Is databases safe to install?

SaferSkills independently audited databases (MCP Server) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.

CategoryWeightCategory scoreContribution

Securityprompt, exec, net, exfil, eval

35%

100

35.0 pts

Supply chainhash, typosquat, maintainer, lockfile

20%

100

20.0 pts

Maintenancestaleness, pinning, CI

15%

100

15.0 pts

TransparencySKILL.md, perms, README

15%

100

15.0 pts

Communityinstalls, verify, response

15%

100

15.0 pts

Findings & checks · 0 flagged

Securityscore 100 · 0 findings

✓—All security checks passedNo findings in this category for the latest scan.pass

Supply chainscore 100 · 0 findings

✓—All supply chain checks passedNo findings in this category for the latest scan.pass

Maintenancescore 100 · 0 findings

✓—All maintenance checks passedNo findings in this category for the latest scan.pass

Transparencyscore 100 · 0 findings

✓—All transparency checks passedNo findings in this category for the latest scan.pass

Communityscore 100 · 0 findings

✓—All community checks passedNo findings in this category for the latest scan.pass

The primary manifest — the file an agent reads to learn what this artifact does.

README.md · 1 file

README.md44.6 KB · Markdown

<br>

<br>

📢 Featured in awesome-claude-skills (5.7k ⭐)

<br>

Read in: English · Türkçe

<h3>🧬 210 purpose-built Claude AI skills for faculty, researchers & academicians</h3> <p><em>Organized across 16 research domains — from Turkish academia to bioinformatics to digital humanities</em></p> <p><em>210/210 ship executable evals · deterministic citation-existence verifier · per-domain bundles for claude.ai</em></p>

<p> <b>Research Pipeline</b> · <b>Scientific Databases</b> · <b>Bioinformatics</b> · <b>Data Science</b> · <b>Visualization</b> · <b>Clinical Research</b> · <b>and more</b> </p>

<p> <a href="skills/"><b>Explore Skills »</b></a> · <a href="#-quick-start">Quick Start</a> · <a href="#%EF%B8%8F-domain-overview">Domain Overview</a> · <a href="CONTRIBUTING.md">Contributing</a> · <a href="https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/issues">Report Bug</a> </p>

<br>

<hr>

<table><tr><td> <b>Built by</b> <a href="https://github.com/AlterLab-IEU"><b>AlterLab Creative Technologies Laboratory</b></a> <br><br> <em>Not tied to any specific university — these skills work for any researcher, anywhere.</em> </td></tr></table>

</div>

<br>

<div align="center"> <table> <tr> <td align="center" width="25%"> <h3>🎯</h3> <h3>Plug & Play</h3> <p>Drop a <code>.md</code> skill file into<br>Claude Projects or Claude Code<br>and get instant expertise</p> </td> <td align="center" width="25%"> <h3>🧠</h3> <h3>Domain Expert</h3> <p>Each skill transforms Claude<br>into a specialized research<br>assistant with deep knowledge</p> </td> <td align="center" width="25%"> <h3>🔬</h3> <h3>Real Frameworks</h3> <p>Built on actual scientific<br>methods, tools, and professional<br>output templates</p> </td> <td align="center" width="25%"> <h3>🌐</h3> <h3>Universal</h3> <p>Works for any researcher<br>at any institution —<br>no vendor lock-in</p> </td> </tr> </table> </div>

<br>

🚀 What's New in v2.2.0

🧠 Research-backed elevation of 191 skills — 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) — composes AlterLab skills into multi-agent workflows (subagent fan-out, pipelines, judge panels, adversarial verification), lifting the corpus to 210 skills. → Core Pipeline

🇹🇷 Turkish-academia flagship (12 skills) — the deepest Turkish-academia suite in any skills library: DergiPark, TR Dizin, YÖK Tez, YÖK Akademik, YÖKATLAS, TÜBİTAK 1001/1002-A proposals, doçentlik eligibility, akademik teşvik scoring, Turkish APA-7 style, TR research ethics, KVKK data-management plans, and TÜBİTAK Aperta — each wired to a verified national-platform endpoint. → Turkish Academia
🎓 Faculty Life (6 skills) — syllabus AI policy, post-award grant reporting, recommendation letters, AACSB/ABET accreditation (AoL), REDCap/CDISC capture, and preprint deposition. → Faculty Life
🧪 Methodology (3 skills) — superpowers-style rigor (Iron Laws, Excuse-vs-Reality tables) applied to research methods: pre-registration discipline, statistical-test-selection guard, and results-reporting transparency. → Methodology
🧬 Bioinformatics grew 25 → 30 — production pipelines: nf-core/sarek variant calling, QIIME 2 amplicon, salmon/kallisto RNA-seq quant, NCBI BLAST+, and Squidpy spatial transcriptomics. → Bioinformatics
✅ Day-one evals on all 26 new skills — coverage stays 210 / 210; the shape + coverage gate runs in CI on every PR. → docs/evals.md

