Results for “g-suite”

Builds INTERACTIVE charts with the Plotly Python library (plotly.express / graph_objects) — hover tooltips, zoom/pan, animations, rangesliders, 3D rotation, and standalone HTML/web-embeddable output. Use when a chart must be interactive or web-embedded, for dashboards (incl. Dash), exploratory data analysis, or rotatable 3D plots. For static publication figures defer to alterlab-matplotlib; for static statistical charts (heatmaps, distributions) defer to alterlab-seaborn; for diagrams/schematics defer to alterlab-scientific-viz. 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.

Provide direct REST API access to KEGG (academic use only) for pathway analysis, gene-to-pathway and compound-to-pathway mapping, metabolic reactions, KEGG Orthology (KO), drug-drug interactions, and ID conversion. Use when querying KEGG pathways, mapping genes/compounds to metabolic maps, or running KEGG pathway enrichment via raw HTTP/REST; for protein-protein interaction networks prefer alterlab-string-db, for protein sequences and annotations prefer alterlab-uniprot, and for Python workflows spanning many databases prefer bioservices instead. 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.

Loads Therapeutics Data Commons (TDC, PyTDC) AI-ready drug-discovery datasets and benchmarks — ADME, toxicity, drug-target interaction (DTI), scaffold splits, and molecular oracles for therapeutic ML and pharmacological prediction. Use when fetching a standardized benchmark dataset, applying scaffold or cold-split evaluation, or sourcing labeled molecules for ADMET, toxicity, or DTI modeling. Sources data, splits, and oracles only — defer molecular featurization (ECFP/fingerprints), model training, and transformers to a molecular-ML skill (e.g. deepchem). 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.

Query the STRING API for protein-protein interactions (59M proteins, 20B interactions across 5000+ species), building interaction networks, discovering functional partners, and running GO/KEGG/Pfam enrichment on protein lists. Use when constructing a protein-protein interaction network, expanding from seed proteins to functional partners, or running PPI-based enrichment for systems biology; for curated metabolic pathway maps and reactions prefer alterlab-kegg, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.

Python language (3.10-3.14). Covers typing, async, and modern patterns. Use when writing Python applications. USE WHEN: user mentions "python", "type hints", "dataclasses", "async/await", asks about "asyncio", "context managers", "match statement", "walrus operator", "PEP 695", "type parameter", "generic" DO NOT USE FOR: FastAPI framework - use `backend-fastapi` skill instead DO NOT USE FOR: Django framework - use Django-specific skill DO NOT USE FOR: Package management - use `python-packaging` skill DO NOT USE FOR: Linting/type checking config - use `python-quality` skill

Supervises theses and dissertations end to end — structure guidance from proposal through defense, chapter-by-chapter writing support (introduction, literature review, methodology, results, discussion), supervision strategies, committee management, defense and viva voce preparation, timeline planning, feedback integration, examiner-expectation guidance, and formatting (APA 7, Chicago, university styles). Use when the request mentions thesis, dissertation, supervision, defense preparation, viva, proposal defense, thesis structure, thesis chapter, literature review chapter, methodology chapter, results chapter, discussion chapter, thesis timeline, committee, thesis formatting, or dissertation proposal. Part of the AlterLab Academic Skills suite.

Run full computational-pathology workflows with PathML — whole-slide-image (WSI) analysis across 160+ slide formats, multiplexed immunofluorescence (CODEX, Vectra, MERFISH), nucleus segmentation/classification (HoVer-Net, HACTNet), tissue- and cell-graph construction, HDF5 dataset management, and deep-learning model training on pathology data. Use when the user builds end-to-end deep-learning pathology pipelines, analyzes multiplexed or spatial-proteomics slides, or segments nuclei. For lightweight H&E slide preprocessing, tissue masking, or plain Random/Grid/Score tile extraction prefer alterlab-histolab instead. 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.

Access NCBI GEO (Gene Expression Omnibus) for gene expression and functional genomics data — search and download microarray and RNA-seq datasets by GSE, GSM, GPL, or GDS accession and retrieve SOFT, MINiML, and series matrix files. Use when locating public expression datasets, fetching processed expression matrices, downloading a study's supplementary files, or sourcing per-study transcriptomics data for differential-expression analysis. For raw FASTQ sequencing reads by SRA/ENA run accession use alterlab-ena; for reference tissue-expression baselines (median TPM across human tissues) use alterlab-gtex; for cancer cohort somatic mutations and copy-number use alterlab-cbioportal. 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.

