scanner included Pre-run audit available

Click or tap to explore — scroll the page freely

Things people build with this

USE CASE 1

Install all 139 research skills into Claude Code to immediately give your AI assistant working knowledge of bioinformatics, molecular modeling, and other scientific tools

USE CASE 2

Pick individual skills by name to extend your agent with a specific workflow like literature review, citation management, or a genomics pipeline

USE CASE 3

Audit the skill content with the bundled Cisco AI scanner before installing in a sensitive research environment to check for unintended shell commands or network calls

Tech stack

PythonnpxCLI

Getting it running

Difficulty · easy Time to first run · 5min

Skills can instruct AI agents to run shell commands, install packages, or make network requests, run the included security scan before using in sensitive environments.

Use, modify, and distribute freely for any purpose as long as you keep the original copyright notice.

In plain English

This repository is a collection of 139 packaged skill directories for AI coding agents, focused on scientific and academic work. Each skill teaches an AI agent how to use a specific tool, library, or research workflow. The collection covers a wide range of fields: bioinformatics and genomics, drug discovery and molecular modeling, clinical research, geospatial science, materials science, physics, astronomy, and more. It also includes skills for tasks like literature review, scientific writing, citation management, and AI model interpretation. Each skill directory holds a SKILL.md file that describes what the agent should do, along with optional scripts, reference files, example data, or tests. The skill format is designed to be portable across different AI coding agents. The repository explicitly supports three agents: Claude Code (Anthropic), Codex (OpenAI), and OpenCode. Installation is handled via a command-line tool called npx skills, which copies the selected skill directories into the agent's local configuration folder. You can install all 139 skills at once or pick individual ones by name. The install paths differ by agent. Claude Code reads skills from .claude/skills/ inside your project or from ~/.claude/skills/ for a user-level install. Codex uses .agents/skills/ for projects. OpenCode has its own native paths but also reads from the Claude Code and shared agent paths. After installing, a Python validation script checks compatibility so you can confirm the skills landed correctly before using them. The README includes a security caution worth noting: skills can instruct an AI agent to run shell commands, install packages, make network requests, read environment variables, or modify files. The repository includes a pre-run security scan of its own skill directories, and you can run the Cisco AI skill scanner yourself to audit the content before installing anything. This is a fork of an upstream open-source skills collection, cleaned up to remove organization-specific install paths and tracking. It carries an MIT license, and the original copyright notice is preserved as the license terms require.

Copy-paste prompts

Prompt 1

I installed the academic-skills collection into Claude Code, how do I activate the bioinformatics skill and ask it to run a sequence alignment pipeline on my FASTA files?

Prompt 2

Which academic skills cover drug discovery and molecular modeling? Show me the npx command to install just those ones by name

Prompt 3

I want to create a new skill for my own research workflow using the academic-skills format, what goes in SKILL.md and what optional supporting files can I include?

Prompt 4

Run the Cisco AI skill scanner on the academic-skills collection and explain any findings before I install it into my Claude Code environment

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