# AlterLab Academic Skills > 210 evaluated academic Claude/agent skills across 16 research domains β€” bioinformatics, cheminformatics, data science, databases, clinical, Turkish academia & more. Every skill ships an executable eval (agentskills.io schema). Citation verifier + researchβ†’writeβ†’reviewβ†’publish pipeline. Claude Code, Cursor, Codex, Gemini CLI & Copilot. - **Type:** MCP server - **Install:** `agentstack add mcp-alterlab-ieu-alterlab-academic-skills` - **Verified:** Pending review - **Seller:** [AlterLab-IEU](https://agentstack.voostack.com/s/alterlab-ieu) - **Installs:** 0 - **Category:** [AI & ML](https://agentstack.voostack.com/c/ai-and-ml) - **Latest version:** 0.1.0 - **License:** MIT - **Upstream author:** [AlterLab-IEU](https://github.com/AlterLab-IEU) - **Source:** https://github.com/AlterLab-IEU/AlterLab-Academic-Skills - **Website:** https://alterlab-ieu.github.io/AlterLab-Academic-Skills/ ## Install ```sh agentstack add mcp-alterlab-ieu-alterlab-academic-skills ``` Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent. ## About > πŸ“’ **Featured in** [awesome-claude-skills](https://github.com/BehiSecc/awesome-claude-skills) (5.7k ⭐) **Read in:** [English](README.md) Β· [TΓΌrkΓ§e](README.tr-TR.md) 🧬 210 purpose-built Claude AI skills for faculty, researchers & academicians Organized across 16 research domains β€” from Turkish academia to bioinformatics to digital humanities 210/210 ship executable evals Β· deterministic citation-existence verifier Β· per-domain bundles for claude.ai Research Pipeline Β· Scientific Databases Β· Bioinformatics Β· Data Science Β· Visualization Β· Clinical Research Β· and more Explore Skills Β» Β· Quick Start Β· Domain Overview Β· Contributing Β· Report Bug Built by AlterLab Creative Technologies Laboratory Not tied to any specific university β€” these skills work for any researcher, anywhere. 🎯 Plug & Play Drop a .md skill file intoClaude Projects or Claude Codeand get instant expertise 🧠 Domain Expert Each skill transforms Claudeinto a specialized researchassistant with deep knowledge πŸ”¬ Real Frameworks Built on actual scientificmethods, tools, and professionaloutput templates 🌐 Universal Works for any researcherat any institution β€”no vendor lock-in ## πŸš€ What's New in v2.2.0 - 🧠 **Research-backed elevation of 191 skills** β€” a corpus-wide accuracy and depth pass over every pre-existing skill: corrected regulation/API details, slimmed oversized bodies into `references/`, and version-bumped touched skills. - 🧩 **New core skill: Workflow Orchestration** (`alterlab-workflow-orchestration`) β€” composes AlterLab skills into multi-agent workflows (subagent fan-out, pipelines, judge panels, adversarial verification), lifting the corpus to **210 skills**. β†’ [Core Pipeline](#-core-pipeline--9-skills) - πŸ‡ΉπŸ‡· **Turkish-academia flagship (12 skills)** β€” the deepest Turkish-academia suite in any skills library: DergiPark, TR Dizin, YΓ–K Tez, YΓ–K Akademik, YΓ–KATLAS, TÜBΔ°TAK 1001/1002-A proposals, doΓ§entlik eligibility, akademik teşvik scoring, Turkish APA-7 style, TR research ethics, KVKK data-management plans, and TÜBΔ°TAK Aperta β€” each wired to a verified national-platform endpoint. β†’ [Turkish Academia](#-turkish-academia--national-platforms--scholarly-workflow-12-skills) - πŸŽ“ **Faculty Life (6 skills)** β€” syllabus AI policy, post-award grant reporting, recommendation letters, AACSB/ABET accreditation (AoL), REDCap/CDISC capture, and preprint deposition. β†’ [Faculty Life](#-faculty-life--teaching-service--the-academic-career-6-skills) - πŸ§ͺ **Methodology (3 skills)** β€” superpowers-style rigor (Iron Laws, Excuse-vs-Reality tables) applied to research