Results for “c-suite”

Winston - versatile logging library for Node.js with multiple transports, custom formatting, and log rotation. Supports structured logging, custom levels, and enterprise integration. USE WHEN: user mentions "winston", "node.js logging", "multiple transports", "log rotation", asks about "how to log to multiple destinations", "rotate log files in Node.js", "custom log formats" DO NOT USE FOR: Pino logging - use `pino` instead, Python logging - use `python-logging` instead, Java logging - use `slf4j` or `logback` instead

Java logging with SLF4J facade, Logback, and Log4j2 implementations. Covers configuration, log levels, structured logging, async logging, and production best practices for Spring Boot applications. USE WHEN: user mentions "java logging", "spring boot logging", "slf4j setup", asks about "how to log in java", "logback vs log4j2", "java logging best practices" DO NOT USE FOR: Node.js logging - use `nodejs-logging` instead, Python logging - use `python-logging`, Kotlin-specific logging - similar but has nuances

Node.js logging with Winston, Pino, and built-in console. Covers structured logging, log levels, transports, async logging, and production best practices for Express/NestJS applications. USE WHEN: user mentions "node.js logging", "express logging", "nestjs logging", asks about "how to log in node", "winston vs pino", "node logging best practices" DO NOT USE FOR: Python logging - use `python-logging` instead, Java logging - use `slf4j` or `logback`, Browser logging - different environment and APIs

Python logging with the standard library logging module and structlog. Covers log levels, handlers, formatters, structured logging, and production best practices for FastAPI/Django applications. USE WHEN: user mentions "python logging", "fastapi logging", "django logging", asks about "how to log in python", "python logging module", "logging configuration python" DO NOT USE FOR: Node.js logging - use `nodejs-logging` instead, Java logging - use `slf4j` or `logback`, structlog-specific - use `structlog` skill for deep dive

Prisma ORM for Node.js/TypeScript. Covers schema definition, migrations, and type-safe queries. Use when working with Prisma. USE WHEN: user mentions "prisma", "schema.prisma", "prisma migrate", "prisma generate", "prisma studio", "@prisma/client", asks about "how to define models in prisma", "prisma relations", "prisma transactions", "type-safe database queries" DO NOT USE FOR: raw SQL queries - use `database-query` MCP; Drizzle ORM - use `drizzle` skill; TypeORM - use `typeorm` skill; SQLAlchemy - use `sqlalchemy` skill

Drizzle ORM for TypeScript. Covers schema definition, queries, and migrations. Use for type-safe SQL with minimal overhead. USE WHEN: user mentions "drizzle", "drizzle-orm", "drizzle-kit", "pgTable", "mysqlTable", asks about "lightweight orm", "sql-like orm", "drizzle schema", "drizzle migrations", "drizzle studio", "type-safe sql builder" DO NOT USE FOR: Prisma projects - use `prisma` skill; TypeORM - use `typeorm` skill; raw SQL - use `database-query` MCP; SQLAlchemy - use `sqlalchemy` skill; NoSQL databases - use `mongodb` skill

Apache Pulsar cloud-native messaging and streaming. Covers topics, subscriptions, Pulsar Functions, and geo-replication. Use for multi-tenant, geo-distributed messaging systems. USE WHEN: user mentions "pulsar", "bookkeeper", "multi-tenancy", "geo-replication", "pulsar functions", asks about "cloud-native streaming", "tenant isolation", "global messaging" DO NOT USE FOR: simple queues - use `rabbitmq` or `sqs`; AWS-native - use `sqs`; Azure-native - use `azure-service-bus`; GCP-native - use `google-pubsub`; lightweight - use `nats`; JMS - use `activemq`

SLF4J - Simple Logging Facade for Java. Standard logging API that abstracts underlying implementation (Logback, Log4j2). Provides parameterized logging and MDC support. USE WHEN: user mentions "slf4j", "java logging api", "parameterized logging", asks about "how to log in Java", "logger facade", "MDC in java", "logging best practices java" DO NOT USE FOR: Logback configuration - use `logback` instead, Log4j2 configuration - use Log4j2 skill, Node.js logging - use `winston` or `pino` instead, Python logging - use `python-logging` instead

