Results for “c-suite”

Run the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensionality reduction (PCA, UMAP, t-SNE), Leiden/Louvain clustering, marker/differential expression, PAGA trajectories, and plotting. Use when analyzing scRNA-seq data through clustering, cell-type annotation, DE, or pseudotime workflows; for building or reading the .h5ad data structure itself (layers, obs/var, concatenation, backed mode) prefer alterlab-anndata instead, and for RNA velocity from spliced/unspliced counts prefer alterlab-scvelo instead. Part of the AlterLab Academic Skills suite.

Kotlin language fundamentals. Covers null safety, coroutines, flow, sealed classes, data classes, scope functions, and Kotlin 2.x features (K2 compiler, context parameters). Use for Kotlin/JVM, Kotlin/Native, Kotlin/JS work. USE WHEN: user mentions "Kotlin", "coroutines", "suspend", "Flow", "sealed class", "data class", "scope functions", "K2 compiler", "ksp", "Kotlin 2.x" DO NOT USE FOR: Kotlin Multiplatform setup - use `mobile/kotlin-multiplatform` DO NOT USE FOR: Compose UI - use `frontend-frameworks/compose-multiplatform` DO NOT USE FOR: Spring Boot Kotlin - use `spring-boot` framework skill

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.

Builds, simulates, and runs quantum circuits with Cirq, Google Quantum AI's framework for NISQ hardware, noise-aware low-level circuit design, and noise characterization. Use when targeting Google Quantum AI processors (Sycamore/Weber), designing noise-aware NISQ circuits, or running characterization experiments (randomized benchmarking, XEB). For IBM Quantum hardware and Qiskit Runtime prefer alterlab-qiskit; 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.

User-Mode Driver Framework v2 (UMDF). User-mode driver model that uses the same WDF object model as KMDF but runs in a host process (WUDFHost.exe) protected by the reflector. Required for some categories (Indirect Display Drivers, many sensor and camera drivers) and recommended for any driver that doesn't strictly need kernel mode. USE WHEN: user mentions "UMDF", "WUDFHost", "user-mode driver", "reflector", "IDD", "ISensor", "WDFHOST", "UMDF v2", "FX2" DO NOT USE FOR: KMDF (use `wdf-kmdf`), classic UMDF v1 (deprecated, COM-based)

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.

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.

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.

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.

Query NCBI ClinVar via the E-utilities API or FTP for the clinical significance (pathogenicity) of human germline genetic variants, searching by gene, variant, condition, or genomic position and interpreting ACMG/AMP classifications and review-status star ratings. Use when assessing whether a variant is pathogenic, likely pathogenic, VUS, likely benign, or benign, resolving conflicting interpretations, or annotating a VCF with ClinVar clinical significance. For population allele frequencies by ancestry use alterlab-gnomad; for somatic cancer mutation frequencies use alterlab-cosmic. 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.

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.

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.

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`

Query the GTEx (Genotype-Tissue Expression) portal v2 REST API for tissue-specific gene expression (median TPM across 54 human tissues), expression QTLs (eQTLs), and splicing QTLs (sQTLs). Use when checking which tissues express a gene, finding which gene a non-coding/GWAS variant regulates via eQTLs, or interpreting variant regulatory effects across tissues. NOT for curated trait-variant associations (use alterlab-gwas), population allele frequencies or variant constraint (use alterlab-gnomad), or gene/transcript structure and ID mapping (use alterlab-ensembl). 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.

Create cross-platform agent skills from workflow descriptions. Activates when users ask to create an agent, automate a repetitive workflow, create a custom skill, or need advanced agent creation. Triggers on phrases like create agent for, automate workflow, create skill for, every day I have to, daily I need to, turn process into agent, need to automate, create a cross-platform skill, validate this skill, export this skill, migrate this skill. Supports single skills, multi-agent suites, transcript processing, template-based creation, interactive configuration, cross-platform export, and spec validation.

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.

Submits and tracks protein-testing experiments on the Adaptyv Bio Foundry cloud lab (wet-lab validation), and optimizes protein sequences before submission with computational tools (NetSolP, SoluProt, SolubleMPNN, ESM). Use when designing proteins that need wet-lab validation - binding/affinity screening, expression testing, thermostability, or fluorescence assays - or when submitting experiments to the Foundry API, browsing the target catalog, tracking experiment status, retrieving results, or pre-screening sequences for solubility/expression. Triggers on "Adaptyv", "Foundry API", "cloud lab", "biolayer interferometry / BLI", "wet-lab validation". Part of the AlterLab Academic Skills suite.

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`

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

Access the RCSB Protein Data Bank (PDB) for EXPERIMENTALLY determined 3D structures (X-ray, cryo-EM, NMR) of proteins and nucleic acids — searching by text, sequence, or structure similarity and downloading coordinates in PDB/mmCIF format with metadata. Use when retrieving a structure by PDB ID, running sequence or structure similarity searches, or obtaining experimental coordinates for structural biology and drug discovery; for AI-PREDICTED structures of proteins lacking experimental data prefer alterlab-alphafold-db, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.

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`

Kotest — flexible, idiomatic Kotlin testing framework. Multiple specification styles (StringSpec, FunSpec, BehaviorSpec, DescribeSpec, FeatureSpec, FreeSpec), rich matcher library, property-based testing, data-driven tests, coroutine support, KMP-friendly. Drop-in alternative or complement to JUnit. USE WHEN: user mentions "Kotest", "io.kotest", "shouldBe", "StringSpec", "BehaviorSpec", "DescribeSpec", "kotest property testing", "Arb.list", "forAll", "kotest matchers", "kotlin tests" DO NOT USE FOR: JUnit-specific patterns - use junit skill (or framework-specific test skills) DO NOT USE FOR: Flow testing - use `testing/turbine` DO NOT USE FOR: Compose snapshot tests - use `testing/compose-snapshot` DO NOT USE FOR: Mobile E2E - use `testing/maestro`

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.

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).

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.

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.

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.

Co-fold biomolecular complexes with Boltz-2, an open AlphaFold3-style model — predict protein + ligand (SMILES/CCD), protein + nucleic-acid, and multi-chain structures in one pass, with binding-affinity prediction. Use when folding a protein together with a small-molecule ligand, predicting a holo (ligand-bound) complex or its binding affinity, or co-folding protein–DNA/RNA assemblies. For protein-only or protein–protein folding without ligands prefer alterlab-alphafold; for antibody–antigen complexes prefer alterlab-chai; to dock a ligand into a FIXED receptor structure prefer alterlab-diffdock; to look up an existing structure prefer alterlab-pdb. Part of the AlterLab Academic Skills suite.

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.

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.

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.

Maestro — declarative E2E mobile UI testing framework by mobile.dev. YAML-based flow files, single tool for Android + iOS (and Compose Multiplatform / Flutter / React Native). Built-in cloud runner, recording mode, JS scripting for complex assertions, screen state diffing, no flakiness from explicit waits. USE WHEN: user mentions "Maestro", "maestro test", "mobile E2E", "cross-platform UI test", "maestro studio", "mobile.dev cloud", ".maestro" folder, "launchApp" YAML DO NOT USE FOR: web E2E - use `testing/playwright` DO NOT USE FOR: unit tests - use `testing/kotest`, `testing/vitest`, etc. DO NOT USE FOR: instrumented Android tests - use Espresso/Compose Test DO NOT USE FOR: snapshot tests - use `testing/compose-snapshot`

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.