methods: pre-registration discipline, statistical-test-selection guard, and results-reporting transparency. β†’ [Methodology](#-methodology--research-rigor--discipline-gates-3-skills) - 🧬 **Bioinformatics grew 25 β†’ 30** β€” production pipelines: nf-core/sarek variant calling, QIIME 2 amplicon, salmon/kallisto RNA-seq quant, NCBI BLAST+, and Squidpy spatial transcriptomics. β†’ [Bioinformatics](#-bioinformatics--genomics-proteomics--molecular-biology-30-skills) - βœ… **Day-one evals on all 26 new skills** β€” coverage stays **210 / 210**; the shape + coverage gate runs in CI on every PR. β†’ [`docs/evals.md`](docs/evals.md) Previously β€” What's New in v2.0 - βœ… **Full-corpus executable evals** β€” schema + trigger-coverage are CI-gated on every PR; the behavioral pass (claude CLI + LLM judge) runs on demand via `workflow_dispatch`. β†’ [`docs/evals.md`](docs/evals.md) - πŸ”Ž **Deterministic citation-existence verifier** that catches hallucinated references against Crossref / OpenAlex / Semantic Scholar / arXiv β€” no LLM guesswork in the gate. β†’ [Headline feature](#-headline-feature--alterlab-citation-verifier) - πŸ“¦ **Per-domain `claude.ai` bundles on every Release** β€” each `dist/.zip` clears the 200-file / 30 MB caps. β†’ [Releases](https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/releases) - 🌐 **Live searchable catalog** to browse every skill in the browser. β†’ [Browse the Catalog](#-browse-the-catalog) - πŸ€– **35 registered subagents + slash commands + a bundled academic MCP** wiring PubMed / OpenAlex / Crossref / Zotero. β†’ [MCP & Slash Commands](#-mcp--slash-commands) - πŸ“œ **Honest provenance** β€” upstream K-Dense fork credited in [`THIRD_PARTY_NOTICES.md`](THIRD_PARTY_NOTICES.md) and a machine-readable [`CITATION.cff`](CITATION.cff). β†’ [Cite This Repository](#-cite-this-repository) ## πŸ“‹ Table of Contents Click to expand / collapse - [πŸš€ What's New in v2.2.0](#-whats-new-in-v220) - [🎯 What Is This?](#-what-is-this) - [πŸ†• v2.0 Highlights](#-v20-highlights) - [✨ Key Features](#-key-features) - [πŸ—‚οΈ Domain Overview](#%EF%B8%8F-domain-overview) - [πŸ”Ž Browse the Catalog](#-browse-the-catalog) - [πŸš€ Quick Start](#-quick-start) - [⚑ Core Pipeline β€” 9 Skills](#-core-pipeline--9-skills) - [πŸ“š All 210 Skills](#-all-210-skills) - [πŸ—οΈ Project Structure](#%EF%B8%8F-project-structure) - [βš™οΈ How Skills Work](#%EF%B8%8F-how-skills-work) - [πŸ’‘ Usage Examples](#-usage-examples) - [βš–οΈ How It Compares](#%EF%B8%8F-how-it-compares) - [🀝 Contributing](#-contributing) - [πŸ“– Cite This Repository](#-cite-this-repository) - [πŸ“œ License](#-license) - [πŸ™ Credits](#-credits) ## 🎯 What Is This? A comprehensive suite of **210 purpose-built Claude AI skills** for faculty members, academicians, and researchers β€” organized into **16 domain categories** spanning the full academic research lifecycle. Each skill transforms Claude into a **domain-specific expert assistant** tailored to academic research, scientific computing, and scholarly publishing workflows. > [!TIP] > **How it works:** Each skill is a structured `SKILL.md` file. Install the collection as a Claude Code plugin, or copy a skill directory into `~/.claude/skills/` (or a project's `.claude/skills/`) β€” and Claude becomes your research expert, with real scientific frameworks, professional output templates, and deep domain knowledge. A loose `.md` file does **not** auto-load. ## πŸ†• v2.0 Highlights > *v2.0 is the "Trust & Reach" release β€” it turns the loudest objection to academic skills ("just prompts, no evals") into the headline differentiator.