Results for “sui”

Nonlinear dimensionality reduction with UMAP — fast manifold learning for 2D/3D visualization, clustering preprocessing (e.g., HDBSCAN), and supervised or parametric UMAP. Use when projecting high-dimensional data to low dimensions for visualization, embedding generation, or as a preprocessing step before clustering. Part of the AlterLab Academic Skills suite.

Search the bioRxiv preprint server and retrieve paper metadata or download PDFs via its API. Use when finding life sciences preprints by keywords, authors, DOI, date ranges, or categories, or when conducting a biology literature review of not-yet-peer-reviewed work. Part of the AlterLab Academic Skills suite.

Bayesian modeling and probabilistic programming with PyMC — hierarchical models, MCMC (NUTS) sampling, variational inference, LOO/WAIC model comparison, and posterior predictive checks. Use when fitting Bayesian or hierarchical models, estimating posteriors and credible intervals, running probabilistic inference, or comparing models with LOO/WAIC. Part of the AlterLab Academic Skills suite.

Multi-objective optimization with pymoo — NSGA-II, NSGA-III, MOEA/D, Pareto-front computation, constraint handling, and standard benchmarks (ZDT, DTLZ). Use when solving multi-objective or constrained optimization problems, computing Pareto-optimal trade-offs, or tackling engineering design problems with competing objectives. Part of the AlterLab Academic Skills suite.

OS command injection occurs when user input is passed unsanitized to a system shell via dangerous APIs: Java `Runtime.exec()`, Python `os.system/subprocess`, PHP `system/shell_exec/exec/proc_open`, C `system/exec`. Detect via pipe `|`, semicolon `;`, `&&`, `||`, backtick, `$()` operators, and time-delay payloads (`sleep 5`). Tools: Commix, Burp Suite, OWASP WebGoat.

Queries the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biomedical relationships across genes, drugs, diseases, phenotypes, pathways, and biological processes. Use when exploring drug-disease or gene-disease links, building disease-centric knowledge subgraphs, or sourcing relations for drug repurposing and precision-medicine analyses. Part of the AlterLab Academic Skills suite.

xUnit.net testing framework with Fact, Theory, fixtures, DI, and mocking with Moq and NSubstitute. Covers .NET testing best practices. USE WHEN: user mentions "xUnit", ".NET testing", "Fact", "Theory", "InlineData", "Moq", "NSubstitute", "C# unit test" DO NOT USE FOR: NUnit - use `nunit`, Vitest - use `vitest`, Jest - use `jest`, Playwright - use `playwright`

Detect and exploit Cross-Site Request Forgery vulnerabilities by testing for missing or predictable CSRF tokens, absent SameSite cookie attributes, and JSON endpoints accepting text/plain Content-Type, with payloads and bypass techniques for security testing.

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 gnomAD (Genome Aggregation Database) for population allele frequencies and gene constraint scores (pLI, LOEUF) reflecting loss-of-function intolerance. Use when checking how common a variant is across populations, filtering rare-disease candidate variants, assessing variant pathogenicity, or identifying loss-of-function intolerant genes. Part of the AlterLab Academic Skills 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.

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.

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.

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.

pnpm package manager. Fast, disk-efficient with excellent monorepo support. Use when managing dependencies or setting up monorepos. USE WHEN: user mentions "pnpm", "pnpm workspace", "pnpm-workspace.yaml", asks about "pnpm commands", "pnpm install", "workspace protocol" DO NOT USE FOR: npm (use standard npm commands), yarn (use yarn commands), bun package manager

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

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.

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.

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.

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.

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.

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.

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

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.

Use when a feature's screens and flows are drafted and the design phase needs a navigable wireframe — a multi-screen greyscale Astro prototype where buttons and links actually work, suitable for the design gate and moderated user testing. In the A-Team pipeline it is conducted by ateam-design and consumes design.md's

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."

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 BRENDA enzyme database via its SOAP API to retrieve kinetic parameters (Km, kcat, Ki), reaction equations, organism data, and substrate-specific enzyme information indexed by EC number. Use when looking up enzyme kinetics, turnover numbers, or substrate specificity for biochemical research and metabolic pathway analysis. Part of the AlterLab Academic Skills suite.

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.

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.

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.

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.