alterlab-ieu/alterlab-academic-skills

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alterlab-opentargets Query the Open Targets Platform GraphQL API for target-disease associations, tractability and safety data, genetics/o…

alterlab-ieu/alterlab-academic-skills

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alterlab-opentrons Writes liquid-handling protocols for Opentrons OT-2 and Flex robots using the official Opentrons Protocol API v2, wit…

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alterlab-paper-2-web Converts academic papers into promotional and presentation formats — interactive websites (Paper2Web), presentation v…

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alterlab-paper-reviewer Simulates a full multi-reviewer journal review PANEL — 5 personas (Editor-in-Chief + 3 peer reviewers + a Devil's Adv…

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alterlab-paper-writer Drafts and revises academic papers through a 12-agent pipeline with hardened LaTeX output (apa7 document class, justi…

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alterlab-parallel-web Search the web, run deep research, and extract content from known URLs via the Parallel Web Systems Chat API (OpenAI-…

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alterlab-pdb Access the RCSB Protein Data Bank (PDB) for EXPERIMENTALLY determined 3D structures (X-ray, cryo-EM, NMR) of proteins…

alterlab-ieu/alterlab-academic-skills

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8

alterlab-pennylane Trains and differentiates quantum circuits with PennyLane, a hardware-agnostic quantum machine-learning framework wit…

alterlab-ieu/alterlab-academic-skills

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alterlab-perplexity Run AI web searches with real-time, citation-grounded answers using Perplexity Sonar models (sonar, sonar-pro, sonar-…

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alterlab-polars Fast in-memory DataFrame analytics with Polars — lazy evaluation, parallel execution, and an Apache Arrow backend for…

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alterlab-primekg Queries the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biomedical relationships across genes, drugs,…

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alterlab-protocolsio Manages scientific protocols through the protocols.io API v3 — search, create, update, and publish protocols (with DO…

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alterlab-pubchem Query PubChem via the PUG-REST API and PubChemPy across 110M+ compounds, searching by name, CID, or SMILES and retrie…

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alterlab-pufferlib Scales reinforcement learning with PufferLib — high-throughput parallel training (PuffeRL), vectorized environments, …

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alterlab-pydicom Reads, writes, and manipulates DICOM (Digital Imaging and Communications in Medicine) medical imaging files with the …

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alterlab-pyhealth Develops, tests, and deploys clinical machine learning models with the PyHealth healthcare AI toolkit. Use when worki…

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alterlab-pylabrobot Programs lab automation with PyLabRobot, a vendor-agnostic Python framework that unifies control across Hamilton, Tec…

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alterlab-pymoo Multi-objective optimization with pymoo — NSGA-II, NSGA-III, MOEA/D, Pareto-front computation, constraint handling, a…

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alterlab-pytdc Loads Therapeutics Data Commons (TDC, PyTDC) AI-ready drug-discovery datasets and benchmarks — ADME, toxicity, drug-t…

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alterlab-pytorch-lightning Scalable deep-learning training with PyTorch Lightning — organize PyTorch code into LightningModules, configure Train…

alterlab-ieu/alterlab-academic-skills

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21

alterlab-pyzotero Interact with Zotero reference management libraries using the pyzotero Python client — retrieve, create, update, and …

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alterlab-qiskit Builds, transpiles, and runs quantum circuits with Qiskit, IBM's quantum computing framework, including Qiskit Runtim…

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alterlab-rdkit Provides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsing, des…

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alterlab-reactome Query the Reactome REST API for pathway analysis, over-representation/enrichment, gene-to-pathway mapping, disease pa…

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25

alterlab-rowan Drives the Rowan cloud quantum-chemistry platform via its Python API for computational chemistry — pKa prediction, ge…

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alterlab-scientific-slides Builds slide decks for research talks in PowerPoint and LaTeX Beamer, providing slide structure, design templates, ti…

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alterlab-scientific-thinking Evaluate scientific claims and evidence quality using evidence grading frameworks (GRADE, Cochrane Risk of Bias), ass…

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alterlab-scikit-learn Classical machine learning in Python with scikit-learn — algorithms, preprocessing, pipelines, and best-practice refe…

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alterlab-simpy Process-based discrete-event simulation in Python with SimPy — processes, queues, shared resources, and time-based ev…

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alterlab-link-health Audits and repairs Markdown link health across a skills repo via a four-tier pipeline (config hardening, intra-repo f…

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alterlab-qiime2-amplicon Runs 16S/ITS amplicon (microbiome) analysis with the QIIME 2 amplicon distribution (2026.1; renamed to "qiime2" in 20…

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alterlab-citation-graph Free, key-less ResearchRabbit analog — builds a citation and co-citation graph around one or more seed papers using t…

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alterlab-blast Runs NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parse_seqids), blastn/blastp/blas…

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alterlab-citation-verifier Verifies that every entry in a bibliography ACTUALLY EXISTS by cross-checking it against four keyless public scholarl…

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alterlab-pdf-extract Free Elicit-columns analog — ingest N PDFs (or any MarkItDown-supported document) and build a per-paper evidence tabl…

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alterlab-squidpy-spatial Analyzes spatial transcriptomics with squidpy (1.8.x) on AnnData and SpatialData objects, routing platforms correctly…

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alterlab-recommendation-letters Drafts evidence-anchored academic reference and recommendation letters across types — graduate admission, faculty hir…

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alterlab-rnaseq-quant Quantifies bulk RNA-seq transcript abundance with salmon (v1.11.4 selective alignment) and kallisto (v0.52.0, kb-pyth…

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alterlab-syllabus-ai-policy Drafts course-level generative-AI use policies and syllabus statements: assigns each graded task a permitted/restrict…

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alterlab-tubitak-proposal Scaffolds TÜBİTAK ARDEB national research proposals (1001 Bilimsel ve Teknolojik Araştırma Projeleri and 1002-A Hızlı…

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alterlab-dergipark Harvests article metadata, abstracts, and full-text PDFs from DergiPark (TÜBİTAK ULAKBİM's national journal-hosting p…

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alterlab-nf-core-sarek Runs FASTQ-to-VCF germline and somatic variant calling via the Nextflow nf-core/sarek pipeline pinned to -r 3.8.1 — b…

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alterlab-results-transparency Enforces results-reporting transparency as a discipline gate built on the Iron Law "NO RESULTS CLAIM WITHOUT REPORTIN…

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alterlab-skill-name <Verb-led statement of what the skill does, naming the real tools/libraries/databases/methods>. Use when <concrete tr…

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alterlab-test-selection-guard Enforces statistical-test selection as a discipline, holding the Iron Law NO TEST CHOSEN AFTER SEEING THE P-VALUE: ro…

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alterlab-accreditation-aol Scaffolds program-level Assurance-of-Learning (AoL) documentation for AACSB (2020 Standard 5) and ABET (Criterion 3 S…

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alterlab-grant-reporting Drafts post-award grant deliverables across funder formats — NIH RPPR (Annual/Interim/Final via eRA Commons), NSF ann…

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alterlab-preregistration-discipline Enforces pre-registration discipline with the Iron Law NO DATA ANALYSIS WITHOUT A PRE-REGISTERED ANALYSIS PLAN FIRST,…

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alterlab-tr-academic-style Formats manuscripts for Turkish journals: TR Dizin submission rules (TR Dizin mandates a set abstract word limit, two…

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alterlab-workflow-orchestration Composes existing AlterLab skills into multi-agent agentic workflows using current Claude Code subagent and Claude Ag…

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