Scales reinforcement learning with PufferLib — high-throughput parallel training (PuffeRL), vectorized environments, and native multi-agent systems achieving 2-10x speedups over standard implementations. Use when scaling RL to millions of steps per second, running vectorized or multi-agent setups, building custom PufferEnv tasks, or integrating game environments (Atari, Procgen, NetHack, PettingZoo). For standard single-agent algorithm implementations (PPO/SAC/DQN) or quick prototyping prefer alterlab-stable-baselines3. Part of the AlterLab Academic Skills suite.

tRPC for type-safe APIs. Covers routers, procedures, and React Query integration. Use for end-to-end type-safe APIs. USE WHEN: user mentions "tRPC", "type-safe API", "end-to-end types", "procedures", "tRPC router", "tRPC React Query", asks about "how to build type-safe API", "tRPC with Next.js", "tRPC middleware", "tRPC context" DO NOT USE FOR: REST APIs - use `rest-api` instead; GraphQL - use `graphql` instead; OpenAPI specs - use `openapi` instead; Non-TypeScript projects

Designs courses and teaching materials using backward design (Wiggins & McTighe), constructive alignment (Biggs), and Bloom's taxonomy alignment, generating rubrics, formative and summative assessments, syllabi, lesson plans, inclusive-pedagogy guidance, and online/hybrid course architecture. Use when the request mentions course design, syllabus, learning outcomes, rubric, assessment design, lesson plan, backward design, constructive alignment, Bloom's taxonomy, curriculum mapping, course redesign, inclusive pedagogy, hybrid course, or online course design. Part of the AlterLab Academic Skills suite.

Agent-driven RAG patterns. Self-RAG, Corrective RAG (CRAG) with web fallback, Adaptive RAG with routing classifier, ReAct with retrieval tool, multi-hop retrieval, plan-and-execute, LangGraph state machines for RAG. USE WHEN: user mentions "agentic RAG", "Self-RAG", "Corrective RAG", "CRAG", "Adaptive RAG", "multi-hop retrieval", "LangGraph RAG", "ReAct RAG", "plan and execute RAG" DO NOT USE FOR: static retrieval pipelines - use `rag-architecture`; query rewriting only - use `query-transformations`; evaluation - use `rag-evaluation`

Logback - flexible and powerful logging framework for Java and Spring Boot applications. Successor to Log4j with native SLF4J support, async logging, and automatic file rotation. USE WHEN: user mentions "logback", "spring boot logging", "java logging configuration", asks about "logback-spring.xml", "rolling file appender", "async logging in java" DO NOT USE FOR: SLF4J API usage - use `slf4j` instead, Log4j2 - use separate Log4j2 skill, Node.js logging - use `winston` or `pino` instead, Python logging - use `python-logging` instead

Access the COSMIC catalogue of somatic mutations in cancer to query somatic mutations, the Cancer Gene Census, mutational signatures, and gene fusions (authentication required). Use when curating known cancer driver genes, looking up recurrent somatic mutations in a gene, or interpreting mutational signatures for cancer research and precision oncology. Not for germline pathogenicity calls (use alterlab-clinvar) or interactive cohort visualization like OncoPrints and survival from study data (use alterlab-cbioportal). Part of the AlterLab Academic Skills suite.

Query ChEMBL via the chembl_webresource_client Python client for curated bioactive molecules and drug-like compound libraries at scale — search compounds by structure or physicochemical properties, retrieve bioactivity measurements (IC50, Ki, EC50), and find inhibitors of a target. Use when screening chemical libraries, mining curated bioactivity for a protein, running SAR studies, or sourcing medicinal-chemistry data; for measured protein-ligand binding affinities (Ki/Kd/IC50) prefer alterlab-bindingdb instead. Part of the AlterLab Academic Skills suite.

Query BindingDB for measured protein-ligand binding affinities (Ki, Kd, IC50, EC50) via its keyless REST API or the full TSV download, searching by target (UniProt ID), compound (SMILES), or pathogen. Use when looking up experimental binding constants, profiling inhibitors of a protein target, doing lead optimization, polypharmacology analysis, or structure-activity relationship (SAR) studies; for curated bioactivity mining or drug-like compound library screening at scale prefer alterlab-chembl instead. Part of the AlterLab Academic Skills suite.