<details> <summary><b>Previously — What's New in v2.0</b></summary> <br>

✅ Full-corpus executable evals — schema + trigger-coverage are CI-gated on every PR; the behavioral pass (claude CLI + LLM judge) runs on demand via workflow_dispatch. → docs/evals.md
🔎 Deterministic citation-existence verifier that catches hallucinated references against Crossref / OpenAlex / Semantic Scholar / arXiv — no LLM guesswork in the gate. → Headline feature
📦 Per-domain `claude.ai` bundles on every Release — each dist/<domain>.zip clears the 200-file / 30 MB caps. → Releases
🌐 Live searchable catalog to browse every skill in the browser. → Browse the Catalog
🤖 35 registered subagents + slash commands + a bundled academic MCP wiring PubMed / OpenAlex / Crossref / Zotero. → MCP & Slash Commands
📜 Honest provenance — upstream K-Dense fork credited in THIRD_PARTY_NOTICES.md and a machine-readable CITATION.cff. → Cite This Repository

</details>

<br>

📋 Table of Contents

<details open> <summary><b>Click to expand / collapse</b></summary> <br>

🚀 What's New in v2.2.0
🎯 What Is This?
🆕 v2.0 Highlights
✨ Key Features
🗂️ Domain Overview
🔎 Browse the Catalog
🚀 Quick Start
⚡ Core Pipeline — 9 Skills
📚 All 210 Skills
🏗️ Project Structure
⚙️ How Skills Work
💡 Usage Examples
⚖️ How It Compares
🤝 Contributing
📖 Cite This Repository
📜 License
🙏 Credits

</details>

<br>

🎯 What Is This?

A comprehensive suite of 210 purpose-built Claude AI skills for faculty members, academicians, and researchers — 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/) — 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.

<br>

🆕 v2.0 Highlights

v2.0 is the "Trust & Reach" release — it turns the loudest objection to academic skills ("just prompts, no evals") into the headline differentiator.

	What	Detail
✅	Executable evals across the corpus	210 / 210 skills ship `evals/evals.json` on the canonical agentskills.io schema, validated in CI. See `docs/evals.md`.
🔎	Citation-existence verifier	New core skill `alterlab-citation-verifier` — 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.
📦	Per-domain bundles for claude.ai	`dist/<domain>.zip` bundles (one per domain) attached to each Release — each clears claude.ai's 200-file / 30 MB caps and vendors the shared handoff contracts.
🔌	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` — drive the core pipeline directly.
🗂️	Generated catalog	A machine-readable `skills.json` is generated from skill frontmatter; a CI gate keeps every count in this README honest.
📜	Honest provenance	Upstream K-Dense fork credited in `THIRD_PARTY_NOTICES.md` + `PROVENANCE.md` / `CITATION.cff`.

🔎 Headline feature — `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.

<br>

✨ Key Features

	Feature	Description
🔬	Research-Ready	Skills built on real scientific methods, databases, and professional frameworks used by working researchers
🤖	Multi-Agent Pipelines	Core skills chain together: Research → Write → Review → Publish in a seamless workflow
📊	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
📝	Publication-Quality Output	LaTeX papers, conference posters, grant proposals, scientific visualizations — all formatted to professional standards
🔄	Mix & Match	Combine multiple skills in one Claude Project for a multi-expert research team

