Results for “c-suite”

Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs), searching by TF name, species, or class, scanning DNA sequences for binding sites, and comparing matrices. Use when doing motif analysis, regulatory genomics, transcription factor binding prediction, or interpreting regulatory/non-coding GWAS variants. Part of the AlterLab Academic Skills suite.

Build complete mass-spectrometry workflows with pyOpenMS — feature detection, peptide identification, protein quantification, and full LC-MS/MS pipelines across many MS file formats (mzML, mzXML) and algorithms. Use for comprehensive proteomics and MS data processing — for simple spectral comparison and metabolite identification use matchms. Part of the AlterLab Academic Skills suite.

Python performance profiling with cProfile, tracemalloc, and line_profiler. Use for identifying bottlenecks and memory issues. USE WHEN: user mentions "Python profiling", "cProfile", "memory profiling", asks about "Python performance", "tracemalloc", "line_profiler", "py-spy", "Python optimization", "Python memory leak" DO NOT USE FOR: Java/Node.js profiling - use respective skills instead

Query and analyze scholarly literature using the OpenAlex API across 240M+ works, retrieving papers, authors, institutions, citations, and open access status. Use when searching academic papers, tracking citations, finding works by author or institution, analyzing research trends, discovering open access publications, or running bibliometric analysis. Part of the AlterLab Academic Skills suite.

Reflected XSS occurs when user-supplied input is echoed in an HTTP response without sanitization, allowing script execution in the victim's browser. Detect via injecting `<script>alert(1)</script>`, event handlers like `onfocus`, HTML entity bypass, and encoding variants. Tools: Burp Suite, OWASP ZAP, PHP Charset Encoder (PCE), Hackvertor, XSS-Proxy, ratproxy.

Query the openFDA API for drugs, medical devices, adverse event reports, recalls, regulatory submissions (510k, PMA), and substance identification (UNII). Use when searching FDA safety data, pharmacovigilance and adverse-event signals, device clearances, drug labels, or recall records for regulatory data analysis and safety research. Part of the AlterLab Academic Skills suite.

Query the Reactome REST API for pathway analysis, over-representation/enrichment, gene-to-pathway mapping, disease pathways, molecular interactions, and expression analysis. Use when running pathway enrichment on a gene list, mapping genes to curated biological pathways, or exploring disease pathways for systems biology studies. Part of the AlterLab Academic Skills suite.

Multi-agent board meeting protocol for strategic decisions. Runs a structured 6-phase deliberation: context loading, independent C-suite contributions (isolated, no cross-pollination), critic analysis, synthesis, founder review, and decision extraction. Use when the user invokes /cs:board, calls a board meeting, or wants structured multi-perspective executive deliberation on a strategic question.

Chunked, compressed N-dimensional arrays for cloud storage with Zarr — parallel I/O, S3/GCS integration, and NumPy/Dask/Xarray compatibility. Use when storing or reading large N-D scientific arrays, streaming chunked data to/from cloud object stores, or building large-scale scientific computing pipelines. Part of the AlterLab Academic Skills suite.

Discover, profile, and evaluate MCP servers for a given domain or purpose. Use when searching for MCP servers to add to a project, comparing server capabilities, enriching the local registry cache, or evaluating whether a server suite covers a stated need. Covers cache-first discovery, remote registry scanning, deep server profiling, and gap analysis.

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.

Zod TypeScript schema validation library for runtime type checking. USE WHEN: user mentions "Zod", "schema validation", "form validation", "API validation", "type-safe validation", asks about "runtime validation", "React Hook Form validation" DO NOT USE FOR: Yup projects (use yup skill), class-validator/NestJS DTOs (use class-validator skill), PropTypes, compile-time only validation

This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.

This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.

This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.

Access the ZINC database of 230M+ commercially available (purchasable) compounds, searching by ZINC ID or SMILES, running similarity searches, and downloading 3D-ready structures. Use when assembling a compound library for virtual screening, finding purchasable analogs, or obtaining docking-ready 3D structures for drug discovery. Part of the AlterLab Academic Skills suite.

API backend test generation for Nick's stack, especially Next.js App Router APIs with Supabase-aware auth assumptions. Use when testing backend routes, generating API test suites, validating authenticated vs unauthenticated access, checking malformed inputs, or building route-by-route backend coverage for projects that use /app/api or /pages/api.

Query PubChem via the PUG-REST API and PubChemPy across 110M+ compounds, searching by name, CID, or SMILES and retrieving molecular properties, bioactivity, and similarity/substructure matches. Use when looking up a chemical compound, converting names/SMILES to CIDs, fetching physicochemical properties, or running cheminformatics structure searches. Part of the AlterLab Academic Skills suite.