Modern C++ (C++17/20/23) language and standard library. Covers RAII, move semantics, smart pointers, templates, concepts, ranges, coroutines, modules, std::expected, std::format, std::span, std::string_view. USE WHEN: user mentions "C++", "modern C++", "C++17/20/23", "RAII", "smart pointers", "templates", "concepts", "ranges", "move semantics", "std::expected", "std::span", "coroutines", "modules", "STL" DO NOT USE FOR: C (use a C-specific skill), C# (use `csharp`), Objective-C++, Carbon, kernel/no-exception subset (use `cpp-systems`)

Orchestrator for the learn-from suite - auto-detects source type (academic paper, GitHub repo, blog/web article, or in-conversation learnings) and routes to the correct sub-skill for credibility check, security scan, insight extraction, and application. Load when the user says "learn from", "learn from this", "extract insights from", "apply learnings from", "what can we learn from", or provides a URL, file path, or pasted content that should be ingested as knowledge. Single entry point for all learning workflows.

Provides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure/SMARTS search, 2D/3D coordinate generation, similarity, and reaction handling. Use when custom sanitization, specialized fingerprint or descriptor algorithms, reaction enumeration, or conformer generation demand direct API control; for a high-level pandas-friendly wrapper over RDKit prefer alterlab-datamol, and for turning molecules into ML feature vectors prefer alterlab-molfeat. Part of the AlterLab Academic Skills suite.

Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use when creating or wrangling .h5ad/zarr files, managing cell and gene annotations, concatenating batches, or handling layers/obsm/backed-mode; for the QC, normalization, clustering, UMAP, and differential-expression analysis pipeline prefer alterlab-scanpy instead, and for RNA velocity from spliced/unspliced layers prefer alterlab-scvelo instead. Part of the AlterLab Academic Skills suite.

Query the EMBL-EBI InterPro REST API for protein family, domain, and functional-site annotations integrated from member databases (Pfam, PANTHER, PRINTS, SMART, SUPERFAMILY, CDD, ProSite, NCBIfam, and others). Use when predicting protein function, analyzing or comparing domain architecture, classifying a protein by family or homologous superfamily, resolving a Pfam/InterPro accession, or mapping a protein's signatures to GO terms. Not for raw UniProt entry/FASTA retrieval or AlphaFold 3D structures. Part of the AlterLab Academic Skills suite.

Bun JavaScript runtime. Fast all-in-one toolkit with bundler, test runner, package manager. Use when working with Bun projects or considering Node.js alternatives. USE WHEN: user mentions "bun", "bun test", "bun build", asks about "Bun.serve", "bun install", "SQLite in Bun", "bunx", "performance comparison" DO NOT USE FOR: Node.js runtime - use `nodejs` skill instead DO NOT USE FOR: Hono/Elysia frameworks - use framework-specific skills DO NOT USE FOR: Language syntax - use `typescript` or `javascript` skills

Access ClinPGx pharmacogenomics data (the successor to PharmGKB) to query gene-drug interactions, CPIC/DPWG dosing guidelines, drug labels, and pharmacogene records. Use when interpreting pharmacogenes (CYP2D6, CYP2C19, TPMT, DPYD, SLCO1B1), looking up genotype-guided drug dosing, checking PGx drug-safety associations (e.g. HLA-B*57:01 and abacavir), or supporting precision medicine and clinical pharmacogenomics decisions. For star-allele definitions/frequencies see PharmVar; for germline/somatic variant pathogenicity see alterlab-clinvar. Part of the AlterLab Academic Skills 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.

