All Skills

Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing topologies — applicable to social, biological, transportation, citation, and any pairwise-relationship networks. This is classical graph analytics, not deep learning — for training graph neural networks (GCN/message passing, node/edge/graph classification on Cora-style data) use alterlab-torch-geometric instead. Part of the AlterLab Academic Skills suite.

Query Google Data Commons for public statistical data aggregated from global sources, resolving geographic entities and pulling time-series statistics. Use when working with demographic data, economic indicators, health statistics, or environmental data — population counts, GDP figures, unemployment rates, disease prevalence — or when resolving places to DCIDs and exploring relationships between statistical entities. Part of the AlterLab Academic Skills suite.

Query the Open Targets Platform GraphQL API for target-disease associations, tractability and safety data, genetics/omics evidence, and known drugs. Use when identifying or prioritizing therapeutic drug targets, assessing target druggability/safety, or gathering target-disease evidence for drug discovery. Part of the AlterLab Academic Skills suite.

Simulates open quantum systems with QuTiP, the Quantum Toolbox in Python, solving Lindblad master equations (mesolve), Monte Carlo trajectories (mcsolve), and unitary dynamics (sesolve). Use when studying master-equation or Lindblad dynamics, decoherence, dissipation, quantum optics, cavity QED, or open-system time evolution. NOT for circuit-based quantum computing or hardware execution — for IBM Quantum circuits prefer alterlab-qiskit, for Google Quantum AI or NISQ circuits prefer alterlab-cirq, and for gradient-trained quantum ML prefer alterlab-pennylane. Part of the AlterLab Academic Skills suite.

Writes Markdown documents and text-based Mermaid diagrams (flowcharts, sequence, class, ER, gantt, state, and more) with full style guides, 24 diagram-type references, and 9 document templates. Use when authoring a scientific document, report, analysis, or README, or when a diagram should be expressed as version-controllable Mermaid/Markdown text rather than a rendered image. For AI-rendered publication schematics use scientific-schematics instead. Part of the AlterLab Academic Skills suite.

Builds statistical plots with the seaborn Python library and pandas DataFrame integration, on attractive matplotlib-based defaults. Use for quick exploration of distributions, relationships, and categorical comparisons — box plots, violin plots, swarm/strip plots, KDE/histograms, pair plots, joint plots, regression plots, correlation heatmaps, and faceted small multiples (relplot/displot/catplot/lmplot). For interactive/hover/zoom charts defer to alterlab-plotly; for exact journal/manuscript styling (column widths, point fonts, CMYK, vector export) defer to alterlab-scientific-viz; for low-level custom matplotlib figures defer to alterlab-matplotlib (seaborn integrates with it for fine-tuning). Part of the AlterLab Academic Skills suite.

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against ontologies (genes, cell types, diseases, tissues), tracking data lineage and computational workflows, building data lakehouses, or wiring integrations with Nextflow, Snakemake, W&B, or MLflow. Part of the AlterLab Academic Skills suite.

Verifies that every entry in a bibliography ACTUALLY EXISTS by cross-checking it against four keyless public scholarly APIs (Crossref, OpenAlex, Semantic Scholar, arXiv) with a polite mailto identifier, resolving DOI/arXiv IDs, fuzzy-matching title and authors (difflib SequenceMatcher ratio >=0.70), flagging retractions marked in Crossref (update-to) or OpenAlex (is_retracted), and emitting per-entry JSON verdicts mapped to the AlterLab citation-hallucination taxonomy (TF/PAC/IH/PH/SH). Accepts BibTeX, a DOI/arXiv ID list, or free-form references; degrades gracefully offline by emitting 'unverified' verdicts and never silently passing. Use when the request mentions verify citations, check references, fabricated or hallucinated references, fake DOI, retraction check, bibliography audit, or reference existence check. Does NOT write or draft papers — for authoring a manuscript (whose citation-check mode inserts citations) prefer alterlab-paper-writer instead. Part of the AlterLab Academic Skills suite.

Orchestrates the full academic research pipeline (research, write, integrity check, review, revise, re-review, re-revise, final integrity check, finalize), coordinating alterlab-deep-research, alterlab-paper-writer, and alterlab-paper-reviewer into a seamless 10-stage workflow with mandatory integrity verification, two-stage peer review, and reproducible quality gates. Use when the request mentions academic pipeline, research to paper, full paper workflow, paper pipeline, end-to-end paper, research-to-publication, or complete paper workflow. Part of the AlterLab Academic Skills suite.