<br>

🗂️ Domain Overview

	Domain	Skills	Focus Areas
🔄	Core Pipeline	9	Multi-agent research → write → review → publish pipeline + citation verifier + teaching + thesis + workflow orchestration
🗄️	Databases	39	Connectors to scientific databases — PubMed, ChEMBL, UniProt, ClinicalTrials.gov, COSMIC, and more
🧬	Bioinformatics	30	Genomics, proteomics, molecular biology — Scanpy, BioPython, ESM, single-cell analysis, nf-core/sarek, QIIME 2, RNA-seq quant
⚗️	Cheminformatics	12	Chemistry and drug discovery — RDKit, molecular dynamics, docking, ADMET
🏥	Clinical Research	7	Clinical decision support, treatment planning, medical imaging, regulatory
📊	Data Science	22	ML/statistics — scikit-learn, PyTorch Lightning, SHAP, transformers
📈	Visualization	8	Scientific plotting — Matplotlib, Seaborn, Plotly, schematics, infographics
✍️	Writing Tools	13	Scientific writing, citations, grants, posters, academic career
🔧	Lab Integrations	9	Laboratory platforms — Benchling, DNAnexus, Opentrons, Protocols.io
🌍	Domain-Specific	17	Quantum computing, geospatial, materials science, social science methods, digital humanities
📄	Document Tools	2	Markdown & document conversion — MarkItDown, Open Notebook
🔍	Research Tools	14	Search, discovery, Zotero, citation graphs, PDF evidence tables, qualitative methods, ethics, surveys, open science
💰	Finance & Economics	7	FRED, Alpha Vantage, SEC EDGAR, market research
🇹🇷	Turkish Academia	12	National platforms & scholarly workflow — DergiPark, TR Dizin, YÖK Tez/Akademik, YÖKATLAS, TÜBİTAK proposals, doçentlik, teşvik, KVKK, Aperta
🎓	Faculty Life	6	Teaching, service & the academic career — syllabus AI policy, grant reporting, recommendation letters, accreditation, REDCap/CDISC, preprints
🧪	Methodology	3	Research-rigor discipline gates — pre-registration, test-selection guard, results-reporting transparency

<br>

🔎 Browse the Catalog

<em>Search all 210 skills by name, domain, or keyword — no install required.</em>

</div>

<br>

🚀 Quick Start

🌍 Option 1 — Agent Skills (open standard) (Recommended)

npx skills add AlterLab-IEU/AlterLab-Academic-Skills

These are portable Agent Skills following the agentskills.io open standard — 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 for the spec and the list of supporting agents.

⚡ Option 2 — Claude Code Plugin

Add the marketplace once, then install only the domains you need:

/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:

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.

📁 Option 3 — Personal or Project Install (manual)

git clone https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git
# Personal — available in every project:
cp -R AlterLab-Academic-Skills/skills/bioinformatics/alterlab-scanpy ~/.claude/skills/
# Project-scoped — 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/<name>/SKILL.md or .claude/skills/<name>/SKILL.md — a bare git clone alone does not register anything.

🌐 Option 4 — Claude.ai (per-domain bundles)

Every Release ships pre-built `dist/<domain>.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.

Download the domain bundle you need from the Releases page — e.g. bioinformatics.zip, databases.zip, core.zip.
Upload it under Settings → 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).

🛠️ Option 5 — `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:

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.

🔌 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 — 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` — systematic literature review
`/review-paper`	`alterlab-paper-reviewer` — multi-perspective peer review
`/cite-check`	`alterlab-citation-verifier` — deterministic citation-existence gate
`/research-pipeline`	`alterlab-research-pipeline` — full research → publish orchestrator

<br>

[!NOTE] 210 / 210 skills ship executable evals on the canonical agentskills.io schema. Schema and trigger-coverage are validated in CI on every PR; the behavioral pass (claude CLI + LLM judge) runs on demand via workflow_dispatch. See docs/evals.md for how coverage is measured and how to run scripts/run_evals.py locally.

<br>

⚡ Core Pipeline — 9 Skills

The heart of the system — a multi-agent research-to-publication pipeline with 39 specialized agents, plus teaching and thesis supervision tools.

#	Skill	Agents	What It Does
1	🔬 Deep Research	13	Multi-mode research with systematic review, Socratic dialogue, fact-checking
2	📝 Paper Writer	12	Academic paper authoring with LaTeX, bilingual support, 9 writing modes
3	🔍 Paper Reviewer	7	Multi-perspective peer review with Devil's Advocate, 0–100 quality rubrics
4	🔄 Research Pipeline	7	10-stage orchestrator with integrity verification and material passports
5	🔎 Citation Verifier	—	Deterministic citation-existence gate over Crossref / OpenAlex / Semantic Scholar / arXiv
6	🎓 Teaching Design	—	Course design, syllabi, rubrics, Bloom's taxonomy, backward design
7	📋 Thesis Supervisor	—	Dissertation guidance, defense prep, committee management
8	🔗 Link Health	—	Repo link-health audit meta-skill
9	🧩 Workflow Orchestration	—	Composes AlterLab skills into multi-agent workflows: subagent fan-out, pipelines, judge panels, adversarial verification

<br>

📚 All 210 Skills

🗄️ Databases — Scientific Database Connectors (39 Skills)

<details> <summary><b>Click to expand full database skills list</b></summary> <br>