Provide direct REST API access to UniProt (Swiss-Prot/TrEMBL) for protein sequence searches, FASTA retrieval, functional annotations (GO terms, domains), and cross-database ID mapping. Use when looking up a protein entry, fetching a protein FASTA sequence, or mapping accessions between databases over raw HTTP/REST; for EXPERIMENTAL 3D structures prefer alterlab-pdb, for AI-PREDICTED 3D structures prefer alterlab-alphafold-db, for protein-protein interaction networks prefer alterlab-string-db, and for Python workflows spanning many databases prefer bioservices instead. Part of the AlterLab Academic Skills suite.

Swift language fundamentals (5.10+ / 6.x). Covers optionals, value vs reference semantics, protocols & generics, Swift Concurrency (async/await, actors, Sendable, structured tasks), Result Builders, and Apple platform interop. USE WHEN: user mentions "Swift", "SwiftUI", "async/await Swift", "actor", "Sendable", "Codable", "Combine", "Result Builder", "Apple Keychain", "Secure Enclave", "iOS native" DO NOT USE FOR: SwiftUI screen layouts in depth - use SwiftUI-specific skill if exists DO NOT USE FOR: Compose iOS via Skia - use `frontend-frameworks/compose-multiplatform` DO NOT USE FOR: Kotlin/Native ↔ Swift bridging - use `languages/uniffi`

Security controls for RAG. Indirect prompt-injection via retrieved documents, PII detection/redaction (Microsoft Presidio, AWS Comprehend), multi-tenant isolation, ACL-aware retrieval with row-level/metadata filtering, data-leakage prevention, jailbreak hardening on retrieved context, GDPR right-to-be-forgotten in vector DBs. USE WHEN: user mentions "prompt injection RAG", "indirect prompt injection", "PII redaction", "Presidio", "ACL RAG", "row-level security", "multi-tenant RAG isolation", "GDPR vector DB", "right to be forgotten", "jailbreak", "data leakage RAG" DO NOT USE FOR: hallucination detection - use `rag-guardrails`; tenancy scaling patterns - use `rag-production`; audit tracing schema - use `rag-observability`

Assess the test suite of a codebase — where tests are missing, where they exist but are weak, and which gaps actually matter. Use this skill whenever the user asks about test coverage, test quality, "are there enough tests", "where should we add tests", testing gaps, test debt, untested code paths, flaky tests, or generally wants to know whether a codebase is well-tested. Trigger even on casual phrasings ("is this tested?", "what's the test situation?", "audit our tests"). This skill does NOT write tests — it only assesses what exists and identifies what's missing. For test generation, this is the wrong skill.

Structured data + RAG. NL2SQL hybrid patterns (text-to-SQL then execute vs embed rows), table embedding strategies (row-level, schema-level, hybrid), semantic layer integration (Cube, dbt metrics), LangChain SQLDatabaseChain, LlamaIndex PandasQueryEngine, safe SQL execution (read-only, sandboxed), schema-aware retrieval. Full PostgreSQL + pgvector hybrid code. USE WHEN: user mentions "tabular RAG", "NL2SQL", "text to SQL", "RAG on tables", "database RAG", "SQL RAG", "semantic layer", "structured data RAG" DO NOT USE FOR: unstructured doc RAG - use `rag-architecture`; metadata filtering only - use `self-querying-retriever`; KG retrieval - use `graph-rag`

Audits and repairs Markdown link health across a skills repo via a four-tier pipeline (config hardening, intra-repo file-ref fixes, external URL substitutions, residual exclusions) and enforces a Tier 3 substitution guardrail that prevents regressions of previously-passing links; designed for lychee-based GitHub Actions link checkers but generalizes to markdown-link-check and similar tools. Use when the request mentions link audit, dead links, link health, lychee, broken links, link checker, markdown link audit, link-health audit, 404 audit, check-links failing, CI link-check, or 連結健檢, 死鏈, 失效連結, 斷鏈檢查. Part of the AlterLab Academic Skills suite.