Access the AlphaFold DB of 200M+ AI-PREDICTED protein structures — retrieve models by UniProt accession, download PDB/mmCIF files, and analyze prediction confidence metrics (pLDDT, PAE). Use when a UniProt ID needs a computationally predicted 3D structure or when no experimental structure exists, for homology modeling, protein engineering, or structure-based drug discovery; for EXPERIMENTALLY determined structures (X-ray, cryo-EM, NMR) prefer alterlab-pdb, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.

Machine learning on genomic interval data (BED files) with the geniml Python package — region embeddings (Region2Vec), joint region+metadata embeddings (BEDspace/StarSpace), single-cell ATAC-seq embeddings (scEmbed), consensus peak sets / universes (build-universe), tokenization, BEDshift randomization, and BBClient/BEDbase caching. Use when training or using region/cell embeddings, clustering scATAC-seq, building a tokenization universe from BED collections, or any ML/feature-learning task over genomic regions. NOT for plain interval arithmetic (overlap/intersect/merge counts) — that is gtars, not geniml. Part of the AlterLab Academic Skills suite.

Builds, transpiles, and runs quantum circuits with Qiskit, IBM's quantum computing framework, including Qiskit Runtime primitives (Sampler/Estimator), circuit transpilation, and error mitigation on IBM Quantum hardware. Use when targeting IBM Quantum backends, transpiling circuits, running Runtime sessions or batches, or applying resilience/error mitigation. For Google Quantum AI hardware and NISQ circuits prefer alterlab-cirq; for gradient-trained quantum ML and hybrid quantum-classical models prefer alterlab-pennylane; for open-system Lindblad/master-equation dynamics prefer alterlab-qutip. Part of the AlterLab Academic Skills suite.

Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation. Use when analyzing bulk or single-cell RNA-seq transcriptomics to map transcription-factor-to-target-gene regulatory interactions, build adjacency networks, or run the GRN-inference step of a SCENIC pipeline on large datasets. Part of the AlterLab Academic Skills suite.

Extract and preprocess tiles from whole-slide images (WSI) with histolab — OpenSlide-backed slide loading, tissue detection and masks, Random/Grid/Score tile extraction, and image/morphological filters for H&E preprocessing. Use when the user needs lightweight WSI slide preprocessing — building tile datasets for ML training, tissue segmentation, or quick tile-based inspection of histopathology slides. For end-to-end computational-pathology, deep-learning model training, nucleus segmentation, or multiplexed/spatial-proteomics (CODEX, Vectra) pipelines prefer alterlab-pathml instead. Part of the AlterLab Academic Skills suite.

Run differential gene expression analysis on bulk RNA-seq count matrices with PyDESeq2, the Python port of DESeq2 — size-factor normalization, dispersion estimation, Wald tests, FDR (Benjamini-Hochberg) correction, and volcano/MA plots. Use when identifying differentially expressed genes between conditions from raw bulk RNA-seq counts. Part of the AlterLab Academic Skills suite.

Computes mass-spectral similarity and identifies compounds for metabolomics with matchms — comparing mass spectra, scoring similarity (cosine, modified cosine), and searching spectral libraries to annotate unknowns. Use when matching MS/MS spectra, identifying metabolites, or library searching; for full LC-MS/MS proteomics pipelines use pyopenms. Part of the AlterLab Academic Skills suite.

Applies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, and molecular complexity metrics for compound prioritization and library cleanup. Use when filtering or triaging a compound library, flagging PAINS or reactive groups, or assessing drug-likeness of candidate molecules. Part of the AlterLab Academic Skills suite.

Featurizes molecules for machine learning with molfeat (100+ featurizers) — ECFP/MACCS/MAP4 fingerprints, RDKit and Mordred physicochemical descriptors, and pretrained embeddings (ChemBERTa, ChemGPT, GIN) exposed as scikit-learn transformers that convert SMILES into feature vectors. Use when turning molecules into ML-ready feature matrices for QSAR/QSPR or virtual screening, or benchmarking fingerprint against descriptor and embedding representations; for training models and MoleculeNet benchmarks on those features prefer alterlab-deepchem, and for low-level fingerprint or descriptor primitives prefer alterlab-rdkit. Part of the AlterLab Academic Skills suite.

Use DuDuClaw — a self-hosted AI-employee platform — for cross-session memory, team-shared wiki knowledge, task boards, and messaging humans over LINE/Telegram/Discord/Slack. Applies when the user mentions DuDuClaw, asks their agent to remember things durably, or wants to reach people on messaging channels from an agent.

Read and create PDF documents — extract text (and per-page text) from a PDF to JSON/markdown, and render markdown/plain text into a new PDF.