#	Skill	What It Does
1	AlphaFold DB	Protein structure predictions from AlphaFold
2	arXiv	Preprint search and discovery
3	BindingDB	Binding affinity data for drug-target interactions
4	bioRxiv	Biology preprint search and monitoring
5	BRENDA	Enzyme functional data
6	cBioPortal	Cancer genomics data exploration
7	ChEMBL	Bioactive molecules with drug-like properties
8	ClinicalTrials.gov	Clinical trial registry search
9	ClinPGx	Clinical pharmacogenomics data
10	ClinVar	Genomic variation and human health
11	COSMIC	Catalogue of somatic mutations in cancer
12	Data Commons	Google's open knowledge graph
13	DepMap	Cancer dependency mapping
14	DrugBank	Drug and drug target information
15	ENA	European Nucleotide Archive
16	Ensembl	Genome annotation and variation
17	FDA	FDA drug and device data
18	Gene DB	Gene-level data aggregation
19	GEO	Gene Expression Omnibus datasets
20	gnomAD	Genome aggregation and variant frequency
21	GTEx	Tissue-specific gene expression
22	GWAS Catalog	Genome-wide association studies
23	HMDB	Human Metabolome Database
24	Imaging Data Commons	Cancer imaging data
25	InterPro	Protein families and domains
26	JASPAR	Transcription factor binding profiles
27	KEGG	Biological pathways and networks
28	Metabolomics Workbench	Metabolomics data repository
29	Monarch Initiative	Disease-gene associations
30	OpenAlex	Open scholarly metadata
31	Open Targets	Drug target identification
32	PDB	Protein 3D structure database
33	PubChem	Chemical information database
34	PubMed	Biomedical literature search
35	Reactome	Biological pathway database
36	STRING	Protein-protein interaction networks
37	UniProt	Protein sequence and function
38	USPTO	Patent search and analysis
39	ZINC	Commercially-available compounds for docking

</details>

🧬 Bioinformatics — Genomics, Proteomics & Molecular Biology (30 Skills)

<details> <summary><b>Click to expand full bioinformatics skills list</b></summary> <br>

#	Skill	What It Does
1	AnnData	Annotated data matrices for single-cell
2	Arboreto	Gene regulatory network inference
3	BioPython	General-purpose bioinformatics toolkit
4	BioServices	Programmatic access to biological web services
5	CellxGene	Interactive single-cell data exploration
6	COBRApy	Constraint-based metabolic modeling
7	deepTools	NGS data analysis and visualization
8	ESM	Protein language models
9	ETE Toolkit	Phylogenetic tree analysis and visualization
10	FlowIO	Flow cytometry data handling
11	gget	Query genomic databases from Python
12	Glycoengineering	Glycan analysis and engineering
13	HistoLab	Computational histopathology
14	LaminDB	Data lineage and biological data management
15	Neuropixels	Neural probe data processing
16	PathML	Machine learning for pathology
17	Phylogenetics	Evolutionary tree construction
18	PyDESeq2	Differential gene expression analysis
19	pyOpenMS	Mass spectrometry data analysis
20	pysam	SAM/BAM file manipulation
21	Scanpy	Single-cell analysis in Python
22	scikit-bio	Bioinformatics algorithms and data structures
23	scVelo	RNA velocity analysis
24	scvi-tools	Deep generative models for single-cell
25	TileDB-VCF	Population-scale genomic variant storage
26	BLAST	NCBI BLAST+ command-line sequence similarity searches
27	nf-core/sarek	FASTQ-to-VCF germline & somatic variant-calling pipeline
28	QIIME 2 Amplicon	16S/ITS microbiome amplicon analysis
29	RNA-seq Quant	Transcript abundance with salmon & kallisto
30	Squidpy Spatial	Spatial transcriptomics on AnnData/SpatialData

</details>

⚗️ Cheminformatics — Chemistry & Drug Discovery (12 Skills)

<details> <summary><b>Click to expand full cheminformatics skills list</b></summary> <br>

#	Skill	What It Does
1	Datamol	Molecular data manipulation
2	DeepChem	Deep learning for chemistry
3	DiffDock	Diffusion-based molecular docking
4	matchms	Mass spectra matching and similarity
5	MedChem	Medicinal chemistry analysis
6	Molecular Dynamics	MD simulation setup and analysis
7	MolFeat	Molecular featurization
8	PrimeKG	Precision medicine knowledge graph
9	PyTDC	Therapeutics Data Commons access
10	RDKit	Core cheminformatics toolkit
11	Rowan	Computational chemistry workflows
12	TorchDrug	Graph neural networks for drug discovery