Apache Kafka event streaming platform. Covers producers, consumers, topics, partitions, Kafka Streams, and Connect. Use for high-throughput event-driven architectures and real-time data pipelines. USE WHEN: user mentions "kafka", "event streaming", "kafka streams", "consumer groups", "topic partitions", asks about "high throughput messaging", "event sourcing", "log aggregation", "real-time pipelines" DO NOT USE FOR: simple queues - use `rabbitmq` or `activemq`; cloud-native lightweight - use `nats`; AWS-native - use `sqs`; Azure-native - use `azure-service-bus`; GCP-native - use `google-pubsub`

Amazon SQS managed message queue service. Covers standard and FIFO queues, dead-letter queues, and integration patterns. Use for AWS-native serverless and microservices architectures. USE WHEN: user mentions "sqs", "aws queues", "fifo queue", "lambda trigger", "sns to sqs", asks about "aws messaging", "serverless queues", "standard queue", "visibility timeout" DO NOT USE FOR: event streaming - use `kafka` or AWS Kinesis; Azure-native - use `azure-service-bus`; GCP-native - use `google-pubsub`; on-premise - use `rabbitmq` or `activemq`; complex routing - use `rabbitmq`

Caching strategies across the RAG stack. Semantic caching with GPTCache and LangChain, Redis-based embedding-similarity cache, cache key design, TTL/invalidation, partial caching (cache retrieval only), provider-native prompt caching (Anthropic, OpenAI), and hierarchical L1/L2 caches. USE WHEN: user mentions "semantic cache", "GPTCache", "LLM cache", "prompt caching", "Redis vector cache", "cache invalidation for RAG", "reduce LLM cost", "latency reduction LLM" DO NOT USE FOR: retrieval accuracy - use `rag-patterns`; groundedness checks - use `rag-guardrails`; incremental indexing - use `rag-production`

Runs high-performance genomic interval analysis with gtars (databio), a Rust toolkit with Python bindings — the performance-critical backend for the geniml ML library. Use when computing overlaps/jaccard/coverage between BED region sets, indexing intervals with IGD, generating uniwig accumulation/coverage tracks, tokenizing genomic regions for ML, splitting single-cell fragments into pseudobulks, or computing GA4GH refget sequence digests. NOT for training region embeddings (use alterlab-geniml) or non-genomic spatial joins (use alterlab-geopandas). Part of the AlterLab Academic Skills suite.

Knowledge-graph-augmented retrieval. Entity and triple extraction, graph construction (Neo4j, LlamaIndex PropertyGraphIndex), hierarchical community summarization (Microsoft GraphRAG), personalized PageRank (HippoRAG), multi-hop traversal retrieval, and hybrid graph + vector pipelines. USE WHEN: user mentions "GraphRAG", "HippoRAG", "knowledge graph RAG", "entity extraction", "multi-hop reasoning", "Neo4j RAG", "LlamaIndex property graph", "LangChain graph retriever", "triple extraction", "community summarization" DO NOT USE FOR: vanilla vector RAG - use `rag-patterns`; multimodal inputs - use `multimodal-rag`; production indexing ops - use `rag-production`; hallucination checks - use `rag-guardrails`

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.

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.

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

Run RNA velocity analysis with scVelo on single-cell RNA-seq data — estimate cell-state transitions from spliced/unspliced mRNA dynamics, infer trajectory direction, compute latent time, and identify driver genes. Use when adding directionality to trajectories or studying differentiation dynamics from spliced/unspliced layers (velocyto/STARsolo output); for the general QC, clustering, UMAP, and differential-expression analysis pipeline prefer alterlab-scanpy instead, and for .h5ad data-structure I/O and layer wrangling prefer alterlab-anndata instead. Part of the AlterLab Academic Skills suite.

Kernel-Mode Driver Framework (KMDF), the Microsoft-recommended way to write Windows kernel-mode drivers. Covers DriverEntry, EvtDeviceAdd, IRPs and IOCTLs, I/O queues, PnP and Power state machines, IRQL discipline, memory pools, WPP tracing, SAL annotations, and Driver Verifier. USE WHEN: user mentions "KMDF", "WDF kernel", "Windows kernel driver", "DriverEntry", "WdfDriverCreate", "EvtDeviceAdd", "IRP", "IOCTL", "DISPATCH_LEVEL", "PASSIVE_LEVEL", "NTSTATUS", "PoolTag", "WdfRequestComplete" DO NOT USE FOR: UMDF v2 (use `wdf-umdf`), classic WDM-only drivers, file-system filters (FltMgr is a separate framework)

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.

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.