Turbine — small Kotlin testing library for kotlinx.coroutines Flows. Provides ergonomic API to test Flow emissions deterministically: awaitItem, expectMostRecentItem, awaitComplete, awaitError. Works with StateFlow, SharedFlow, Channel-backed flows, combine/map/debounce. KMP-friendly. USE WHEN: user mentions "Turbine", "app.cash.turbine", ".test {}", "awaitItem", "Flow testing", "StateFlow test", "SharedFlow test", "expectMostRecentItem", "cancelAndIgnoreRemainingEvents" DO NOT USE FOR: Mobile E2E - use `testing/maestro` DO NOT USE FOR: Compose snapshot - use `testing/compose-snapshot` DO NOT USE FOR: Generic Kotlin testing - use `testing/kotest` DO NOT USE FOR: Suspend function (non-Flow) testing - use `kotlinx-coroutines-test` directly

Apply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretrained foundation model, generating scGPT embeddings, integrating batches with a transformer, or running zero-shot single-cell inference on an h5ad. For probabilistic latent models (scVI/scANVI) prefer alterlab-scvi-tools; for the standard QC→cluster→UMAP→DE pipeline prefer alterlab-scanpy; for the AnnData data structure itself prefer alterlab-anndata; for protein language models prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

Predict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-function model outputting RNA-seq, CAGE, ATAC, and ChIP coverage across long context, used to score non-coding and regulatory variant effects. Use when predicting functional tracks from a DNA sequence, scoring a non-coding/regulatory variant's effect on expression or chromatin, or doing in-silico mutagenesis of a locus. To LOOK UP a variant's population frequency prefer alterlab-gnomad; for its clinical significance prefer alterlab-clinvar; for protein-structure effects prefer alterlab-alphafold; for single-cell foundation models prefer alterlab-scgpt. Part of the AlterLab Academic Skills suite.

Query cBioPortal via its keyless REST API for cancer genomics across TCGA, GENIE, MSK-IMPACT and hundreds of studies — somatic mutations, copy-number alterations (GISTIC), mRNA/protein expression, structural variants, and patient-level clinical/survival data. Use when asked how often a gene is mutated/amplified/deleted in a tumor type, to profile oncogenes or tumor suppressors across cancers (pan-cancer alteration frequency), to pull patient-level mutations joined to OS/clinical outcomes, or to validate a cancer target from cohort genomics. For germline variant pathogenicity use alterlab-clinvar; for mutational-signature (SBS) decomposition use alterlab-cosmic; for CRISPR/RNAi gene-dependency use alterlab-depmap; for aggregated target-disease evidence use alterlab-opentargets. Part of the AlterLab Academic Skills suite.

Operate Playwright for browser automation end to end: author and debug E2E test suites (robust locators, network interception and mocking, parallel workers, accessibility snapshot checks), wire them into CI, and drive headless browsing and scraping with an extract -> validate -> save loop. Use when writing, running, fixing, or scraping with Playwright, when a Playwright CI failure or JSON report needs triage, or when the bundled pwrun script should analyze a run. Do not use for QA strategy or test framework selection (route to qa-methodology), for frontend component or architecture design (route to frontend-engineering), or for Cloudflare/DDoS-GUARD challenge bypass (use flaresolverr).

proptest — property-based testing for Rust (Hypothesis-style). Generates thousands of random inputs to find counterexamples to invariants, with shrinking to minimal failing case. Critical for crypto, parsers, state machines, and finance code where edge cases matter. Includes strategies (gen functions), regression tracking, and integration with cargo test. Alternative: quickcheck (simpler API, less powerful). USE WHEN: user mentions "proptest", "property-based test", "proptest!", "Strategy", "Arbitrary", "shrink", "quickcheck", "regression file", "fuzz-light", "proptest-derive" DO NOT USE FOR: Generic Rust unit tests - use `testing/rust-testing` DO NOT USE FOR: Fuzzing with mutator (cargo-fuzz, AFL) - use bitcoin/testing/fuzz DO NOT USE FOR: KMP property testing - use `testing/kotest` (has built-in property)