</details>

🏥 Clinical Research — Clinical Decision Support & Medical Tools (7 Skills)

<details> <summary><b>Click to expand full clinical research skills list</b></summary> <br>

#	Skill	What It Does
1	Clinical Decision	Evidence-based clinical decision support
2	Clinical Reports	Structured clinical report generation
3	ISO 13485	Medical device quality management
4	NeuroKit2	Neurophysiological signal processing
5	PyDicom	DICOM medical image handling
6	PyHealth	Healthcare ML pipelines
7	Treatment Plans	Treatment planning and protocol design

</details>

📊 Data Science — ML, Statistics & Data Analysis (22 Skills)

<details> <summary><b>Click to expand full data science skills list</b></summary> <br>

#	Skill	What It Does
1	Dask	Parallel computing and out-of-core data
2	EDA	Exploratory data analysis
3	NetworkX	Network/graph analysis
4	Polars	High-performance DataFrames
5	PufferLib	Reinforcement learning environments
6	PyMC	Bayesian statistical modeling
7	pymoo	Multi-objective optimization
8	PyTorch Lightning	Structured deep learning training
9	scikit-learn	Classical machine learning
10	scikit-survival	Survival analysis
11	SHAP	Model interpretability and feature importance
12	SimPy	Discrete-event simulation
13	Stable-Baselines3	Reinforcement learning algorithms
14	Statistical Analysis	Classical statistical tests and methods
15	statsmodels	Statistical models and econometrics
16	SymPy	Symbolic mathematics
17	TimesFM	Foundation model for time series
18	PyTorch Geometric	Graph neural networks
19	Transformers	Hugging Face transformer models
20	UMAP	Dimensionality reduction
21	Vaex	Out-of-core DataFrames for big data
22	Zarr	Chunked, compressed N-dimensional arrays

</details>

📈 Visualization — Scientific Plotting & Graphics (8 Skills)

<details> <summary><b>Click to expand full visualization skills list</b></summary> <br>

#	Skill	What It Does
1	Generate Image	AI image generation for research figures
2	Infographics	Research infographic design
3	Matplotlib	Publication-quality 2D plots
4	Mermaid	Diagrams and flowcharts as code
5	Plotly	Interactive scientific visualizations
6	Scientific Schematics	Technical diagrams and schematics
7	Scientific Viz	Advanced scientific visualization
8	Seaborn	Statistical data visualization

</details>

✍️ Writing Tools — Scientific Writing, Citations & Publishing (13 Skills)

<details> <summary><b>Click to expand full writing tools skills list</b></summary> <br>

#	Skill	What It Does
1	Academic Career	Academic CV, research statements, tenure dossier
2	Citation Management	Reference formatting and management
3	Hypothesis Generator	Research hypothesis development
4	LaTeX Posters	Conference poster design in LaTeX
5	Literature Review	Systematic literature review assistance
6	Paper-to-Web	Convert papers to web-friendly formats
7	Peer Review	Peer review writing assistance
8	PPTX Posters	Conference posters in PowerPoint
9	Research Grants	Grant proposal writing
10	Scholar Eval	Academic output evaluation
11	Scientific Slides	Research presentation creation
12	Scientific Writing	Academic writing style and structure
13	Venue Templates	Journal/conference formatting templates

</details>

🔧 Lab Integrations — Laboratory Platform Connectors (9 Skills)

<details> <summary><b>Click to expand full lab integration skills list</b></summary> <br>

#	Skill	What It Does
1	Benchling	Molecular biology data platform
2	DNAnexus	Genomic data analysis platform
3	Ginkgo Cloud	Synthetic biology platform
4	LabArchive	Electronic lab notebook
5	LatchBio	Bioinformatics workflow platform
6	OMERO	Biological image management
7	Opentrons	Lab automation and robotics
8	Protocols.io	Protocol sharing and management
9	PyLabRobot	Lab robotics programming

</details>

<details> <summary><b>Click to expand full domain-specific skills list</b></summary> <br>

#	Skill	What It Does
1	Adaptyv	Adaptive experimental design
2	Aeon	Time series classification
3	AstroPy	Astronomy and astrophysics
4	Cirq	Quantum circuit design (Google)
5	FluidSim	Fluid dynamics simulation
6	GeniML	Genomic interval ML
7	GeoMaster	Geospatial analysis mastery
8	GeoPandas	Geospatial data analysis
9	GTARS	Genomic tool for annotation
10	HypoGenic	Hypothesis generation from data
11	Modal	Cloud compute for research
12	PennyLane	Quantum machine learning
13	Pymatgen	Materials science analysis
14	Qiskit	Quantum computing (IBM)
15	QuTiP	Quantum dynamics simulation
16	Social Science Methods	Discourse analysis, QCA, Delphi, process tracing
17	Digital Humanities	Text mining, corpus linguistics, stylometry, OCR