* | | What | Detail | |:---:|:---|:---| | βœ… | **Executable evals across the corpus** | **210 / 210** skills ship `evals/evals.json` on the canonical [agentskills.io](https://agentskills.io) schema, validated in CI. See [`docs/evals.md`](docs/evals.md). | | πŸ”Ž | **Citation-existence verifier** | New core skill `alterlab-citation-verifier` β€” a **deterministic** gate that checks every reference actually exists against four keyless scholarly APIs (Crossref, OpenAlex, Semantic Scholar, arXiv), flags retractions, and maps claim-faithfulness verdicts. See below. | | πŸ“¦ | **Per-domain bundles for claude.ai** | `dist/.zip` bundles (one per domain) attached to each [Release](https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/releases) β€” each clears claude.ai's 200-file / 30 MB caps and vendors the shared handoff contracts. | | πŸ”Œ | **Bundled academic MCP** | The `core` and `databases` plugins ship a `.mcp.json` wiring PubMed / OpenAlex / Crossref / Zotero, with a documented `requests/` fallback when no MCP is available. | | ⌨️ | **Slash commands** | `/lit-review`, `/review-paper`, `/cite-check`, `/research-pipeline` β€” drive the core pipeline directly. | | πŸ—‚οΈ | **Generated catalog** | A machine-readable [`skills.json`](skills.json) is generated from skill frontmatter; a CI gate keeps every count in this README honest. | | πŸ“œ | **Honest provenance** | Upstream K-Dense fork credited in [`THIRD_PARTY_NOTICES.md`](THIRD_PARTY_NOTICES.md) + [`PROVENANCE.md`](PROVENANCE.md) / [`CITATION.cff`](CITATION.cff). | ### πŸ”Ž Headline feature β€” `alterlab-citation-verifier` Around **147 k** hallucinated citations surfaced in published work in 2025. Prompt-only "fact-checking" misses roughly a third of them. `alterlab-citation-verifier` is a **deterministic** core capability that, for every entry in a bibliography: - cross-checks existence against **Crossref + OpenAlex + Semantic Scholar + arXiv** (all keyless), - resolves DOIs / arXiv IDs and matches title + author with a Levenshtein threshold, - flags **Retraction Watch** entries, - maps each verdict to the suite's TF / PAC / IH / PH / SH faithfulness taxonomy, and degrades gracefully to plain `requests` / WebSearch when no MCP or network is present. It rewires the pipeline's bibliography and integrity agents to call it instead of generic web search. ## ✨ Key Features | | Feature | Description | |:---:|:---|:---| | πŸ”¬ | **Research-Ready** | Skills built on real scientific methods, databases, and professional frameworks used by working researchers | | πŸ€– | **Multi-Agent Pipelines** | Core skills chain together: Research β†’ Write β†’ Review β†’ Publish in a seamless workflow | | πŸ“Š | **39 Database Integration Skills** | Instant access to PubMed, ChEMBL, UniProt, ClinicalTrials.gov, COSMIC, and more | | 🧬 | **Deep Domain Coverage** | From single-cell RNA-seq analysis to quantum computing, from clinical trials to digital humanities | | πŸ“ | **Publication-Quality Output** | LaTeX papers, conference posters, grant proposals, scientific visualizations β€” all formatted to professional standards | | πŸ”„ | **Mix & Match** | Combine multiple skills in one Claude Project for a multi-expert research team | ## πŸ—‚οΈ Domain Overview | | Domain | Skills | Focus Areas | |:---:|:---|:---:|:---| | πŸ”„ | **Core Pipeline** | **9** | Multi-agent research β†’ write β†’ review β†’ publish pipeline + citation verifier + teaching + thesis + workflow orchestration | | πŸ—„οΈ | **Databases** | **39** | Connectors to scientific databases β€” PubMed, ChEMBL, UniProt, ClinicalTrials.gov, COSMIC, and more | | 🧬 | **Bioinformatics** | **30** | Genomics, proteomics, molecular biology β€” Scanpy, BioPython, ESM, single-cell analysis, nf-core/sarek, QIIME 2, RNA-seq quant | | βš—οΈ | **Cheminformatics** | **12** | Chemistry and drug discovery β€” RDKit, molecular dynamics, docking, ADMET | | πŸ₯ | **Clinical Research** | **7** | Clinical decision support, treatment planning, medical imaging, regulatory | | πŸ“Š | **Data Science** | **22** | ML/statistics β€” scikit-learn, PyTorch Lightning, SHAP, transformers | | πŸ“ˆ | **Visualization** | **8** | Scientific plotting β€” Matplotlib, Seaborn, Plotly, schematics, infographics | | ✍️ | **Writing Tools** | **13** | Scientific writing, citations, grants, posters, academic career | | πŸ”§ | **Lab Integrations** | **9** | Laboratory platforms β€” Benchling, DNAnexus, Opentrons, Protocols.io | | 🌍 | **Domain-Specific** | **17** | Quantum computing, geospatial, materials science, social science methods, digital humanities | | πŸ“„ | **Document Tools** | **2** | Markdown & document conversion β€” MarkItDown, Open Notebook | | πŸ” | **Research Tools** | **14** | Search, discovery, Zotero, citation graphs, PDF evidence tables, qualitative methods, ethics, surveys, open science | | πŸ’° | **Finance & Economics** | **7** | FRED, Alpha Vantage, SEC EDGAR, market research | | πŸ‡ΉπŸ‡· | **Turkish Academia** | **12** | National platforms & scholarly workflow β€” DergiPark, TR Dizin, YΓ–K Tez/Akademik, YΓ–KATLAS, TÜBΔ°TAK proposals, doΓ§entlik, teşvik, KVKK, Aperta | | πŸŽ“ | **Faculty Life** | **6** | Teaching, service & the academic career β€” syllabus AI policy, grant reporting, recommendation letters, accreditation, REDCap/CDISC, preprints | | πŸ§ͺ | **Methodology** | **3** | Research-rigor discipline gates β€” pre-registration, test-selection guard, results-reporting transparency | ## πŸ”Ž Browse the Catalog Search all 210 skills by name, domain, or keyword β€” no install required. ## πŸš€ Quick Start ### 🌍 Option 1 β€” Agent Skills (open standard) *(Recommended)* ```bash npx skills add AlterLab-IEU/AlterLab-Academic-Skills ``` These are portable **Agent Skills** following the [agentskills.io](https://agentskills.io) open standard β€” they also work in **Cursor, Codex, Gemini CLI, and Copilot**, not Claude only. > [!NOTE] > **Standard: Agent Skills.** This collection conforms to the open Agent Skills standard. See [agentskills.io](https://agentskills.io) for the spec and the list of supporting agents. ### ⚑ Option 2 β€” Claude Code Plugin Add the marketplace once, then install only the domains you need: ```bash /plugin marketplace add AlterLab-IEU/AlterLab-Academic-Skills # No SSH key? Use the HTTPS marketplace path instead: /plugin marketplace add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git /plugin install alterlab-bioinformatics@alterlab-academic-skills /reload-plugins ``` For local development against a clone, point Claude Code at the directory directly: ```bash claude --plugin-dir /path/to/AlterLab-Academic-Skills ``` Available domain plugins: `alterlab-core`, `alterlab-databases`, `alterlab-bioinformatics`, `alterlab-cheminformatics`, `alterlab-clinical-research`, `alterlab-data-science`, `alterlab-visualization`, `alterlab-writing-tools`, `alterlab-lab-integrations`, `alterlab-domain-specific`, `alterlab-document-tools`, `alterlab-research-tools`, `alterlab-finance-economics`, `alterlab-turkish-academia`, `alterlab-faculty-life`, `alterlab-methodology`. ### πŸ“ Option 3 β€” Personal or Project Install (manual) ```bash git clone https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git # Personal β€” available in every project: cp -R AlterLab-Academic-Skills/skills/bioinformatics/alterlab-scanpy ~/.claude/skills/ # Project-scoped β€” only in the current repo: cp -R AlterLab-Academic-Skills/skills/bioinformatics/alterlab-scanpy .claude/skills/ ``` Then restart Claude Code. A skill must live at `~/.claude/skills//SKILL.md` or `.claude/skills//SKILL.md` β€” a bare `git clone` alone does **not** register anything. ### 🌐 Option 4 β€” Claude.ai (per-domain bundles) Every Release ships pre-built **`dist/.zip`** bundles. Each is spec-conformant and clears claude.ai's 200-file / 30 MB caps, and vendors the shared handoff contracts so cross-skill references resolve. 