WebRTC peer-to-peer communication. Signaling, ICE/STUN/TURN, media streams, data channels, screen sharing, and SFU integration (mediasoup, LiveKit). USE WHEN: user mentions "WebRTC", "video call", "peer-to-peer", "P2P", "screen sharing", "data channel", "STUN", "TURN", "mediasoup", "LiveKit" DO NOT USE FOR: server-to-client streaming - use `sse`; chat messaging - use `socket-io`

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.

Mega-composite — full greenfield feature development from idea to live. Chains research-and-decide (validate the idea + capture decision) → scope-and-execute (analysis + plan + implement) → design-build (if UI involved) → fix-the-suite (if tests need work) → merge-confidently → ship-it → knowledge-loop. The single command for "build feature X end-to-end."

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.

Expo framework for React Native. Managed and bare workflows, Expo Router, EAS Build/Submit/Update, config plugins, and Expo SDK modules. USE WHEN: user mentions "Expo", "expo-router", "EAS Build", "expo-cli", "app.json", "expo-config-plugin", "Expo Go" DO NOT USE FOR: bare React Native without Expo - use `react-native`; Flutter - use `flutter`

This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.

Query the Ensembl genome database REST API across 250+ species for gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, and Variant Effect Predictor (VEP) annotations. Use when mapping gene IDs or coordinates, fetching genomic sequence, finding orthologs across species, or predicting variant consequences for genomic research. Part of the AlterLab Academic Skills suite.

Zero-shot univariate time-series forecasting with Google's TimesFM foundation model, producing point forecasts and prediction intervals from CSV/DataFrame/array inputs, with a preflight system checker for RAM/GPU. Use to forecast any univariate series (sales, sensors, energy, vitals, weather) without training a custom model. Part of the AlterLab Academic Skills suite.

Runs time series machine learning with the aeon library — classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search via scikit-learn compatible APIs. Use when working with temporal data, sequential patterns, or time-indexed observations (univariate or multivariate) that need specialized algorithms beyond standard ML approaches. Part of the AlterLab Academic Skills suite.

MySQL relational database. Covers queries, indexes, and optimization. Use when working with MySQL databases. USE WHEN: user mentions "mysql", "mariadb", asks about "AUTO_INCREMENT", "ON DUPLICATE KEY UPDATE", "GROUP_CONCAT", "mysql specific syntax" DO NOT USE FOR: PostgreSQL - use `postgresql` instead, MongoDB - use `mongodb` instead, Oracle - use `oracle` instead, SQL Server - use `sqlserver` instead

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use when identifying cancer-specific genetic vulnerabilities, finding synthetic lethal interactions, checking whether a gene is essential in given cell lines, or validating oncology drug targets. Part of the AlterLab Academic Skills suite.

C# 12 language features including records, pattern matching, nullable reference types, LINQ, async/await, and modern language patterns. USE WHEN: user mentions "C#", "C# records", "pattern matching", "LINQ", "async/await", "nullable reference types", "C# generics", "C# language features" DO NOT USE FOR: TypeScript - use `typescript`, Java - use Java skills, F# or VB.NET specific features

Composite skill — safely refactor a module end-to-end with sequencing, parallel implementation, post-refactor cleanup, and rationale capture. Chains refactor-plan (phased plan + rollback) → three-man-team (architect/builder/reviewer in parallel) → fix-the-suite post-refactor → adr-write → docs-sync. Use for non-trivial refactors that need both careful sequencing and durable record.

This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.

Nx build system and monorepo tools. Advanced task orchestration, generators, and plugins. Use for complex enterprise monorepos with multiple technologies. USE WHEN: user mentions "Nx", "nx.json", "Nx monorepo", "Nx generators", asks about "Nx workspace", "affected commands", "module boundaries" DO NOT USE FOR: Turborepo (use turborepo skill), simple monorepos (Turborepo is simpler), single-package projects

Research Twitter/X profiles, tweets, and trends, then take approved engagement and posting follow-through actions through the AIsa relay. Use when: the user needs Twitter/X research plus likes, follows, unfollows, posting, or post-action follow-through without sharing passwords. Supports relay-based reads, OAuth-approved writes, and media-capable posting flows.

Oracle Database specific features. Covers data types, sequences, synonyms, partitioning, and Oracle-specific SQL syntax. Use for Oracle database work. USE WHEN: user mentions "oracle", "oracle database", "sequences", "synonyms", "DUAL", "SYSDATE", "NVL", "DECODE", "Oracle partitioning", "Oracle specifics" DO NOT USE FOR: PostgreSQL - use `postgresql` instead, SQL Server - use `sqlserver` instead, PL/SQL programming - use `plsql` instead

Access the Human Metabolome Database (HMDB, 220K+ metabolites), searching by name, HMDB ID, or structure to retrieve chemical properties, biomarker data, NMR/MS reference spectra, and associated pathways. Use when identifying a human metabolite, looking up its biomarker or disease associations, matching NMR/MS spectra, or running metabolomics annotation. Part of the AlterLab Academic Skills suite.