</details>

📄 Document Tools — Markdown & Document Conversion (2 Skills)

<details> <summary><b>Click to expand full document tools skills list</b></summary> <br>

#	Skill	What It Does
1	MarkItDown	Convert documents to Markdown
2	Open Notebook	Open-format research notebooks

</details>

🔍 Research Tools — Search, Discovery, Methods & Reference Management (14 Skills)

<details> <summary><b>Click to expand full research tools skills list</b></summary> <br>

#	Skill	What It Does
1	BGPT Search	AI-powered research search
2	Citation Graph	Keyless ResearchRabbit analog — citation & co-citation graphs over OpenAlex
3	Mixed Methods	Mixed-methods research design and integration
4	Open Science	Preregistration, FAIR data, open access publishing
5	Parallel Web	Multi-source parallel web search
6	PDF Extract	Elicit-columns analog — per-paper evidence tables from PDFs
7	Perplexity	Perplexity-powered research queries
8	PyZotero	Zotero reference manager integration
9	Qualitative Methods	Thematic analysis, grounded theory, IPA, coding
10	Research Ethics	IRB applications, informed consent, GDPR
11	Research Lookup	Quick research paper discovery
12	Scientific Brainstorm	Structured research ideation
13	Scientific Thinking	Critical scientific reasoning frameworks
14	Survey Design	Questionnaire construction and validation

</details>

💰 Finance & Economics — Financial Data & Analysis (7 Skills)

<details> <summary><b>Click to expand full finance & economics skills list</b></summary> <br>

#	Skill	What It Does
1	Alpha Vantage	Stock and financial market data
2	Denario	Financial data processing
3	EDGAR Tools	SEC filing search and analysis
4	FRED	Federal Reserve economic data
5	Hedge Fund Monitor	Hedge fund tracking and analysis
6	Market Research	Market analysis and intelligence
7	US Fiscal Data	US government fiscal data

</details>

🇹🇷 Turkish Academia — National Platforms & Scholarly Workflow (12 Skills)

<details> <summary><b>Click to expand full Turkish academia skills list</b></summary> <br>

#	Skill	What It Does
1	DergiPark	Harvest metadata, abstracts & PDFs from DergiPark via OAI-PMH
2	TR Dizin	Search TR Dizin & verify a journal's national-index status
3	YÖK Tez	Search the national graduate-thesis archive for review & originality checks
4	YÖK Akademik	Look up a Turkish academic's YÖKSİS profile, title & affiliation
5	YÖKATLAS	Higher-education program & admission statistics (kontenjan, taban puan)
6	TÜBİTAK Proposal	Scaffold TÜBİTAK 1001/1002-A national research proposals
7	Doçentlik Eligibility	Score a publication list against ÜAK associate-professor criteria
8	Akademik Teşvik	Compute the annual academic-incentive (teşvik) score
9	TR Academic Style	Turkish-journal & TR-Dizin formatting + Turkish APA-7
10	TR Research Ethics	Turkish etik kurul applications & consent-form routing
11	KVKK DMP	KVKK-compliant data-management plans for Turkish research
12	Aperta	TÜBİTAK open-science compliance & deposition into Aperta

</details>

🎓 Faculty Life — Teaching, Service & the Academic Career (6 Skills)

<details> <summary><b>Click to expand full faculty life skills list</b></summary> <br>

#	Skill	What It Does
1	Syllabus AI Policy	Course-level generative-AI use policies & syllabus statements
2	Grant Reporting	Post-award reports — NIH RPPR, NSF, Horizon Europe / ERC
3	Recommendation Letters	Evidence-anchored reference & recommendation letters
4	Accreditation (AoL)	AACSB / ABET assurance-of-learning documentation
5	REDCap / CDISC	Validated data-capture instruments mapped to CDISC standards
6	Preprint Deposition	Deposit preprints to arXiv, bioRxiv, medRxiv, SSRN, OSF

</details>

🧪 Methodology — Research Rigor & Discipline Gates (3 Skills)

<details> <summary><b>Click to expand full methodology skills list</b></summary> <br>

#	Skill	What It Does
1	Pre-registration Discipline	No analysis without a frozen, pre-registered plan
2	Test-Selection Guard	No statistical test chosen after seeing the p-value
3	Results Transparency	No results claim without reporting every analysis run

