All Skills

Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.

Use this skill when users ask about RAG (Retrieval-Augmented Generation), semantic search, document indexing, embeddings, vector databases, or chunking strategies. Trigger phrases include "how does rag-research work", "improve search results", "RAG optimization", "embedding model", "chunking strategy", "vector database".

'Detect codebase bloat through progressive analysis: dead code, duplication,

PDF manipulation toolkit. Extract text/tables, create PDFs, merge/split, fill forms, for programmatic document processing and analysis.

Guide for assistant-ui library - AI chat UI components. Use when asking about architecture, debugging, or understanding the codebase.

Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.

Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.

Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when working with mass spectrometry data, analyzing proteomics experiments, or processing metabolomics datasets.

Use when marking a task as complete, finishing a feature, or claiming a bug is fixed. Ensures functional resolution is verified with evidence before closing.

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Create critical MVP application briefs through ruthless scope-cutting dialogue. Use when user wants to turn business ideas and processes into applications. Ruthlessly cuts scope, challenges overengineering, and focuses on minimum viable product to test hypotheses. Creates structured MVP briefs in .ideas/[name]/app.md. Triggers include "build an app", "MVP for this", "what should the application do", or readiness to design application.

Two modes: (1) Solution Architect — proposes complete architecture from product definition, stack, and specs. (2) Decision Logger — logs individual architecture decisions. Triggers: 'propose architecture', 'log decision', 'architecture choice'.

Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted plots, for exploratory analysis and publication figures.

Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.

Write scientific manuscripts. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), abstracts, for research papers and journal submissions.

Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.

Master advanced Git workflows including rebasing, cherry-picking, bisect, worktrees, and reflog to maintain clean history and recover from any situation. Use when managing complex Git histories, collaborating on feature branches, troubleshooting repository issues, or when initializing a new repository according to our companies specific guidelines.

Statistical modeling toolkit. OLS, GLM, logistic, ARIMA, time series, hypothesis tests, diagnostics, AIC/BIC, for rigorous statistical inference and econometric analysis.

Update project documentation (ADRs, CHANGELOG, running notes) in compact Claude-friendly format

Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.

Statistical analysis toolkit. Hypothesis tests (t-test, ANOVA, chi-square), regression, correlation, Bayesian stats, power analysis, assumption checks, APA reporting, for academic research.

Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats.

Write publication-ready ML/AI papers for NeurIPS, ICML, ICLR, ACL, AAAI, COLM. Use when drafting papers from research repos, structuring arguments, verifying citations, or preparing camera-ready submissions. Includes LaTeX templates, reviewer guidelines, and citation verification workflows.

Autonomous AI agent platform for building and deploying continuous agents. Use when creating visual workflow agents, deploying persistent autonomous agents, or building complex multi-step AI automation systems.