SIMD optimization patterns and learnings for x86_64 and ARM. Use when implementing SIMD code, optimizing vectorized operations, or debugging SIMD issues. Triggers on terms like "SIMD", "AVX", "SSE", "NEON", "vectorization", "intrinsics".
Research best practices via MCP Ref/Context7 and create documentation (guide/manual/ADR). Single research, multiple output types.
Run bioinformatics analyses using Lobster AI - single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and visualization. Use when analyzing genomics data, searching for papers/datasets, or working with H5AD, CSV, GEO/SRA accessions, or biological data. Requires lobster-ai package installed.
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
Comprehensive patient stratification for precision medicine by integrating genomic, clinical, and therapeutic data. Given a disease/condition, genomic data (germline variants, somatic mutations, expression), and optional clinical parameters, performs multi-phase analysis across 9 phases covering disease disambiguation, genetic risk assessment, disease-specific molecular stratification, pharmacogenomic profiling, comorbidity/DDI risk, pathway analysis, clinical evidence and guideline mapping, clinical trial matching, and integrated outcome prediction. Generates a quantitative Precision Medicine Risk Score (0-100) with risk tier assignment (Low/Intermediate/High/Very High), treatment algorithm (1st/2nd/3rd line), pharmacogenomic guidance, clinical trial matches, and monitoring plan. Use when clinicians ask about patient risk stratification, treatment selection, prognosis prediction, or personalized therapeutic strategy across cancer, metabolic, cardiovascular, neurological, or rare diseases.
Pre-built research workflow templates that execute complete multi-step analyses from a single user prompt. Triggers on gene analysis, target validation, literature review, differential expression, clinical queries, researcher profiling, drug repurposing, or molecular dynamics simulation. Use when the user's query matches a Recipe pattern defined in SCIENCE.md.
Synthesize information across multiple sources into a structured document. Processes sources in batches across sessions to handle more data than fits in context. Discovers and queues related sources automatically. Use for research synthesis, topic deep-dives, or consolidating scattered notes. Triggers on "synthesize", "synthesis", "research [topic]".
Develop causal diagrams (DAGs) from social-science research questions and literature, then render publication-ready figures using Mermaid, R, or Python.
Computational text analysis for sociology research using R or Python. Guides you through topic models, sentiment analysis, classification, and embeddings with systematic validation. Supports both traditional (LDA, STM) and neural (BERT, BERTopic) methods.
Remotion animation patterns — spring physics, interpolate, Easing curves, timing, stagger, enter/exit, and complex motion sequences
Cross-reference lab results from sundhed.dk against current PubMed and medRxiv research on optimal ranges. Generates a report comparing your values to the latest evidence-based guidelines, meta-analyses, and preprints.
Copilot for scientific paper review. Use when reviewing a research paper (PDF/LaTeX), guiding section-by-section analysis, logging issues, and generating structured review responses.
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.
Search 78 public scientific, biomedical, materials science, and economic databases via their REST APIs and return structured JSON results. Covers physics/astronomy (NASA, NIST, SDSS, SIMBAD, Exoplanet Archive), earth/environment (USGS, NOAA, EPA, OpenWeatherMap), chemistry/drugs (PubChem, ChEMBL, DrugBank, FDA, KEGG, DailyMed, ZINC, BindingDB), materials science (Materials Project, COD), biology/genomics (Reactome, BRENDA, UniProt, STRING, Ensembl, NCBI Gene, GEO, GTEx, PDB, AlphaFold, InterPro, ChEBI, BioGRID, Gene Ontology, QuickGO, NCBI Protein/Taxonomy, dbSNP, SRA, ENA, gnomAD, UCSC Genome, ENCODE, JASPAR, MouseMine, PRIDE, LINCS L1000, Human Protein Atlas, Human Cell Atlas, RummaGEO, Metabolomics Workbench, EMDB, Addgene), disease/clinical (COSMIC, Open Targets, ClinPGx, ClinicalTrials.gov, OMIM, ClinVar, GDC/TCGA, cBioPortal, DisGeNET, GWAS Catalog, Monarch, HPO), regulatory (FDA, USPTO, SEC EDGAR), economics/finance (FRED, BEA, BLS, Federal Reserve, World Bank, ECB, US Treasury, Alpha Vantage, Data Com
Epistemological tracking system for managing facts, conclusions, and provenance chains with Git integrity and semantic search. Integrates with Quarto for visual provenance analysis. Use when analyzing data from multiple sources, conducting research, working with metrics/surveys, making data-driven conclusions, or tracking complex findings. Triggers on data analysis (analyze data, metrics, survey, research, findings, insights), conclusions (conclude, recommend, decide, infer), quantitative work (percentage, trend, correlation, statistic), source attribution (according to, based on, from source), or any epistemological tracking. Skip for trivial calculations.
Senior Bioprocess and mRNA Manufacturing Engineer specializing in Moderna's platform technology, LNP formulation, IVT processes, and GMP manufacturing. Use when: mRNA-manufacturing, LNP-formulation, process-development, GMP-production, bioprocess-engineering.