</details>

<br>

🏗️ Project Structure

AlterLab-Academic-Skills/
├── 📁 skills/                       # 210 skills across 16 domains
│   ├── 🔄 core/                # 8 pipeline + citation-verifier + teaching + thesis skills
│   ├── 🗄️ databases/           # 39 database connectors
│   ├── 🧬 bioinformatics/      # 30 bio/genomics tools
│   ├── ⚗️ cheminformatics/     # 12 chemistry/drug discovery
│   ├── 🏥 clinical-research/   # 7 clinical/medical tools
│   ├── 📊 data-science/        # 22 ML/statistics tools
│   ├── 📈 visualization/       # 8 plotting/charting tools
│   ├── ✍️ writing-tools/       # 13 scientific writing & career tools
│   ├── 🔧 lab-integrations/    # 9 lab platform connectors
│   ├── 🌍 domain-specific/     # 17 specialized field tools
│   ├── 📄 document-tools/      # 2 file format tools
│   ├── 🔍 research-tools/      # 14 search, methods & ethics tools
│   ├── 💰 finance-economics/   # 7 financial/economic tools
│   ├── 🇹🇷 turkish-academia/    # 12 Turkish national-platform & workflow skills
│   ├── 🎓 faculty-life/        # 6 teaching, service & career skills
│   └── 🧪 methodology/         # 3 research-rigor discipline gates
├── 📁 dist/                          # per-domain .zip bundles for claude.ai (built on release)
├── 📁 scripts/                       # install.sh, gen_catalog.py, run_evals.py, audit_skills.py …
├── 📁 docs/                          # evals, integrity & design docs
├── 📄 skills.json                    # generated machine-readable catalog
├── 📄 README.md                      # This file
├── 📄 CLAUDE.md                      # Project instructions
├── 📄 CONTRIBUTING.md                # Contribution guidelines
├── 📄 THIRD_PARTY_NOTICES.md         # Upstream / K-Dense provenance
└── 📄 LICENSE                        # MIT License

<br>

⚙️ How Skills Work

Each .md skill file follows a consistent structure:

| name          | description                         |
|---------------|-------------------------------------|
| skill-name    | When to activate this skill...      |

# Skill Title

You are **RoleName**, a [role description]...

## Your Identity & Memory
## Your Core Mission
## Frameworks & Methods
## Output Templates
## Quality Standards

[!NOTE] Pro tip: Combine multiple skills in one Claude Project for a multi-expert team. For example, load Deep Research + Paper Writer + Paper Reviewer for a complete research-to-publication workflow.

<br>

💡 Usage Examples

Skills activate automatically based on user intent:

You say...	Skill activated
"Help me research the latest findings on CRISPR gene editing"	`alterlab-deep-research`
"Write an academic paper on machine learning in education"	`alterlab-paper-writer`
"Review my manuscript for methodology issues"	`alterlab-paper-reviewer`
"Search PubMed for recent studies on Alzheimer's biomarkers"	`alterlab-pubmed`
"Analyze my RNA-seq data"	`alterlab-scanpy` + `alterlab-pydeseq2`
"Create a scientific poster for my conference"	`alterlab-latex-posters`
"Design a survey for my social science study"	`alterlab-survey-design`
"Help me with my IRB ethics application"	`alterlab-research-ethics`
"Build a Bayesian model for my clinical trial data"	`alterlab-pymc`
"Guide my PhD student's thesis writing"	`alterlab-thesis-supervisor`

<br>

⚖️ How It Compares

Respectfully, factually — both peers are excellent MIT-licensed projects. This table is about fit, not ranking.

	AlterLab Academic Skills	K-Dense scientific-agent-skills	anthropics/skills
Skills	210	138 (self-reported)	General-purpose examples
Executable evals	210 / 210 shipped; coverage CI-gated, behavioral on demand	Not shipped as an eval harness	Not the project's focus
License	MIT	MIT	MIT
Academic focus	Built for the research lifecycle	Scientific tooling	General / reference
Bundles / marketplace	Per-domain `claude.ai` bundles + Claude Code marketplace	—	—

</div>

Counts verified against skills.json; K-Dense figure is the upstream project's own self-reported count. anthropics/skills is Anthropic's official example collection, scoped to general-purpose demonstrations rather than a fixed academic catalog.

<br>

🔗 Sister Projects

AlterLab-FC-Skills — 72 agentic skills for communication students
AlterLab_GameForge — 34 game dev skills from concept to launch

🤝 Contributing

We welcome contributions! See [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.

