Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design...
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simpy
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Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing...
literature-review
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Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic...
scientific-writing
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Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using...
networkx
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Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities,...
scvi-tools
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Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration...
Document frontend data needs for backend developers. Use when frontend needs to communicate API requirements to backend, or user says 'backend requirements', 'what data do I need', 'API...
pymoo
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Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
web-asset-generator
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Generate web assets including favicons, app icons (PWA), and social media meta images (Open Graph) for Facebook, Twitter, WhatsApp, and LinkedIn. Use when users need icons, favicons, social...
statsmodels
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Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference. Best for econometrics, time...
clarify-spec
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paper-2-web
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This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference...
scientific-slides
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Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any...
histolab
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Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset...
citation-management
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Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries....
bioservices
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Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database...
esm
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Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and...
dspy-rb
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Build type-safe LLM applications with DSPy.rb - Ruby's programmatic prompt framework with signatures, modules, agents, and optimization
uniprot-database
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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+...
datacommons-client
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Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health...