Use when the user requests diagrams, flowcharts, architecture diagrams, ER diagrams, UML / sequence / class diagrams, SysML / MBSE diagrams (block definition, internal block, requirement, parametric), BPMN business process diagrams, swimlane / cross-functional flowcharts, network topology, cloud architecture from Terraform or Kubernetes manifests, ML/DL model figures (Transformer/CNN/LSTM), mind maps, or any visualization. Also use proactively when explaining systems with 3+ components, complex data flows, or relationships that benefit from visual representation. Best suited when the diagram needs custom styling, rich shape vocabulary, swimlanes, or exportable images (PNG/SVG/PDF/JPG). Generates .drawio XML and exports locally via the native draw.io desktop CLI.

Predict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and restraint inputs. Use when predicting an antibody–antigen complex, folding a mixed protein/ligand/nucleic-acid assembly described in one FASTA, or generating a complex with experimental restraints. For binding-affinity prediction or a ligand-focused co-fold prefer alterlab-boltz; for protein-only or protein–protein folding prefer alterlab-alphafold; to dock into a fixed receptor prefer alterlab-diffdock. Part of the AlterLab Academic Skills suite.

Expert texture artist specializing in PBR workflows, Substance suite, Quixel Mixer, and hand-painted techniques for games and film productionUse when "texture artist, PBR textures, Substance Painter, Substance Designer, Quixel Mixer, normal map, roughness map, metallic map, albedo texture, base color map, texture baking, bake normal, texel density, trim sheet, texture atlas, channel packing, material layering, wear and tear, edge wear, hand painted texture, stylized texture, UDIM workflow, height map vs normal, color ID map, material ID, texture seams, tiling texture, seamless texture, texture, pbr, substance-painter, substance-designer, quixel, megascans, normal-map, roughness, metallic, albedo, uv-mapping, baking, trim-sheet, material, hand-painted, stylized, photorealistic, game-art, 3d-art" mentioned.

Simulates a full multi-reviewer journal review PANEL — 5 personas (Editor-in-Chief + 3 peer reviewers + a Devil's Advocate) debate a manuscript and produce a consensus Editorial Decision (accept/minor/major/reject) plus a prioritized Revision Roadmap. Modes: full, re-review (verify revisions addressed prior comments), quick, methodology-focus, Socratic guided. Use for: simulate peer review, mock review panel, editorial review before submission, multiple reviewer perspectives, re-review of a revised manuscript, or 'critique my paper hard'. For a single-reviewer referee report use alterlab-peer-review; for rubric/grade scoring use alterlab-scholar-eval; to write/revise the paper use alterlab-paper-writer. Part of the AlterLab Academic Skills suite.

Orchestrator for the pre-decision business-idea lifecycle — generate ideas, model them, evaluate them, validate them with customers, and only then hand off to product-soul / brainstorming. Routes through `idea-generation`, `business-modeling`, `idea-evaluation`, and `customer-discovery`. Load when the user asks to explore business ideas, find a startup idea, evaluate a venture, validate an idea, says "what business should I start", "should I build this", "is this a good business", "I have a startup idea", "evaluate this venture", "model this business", "validate this idea", "Mom Test this", "Lean Canvas this", "Business Model Canvas", "Value Proposition Canvas", "go/no-go on this idea". Pre-decision suite — once one idea is committed, hands off to `product-soul`. Does NOT design features (use `brainstorming`) or audit built products (use `reality-check`).

Orchestrator for the experimentation skill suite — turn assumptions and product questions into rigorous, well-instrumented experiments and decision-grade readouts. Routes through backlog → spec → runbook → readout based on user need and existing artefacts. Platform-agnostic with PostHog as the primary binding. Load when the user asks to design an experiment, A/B test something, set up an experiment, run a holdout, test a hypothesis, decide what to test next, read out experiment results, analyse a test, or says "should we A/B test this", "experiment on the landing page", "is this lift real", "ship or kill this test", "what should we test next", "build an experiment backlog", "test the pricing page", "validate this with an experiment".