Quick ways to contribute:

🛠️ Improve an existing skill with better frameworks or templates
✨ Create a new skill following the structure above
🐛 Report issues or suggest improvements
📚 Add examples or use cases to documentation

<br>

📖 Cite This Repository

If AlterLab Academic Skills supports your research or teaching, please cite it. A machine-readable CITATION.cff ships in the repo, so GitHub's "Cite this repository" button and most reference managers can import it automatically. The suite is a content fork of K-Dense's scientific-agent-skills (MIT) — see THIRD_PARTY_NOTICES.md and PROVENANCE.md for full provenance.

@software{alterlab_academic_skills_2026,
  title   = {AlterLab Academic Skills},
  author  = {{AlterLab Creative Technologies Laboratory, Izmir University of Economics (IEU)}},
  year    = {2026},
  version = {2.1.0},
  license = {MIT},
  url     = {https://github.com/AlterLab-IEU/AlterLab-Academic-Skills}
}

<details> <summary><b>Prefer CFF? Click to expand the <code>CITATION.cff</code> core</b></summary>

cff-version: 1.2.0
title: "AlterLab Academic Skills"
type: software
version: 2.1.0
date-released: "2026-06-06"
license: MIT
repository-code: "https://github.com/AlterLab-IEU/AlterLab-Academic-Skills"
authors:
  - name: "AlterLab Creative Technologies Laboratory, Izmir University of Economics (IEU)"
    website: "https://github.com/AlterLab-IEU"
    city: "Izmir"
    country: "TR"

</details>

<br>

📜 License

This project is licensed under the [MIT License](LICENSE).

MIT License — Copyright (c) 2026 AlterLab Creative Technologies Laboratory

<br>

🙏 Credits

<b>Built with ❤️ by <a href="https://github.com/AlterLab-IEU">AlterLab Creative Technologies Laboratory</a></b>

<b>210 skills · 16 domains · 210 with executable evals · 1 prompt away from expert-level research</b>

<hr>

<sub>If you find this project useful, please consider giving it a ⭐</sub>

<br>

</div>

<br>

🌟 Star History

</div>

<br>

Is databases safe to install?

🚀 What's New in v2.2.0

📋 Table of Contents

🎯 What Is This?

🆕 v2.0 Highlights

🔎 Headline feature — alterlab-citation-verifier

✨ Key Features

🗂️ Domain Overview

🔎 Browse the Catalog

🚀 Quick Start

🌍 Option 1 — Agent Skills (open standard) (Recommended)

⚡ Option 2 — Claude Code Plugin

📁 Option 3 — Personal or Project Install (manual)

🌐 Option 4 — Claude.ai (per-domain bundles)

🛠️ Option 5 — install.sh (scriptable local install)

🔌 MCP & Slash Commands

⚡ Core Pipeline — 9 Skills

📚 All 210 Skills

🗄️ Databases — Scientific Database Connectors (39 Skills)

🧬 Bioinformatics — Genomics, Proteomics & Molecular Biology (30 Skills)

⚗️ Cheminformatics — Chemistry & Drug Discovery (12 Skills)

🏥 Clinical Research — Clinical Decision Support & Medical Tools (7 Skills)

📊 Data Science — ML, Statistics & Data Analysis (22 Skills)

📈 Visualization — Scientific Plotting & Graphics (8 Skills)

✍️ Writing Tools — Scientific Writing, Citations & Publishing (13 Skills)

🔧 Lab Integrations — Laboratory Platform Connectors (9 Skills)

🌍 Domain-Specific — Quantum, Geospatial, Materials, Social Science & More (17 Skills)

📄 Document Tools — Markdown & Document Conversion (2 Skills)

🔍 Research Tools — Search, Discovery, Methods & Reference Management (14 Skills)

💰 Finance & Economics — Financial Data & Analysis (7 Skills)

🇹🇷 Turkish Academia — National Platforms & Scholarly Workflow (12 Skills)

🎓 Faculty Life — Teaching, Service & the Academic Career (6 Skills)

🧪 Methodology — Research Rigor & Discipline Gates (3 Skills)

🏗️ Project Structure

⚙️ How Skills Work

💡 Usage Examples

⚖️ How It Compares

🔗 Sister Projects

🤝 Contributing

📖 Cite This Repository

📜 License

🙏 Credits

🌟 Star History

Audit the pieces. Scan the whole. Decide.

🔎 Headline feature — `alterlab-citation-verifier`

🛠️ Option 5 — `install.sh` (scriptable local install)