Read, create, and convert Microsoft Word (.docx) documents — extract text and tables, build reports from markdown/JSON, and export to PDF.

Use the DuDuClaw MCP tools (persistent memory, shared wiki, task board, channel messaging) when the user asks to remember something across sessions, share knowledge with their team's AI employees, manage tasks, or message someone on LINE/Telegram/Discord/Slack. Requires a running DuDuClaw gateway (`npx duduclaw onboard` to set up).

Drafts attorney-supervised, state-compliant U.S. Advance Health Care Directives that appoint health care agents, resolve the HIPAA access gap, and record clinically usable treatment preferences. Enforces state-law verification for execution formalities, statutory forms, and special limitations. Addresses adversarial risks from family disputes and institutional challenges. Use when drafting advance directives, health care proxies, living wills, health care powers of attorney, HIPAA medical authorizations, or end-of-life planning documents.

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Drafts a Proprietary Information and Inventions Agreement (PIIA) for employment or consulting relationships. Covers confidentiality, invention assignment with state-law carve-outs, DTSA immunity notice, and prior inventions disclosure. Trigger when onboarding employees/consultants, drafting IP assignment agreements, or creating confidentiality and invention assignment contracts.

Drafts an IRC §2702-compliant Qualified Personal Residence Trust agreement with safe harbor provisions under Rev. Proc. 2003-42 and Treas. Reg. §25.2702-5(c). Generates trust instrument, signature/notarization blocks, property exhibit, beneficiary schedule, and post-execution checklist. Use when drafting a QPRT for estate planning clients transferring a personal or secondary residence with a retained occupancy term to reduce gift tax valuation.

Drafts a Subordination, Non-Disturbance, and Attornment Agreement (SNDA) for commercial real estate. Extracts key terms from lease and loan documents, structures tri-party protections balancing landlord, tenant, and lender interests. Trigger when new financing or refinancing requires subordinating tenant leases to lender liens, drafting non-disturbance protections, or preparing tri-party SNDA agreements.

Drafts a Stormwater Pollution Prevention Plan (SWPPP) compliant with 40 CFR Part 122, EPA Construction General Permit (CGP), and applicable state NPDES requirements for construction projects disturbing one or more acres. Use when drafting SWPPPs, construction stormwater permits, erosion control plans, NPDES compliance documents, or BMP selection memoranda.

Drafts SEC Form D Notice of Exempt Offering for EDGAR filing under Regulation D. Captures issuer details, related persons, offering structure, exemption basis (Rule 504, 506(b), 506(c)), sales compensation, and use of proceeds. Use when filing Form D, preparing an exempt offering notice, or handling Regulation D compliance for unregistered securities.

Installs and configures the case.dev CLI for legal AI workflows including document vaults, OCR, transcription, and search. Use when the user mentions "case.dev", "casedev", needs to authenticate with case.dev, run diagnostics, set focus targets, list API routes, track jobs, or make raw API calls. Gateway skill for all case.dev skills.

Searches the web, legal databases, case law, patents, and case.dev knowledge base via the casedev CLI. Use when the user mentions "search", "legal research", "find cases", "case law", "patent search", "web search", "fetch URL", "webfetch", "legal skills", or needs to research legal topics, find similar cases, or retrieve web content.

Manages case.dev encrypted document vaults for legal workflows. Creates vaults, uploads files and directories, lists and downloads objects, and runs semantic search across vault contents. Use when the user mentions "vault", "upload documents", "document storage", "download files", "vault search", or needs to manage case files and discovery documents.

Drafts SEC Form 10-K Annual Reports under the Securities Exchange Act of 1934. Structures all four Parts with Regulation S-K compliance and GAAP financial integration. Use when drafting 10-K filings, annual reports, or public company annual SEC disclosures.

Drafts ITAR Technology Control Plans (TCPs) for managing USML defense articles and technical data under 22 CFR Parts 120-130. Covers DDTC registration, classification, access controls, deemed export prevention, secure handling, training, audits, and incident response. Use when creating or updating export control compliance plans, technology control plans, or DDTC submission documents.

Compares two document versions and produces AI-powered redline analysis with structured change summaries, risk flags, and clause-by-clause breakdowns. Use when the user mentions "redline", "compare documents", "what changed", "version comparison", "contract diff", "track changes", or needs to understand differences between document versions.

Advises on corporate law matters including entity formation, governance, finance, M&A, securities, venture capital, non-profits, and dissolution. Use when drafting governance documents, structuring transactions, selecting entity types, or navigating fiduciary duties and corporate formalities.