Operate Firebase from the terminal with `firebase-tools`: install/auth the CLI, bootstrap `firebase.json` / `.firebaserc`, run the Emulator Suite, deploy Hosting / Functions / rules / App Hosting, manage preview channels, and handle Firebase admin tasks like auth import/export, Remote Config, App Distribution, and Extensions. Use when the job is Firebase platform/project operation through the CLI. Triggers on: firebase deploy, firebase init, firebase emulators, firebase hosting, firebase functions, firebase firestore, firebase database, firebase auth import, firebase remote config, firebase app distribution, firebase extensions, firebase apphosting, firebase dataconnect, firebase cli, firebase-tools, deploy firebase, firebase preview channel, firebase login, firebase use, firebase target apply. Route backend AI workflow orchestration to `genkit` and direct in-app SDK integration to `genkit` (`client-ai-logic` mode).

Exploratory data analysis (EDA) on a scientific data file — auto-detects the format, runs structure/quality/statistics checks, and writes a markdown EDA report with downstream recommendations. Use when asked to "explore", "analyze", "summarize", "profile", or "QC" a data file, or to understand its structure/content/quality before deciding what analysis to run. Covers tabular (.csv .tsv .xlsx .parquet), arrays (.npy .npz .hdf5 .h5 .mat .fits), sequence/genomics (.fasta .fastq .sam .bam .vcf .bed .gff .gtf .h5ad), microscopy (.tif .nd2 .czi .lif .ims .dcm .nii), spectroscopy/MS (.mzML .mzXML .mgf .fid .jdx), chemistry (.pdb .cif .mol .sdf .xyz .gro), and proteomics/metabolomics (.pepXML .mzid .mzTab). For zero-shot forecasting of a series use alterlab-timesfm; to create/configure a chunked cloud array store use alterlab-zarr. Part of the AlterLab Academic Skills suite.

Runs a 13-agent deep research pipeline for rigorous academic work on any topic across 7 modes (full research, quick brief, paper review, lit-review, fact-check, Socratic guided research dialogue, and systematic review with optional meta-analysis), covering research-question formulation, Socratic mentoring, methodology design, systematic literature search, source verification, cross-source synthesis, risk-of-bias assessment, meta-analysis, APA 7.0 report compilation, editorial and devil's-advocate review, ethics review, and post-research literature monitoring. Use when the request mentions research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, guide my research, help me think through, or 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 事實查核, 引導我的研究, 幫我釐清, 幫我想想, 我不確定要研究什麼, 研究方向, 研究主題. Part of the AlterLab Academic Skills suite.

Runs NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parse_seqids), blastn/blastp/blastx/tblastn with tabular -outfmt 6/7 for parsing, correct -task choice (megablast vs blastn vs blastn-short), -taxids/-negative_taxids taxonomic scoping, and -mt_mode multithreading; plus a DIAMOND blastp --ultra-sensitive path for large protein searches. Warns that -max_target_seqs is a heuristic keep-count, not a top-N best-hits filter. Use when the user wants command-line BLAST, makeblastdb, a local BLAST database, blastn/blastp/blastx/tblastn searches, or DIAMOND protein search. For the Bio.Blast web NCBIWWW API prefer alterlab-biopython; for quick one-liner database lookups prefer alterlab-gget. Part of the AlterLab Academic Skills suite.

UniFFI by Mozilla — generates idiomatic Kotlin, Swift, Python, and Ruby bindings from a Rust crate. Covers UDL definition, proc-macro mode, async support, callback interfaces, error handling, custom types, and the Kotlin Multiplatform fork (uniffi-kotlin-multiplatform-bindings) used by BDK, Breez SDK, CDK, LWK. USE WHEN: user mentions "UniFFI", "Rust to Kotlin", "Rust to Swift", "FFI bindings", "uniffi-rs", "UDL file", "uniffi-bindgen", "BDK bindings", "Breez SDK bindings", "kotlin-multiplatform-bindings", "Mozilla UniFFI" DO NOT USE FOR: Raw C FFI - use `languages/swift` interop quick-ref + Rust core DO NOT USE FOR: WebAssembly bindings - use wasm-bindgen DO NOT USE FOR: Flutter/Rust bridge - use `flutter_rust_bridge` skill if exists DO NOT USE FOR: React Native - use `uniffi-bindgen-react-native` (out of scope here)