1. Download the domain bundle you need from the [Releases page](https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/releases) β€” e.g. `bioinformatics.zip`, `databases.zip`, `core.zip`. 2. Upload it under **Settings β†’ Capabilities** (requires a plan with code execution). Skills do not sync between claude.ai and Claude Code. To zip a single skill yourself instead, archive its directory (`zip -r alterlab-scanpy.zip skills/bioinformatics/alterlab-scanpy`). ### πŸ› οΈ Option 5 β€” `install.sh` (scriptable local install) The bundled installer copies whole domains and/or individual skills into the right local directory (`~/.claude/skills/` or the cross-tool `~/.agents/skills/`), idempotently: ```bash git clone https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git cd AlterLab-Academic-Skills scripts/install.sh --list # show every domain / skill scripts/install.sh bioinformatics # whole domain scripts/install.sh databases/alterlab-pubmed # one skill scripts/install.sh --project core # into ./.claude/skills scripts/install.sh # install everything ``` Then restart your agent to load them. ### πŸ”Œ MCP & Slash Commands The `core` and `databases` plugins ship a `.mcp.json` that wires the **PubMed / OpenAlex / Crossref / Zotero** academic MCP servers, with a documented `requests/` fallback when no MCP host is available β€” so the citation verifier and database skills work online or offline. Install either plugin (Option 2) to pick the MCP up automatically. Installing the `core` plugin also registers these slash commands: | Command | Drives | |:---|:---| | `/lit-review` | `alterlab-deep-research` β€” systematic literature review | | `/review-paper` | `alterlab-paper-reviewer` β€” multi-perspective peer review | | `/cite-check` | `alterlab-citation-verifier` β€” deterministic citation-existence gate | | `/research-pipeline` | `alterlab-research-pipeline` β€” full research β†’ publish orchestrator | > [!NOTE] > **210 / 210 skills ship executable evals** on … ## Source & license This open-source MCP server is cataloged on AgentStack and links to its original source β€” we do not rehost the code. - **Author:** [AlterLab-IEU](https://github.com/AlterLab-IEU) - **Source:** [AlterLab-IEU/AlterLab-Academic-Skills](https://github.com/AlterLab-IEU/AlterLab-Academic-Skills) - **License:** MIT - **Homepage:** https://alterlab-ieu.github.io/AlterLab-Academic-Skills/ Install and usage instructions live in the source repository linked above. ## Pricing - **Free** β€” Free ## Security capabilities Automated source analysis of v0.1.0 β€” what this tool can access: - **Network access:** no - **Filesystem access:** no - **Shell / process execution:** no - **Environment & secrets:** no - **Dynamic code execution:** yes *"Yes" means the capability is present in the source β€” more access means more to trust, not that it is unsafe.* ## Versions - **0.1.0** β€” security scan: flagged β€” Imported from the upstream source. ## Links - Listing page: https://agentstack.voostack.com/l/mcp-alterlab-ieu-alterlab-academic-skills - Seller: https://agentstack.voostack.com/s/alterlab-ieu - Browse the marketplace: https://agentstack.voostack.com/browse --- Listed on AgentStack β€” the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.