Results for “g-suite”

The AlterLab front door and multi-agent launcher — routes a task to the right AlterLab skill(s) when the user invokes the suite without naming one, and for a multi-stage goal (or on the keyword 'alterflow', aliases 'alterresearch' / 'ultralab') it CLARIFIES the goal with a few questions, SELECTS the skills the task needs, and runs a dynamic multi-agent workflow composing them (via alterlab-workflow-orchestration, alterlab-research-pipeline, or alterlab-ssci-orchestrator). Triggers on 'use AlterLab skills', 'which AlterLab skill for X', 'is there an AlterLab skill for…', a multi-stage research goal, 'alterflow …', or any generic AlterLab request where the user does not know skill names. It always asks clarifying questions before executing a multi-step run. Use when someone references AlterLab generically, describes a multi-stage goal, or fires the alterflow keyword; when the user already names a specific skill, defer to that skill directly. Part of the AlterLab Academic Skills suite.

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`

Queries the FRED (Federal Reserve Economic Data) API for 800,000+ economic time series from 100+ sources, covering GDP, unemployment, inflation, interest rates, exchange rates, housing, and regional data. Use for macroeconomic analysis, financial research, policy studies, economic forecasting, fetching U.S. or international economic indicators by FRED series ID, and academic research requiring historical economic time series. Part of the AlterLab Academic Skills suite.

AI-powered financial analysis suite. Generates executive CFO briefings from QuickBooks exports (P&L, Balance Sheet, General Ledger, Cash Flow, etc.) with anomaly detection, burn rate, runway analysis, and scenario modeling. Also estimates codebase development costs with organizational overhead and AI ROI analysis. Triggers on: 'CFO briefing', 'financial analysis', 'cost briefing', 'expense review', 'runway analysis', 'burn rate', 'cost estimate', 'how much would this cost to build', 'development cost', 'Claude ROI'.

Product orchestrator for Prodig Suites that guides product planning, routes work to specialists, and coordinates execution across the product lifecycle. Use when the user is shaping a digital product, deciding next steps, or needs help choosing the right Prodig specialist or workflow. Triggers: 'prodig', 'digital product', 'product idea', 'product planning', 'which product agent should I use', 'SaaS planning', 'course creation', 'template pack', 'productized service'.

Project Lombok for reducing Java boilerplate. Covers annotations for getters, setters, constructors, builders, logging, and more. Based on production patterns from castellino and gestionale-presenze projects. USE WHEN: user mentions "lombok", "@Data", "@Builder", "@Slf4j", asks about "boilerplate reduction", "getters/setters", "@RequiredArgsConstructor", "@Value" DO NOT USE FOR: Java language features - use `java` skill instead DO NOT USE FOR: MapStruct integration - use `mapstruct` skill DO NOT USE FOR: Spring annotations - use `backend-spring-boot` skill

Unity XR — XR Interaction Toolkit 3.x (Interactor/Interactable/Manipulation), AR Foundation (planes, anchors, image tracking, body tracking), OpenXR, hand tracking on Quest/Vision OS. USE WHEN: VR/AR/MR projects, integrating XR controllers, AR plane detection, XR locomotion, hand tracking, eye tracking, OpenXR features. DO NOT USE FOR: regular 3D gameplay (use `unity-physics-anim`); rendering pipeline (use `unity-rendering` — XR has URP-specific considerations).

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.

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.

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.

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`

Detect and exploit session fixation (WSTG-SESS-01, WSTG-SESS-03) and session exposure (WSTG-SESS-04) by testing whether the server issues a new session token post-authentication, whether pre-login tokens remain valid after login, and whether session IDs are transmitted over HTTP or included in GET parameters. Analyze token randomness via Burp Sequencer. Test JSESSIONID, ASP.NET Forms Auth cookies. Tools: OWASP ZAP, Burp Suite Repeater/Sequencer, JHijack.

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.

Scales pandas/NumPy workflows beyond memory with Dask distributed computing — parallel DataFrames, arrays, delayed task graphs, and cluster execution. Use when existing pandas/NumPy code must run on larger-than-RAM data or across clusters, for parallel file processing, distributed ML, or integration with existing pandas code. For out-of-core analytics on a single machine prefer vaex; for in-memory speed prefer polars. Part of the AlterLab Academic Skills suite.

Java language (17+). Covers modern features, patterns, and best practices. Use when writing Java applications, Spring Boot backends, or enterprise systems. USE WHEN: user mentions "java", "records", "sealed classes", "streams", asks about "pattern matching", "switch expressions", "Optional", "collections", "generics" DO NOT USE FOR: Spring Boot specifics - use `backend-spring-boot` skill instead DO NOT USE FOR: Lombok annotations - use `lombok` skill instead DO NOT USE FOR: MapStruct - use `mapstruct` skill instead

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

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.

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.

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.

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`

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`

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.

Orchestrator for the eval-output skill suite — evaluate LLM and agent outputs for quality, accuracy, helpfulness, and safety using structured rubrics and LLM-as-judge techniques. Load when the user says "evaluate this output", "score this response", "run an eval", "LLM as judge", "evaluate agent output", "how good is this response", "rate this answer", "eval this", or provides an LLM output that should be assessed for quality. Single entry point for all output evaluation workflows.

Drives the Rowan cloud quantum-chemistry platform via its Python API for computational chemistry — pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2), with cloud compute and no local setup. Use when running DFT or semiempirical methods, neural network potentials (AIMNet2), molecular property or protein-ligand binding predictions, or automated computational chemistry pipelines. Part of the AlterLab Academic Skills suite.

Wraps RDKit in a high-level, pandas-friendly datamol interface with sensible defaults for everyday drug discovery — SMILES/SDF loading into DataFrames, molecule standardization, descriptors, fingerprints, Butina clustering, 3D conformer generation, scaffold analysis, and parallel batch processing, returning native rdkit.Chem.Mol objects. Use when running standard cheminformatics pipelines on molecule tables with minimal boilerplate; for low-level control, custom sanitization, or specialized algorithms prefer alterlab-rdkit. Part of the AlterLab Academic Skills suite.

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

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.

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`

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.

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.

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.

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.

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.

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.

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.