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Agent skills
research-tools

Topic: research-tools

81 skills in this topic.

biostatistics Performs biostatistical analyses specialized for clinical and biomedical research including survival analysis, Kaplan-Meier estimation, Cox proportional hazards regression, longitudinal data modeling, and diagnostic test evaluation; trigger when users discuss clinical outcomes, survival curves, or biomedical study statistics.
beita6969/ScienceClaw 571
post-processing Extract, analyze, and visualize simulation output data. Use for field extraction, time series analysis, line profiles, statistical summaries, derived quantity computation, result comparison to references, and automated report generation from simulation results.
beita6969/ScienceClaw 571
computational-pathology-agent COPYRIGHT NOTICE
beita6969/ScienceClaw 571
brainstorming You MUST use this before any creative work - creating features, building components, adding functionality, or modifying behavior. Explores user intent, requirements and design before implementation.
beita6969/ScienceClaw 571
scientific-visualization Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick exploration use seaborn or plotly directly.
beita6969/ScienceClaw 571
pubmed-database Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
beita6969/ScienceClaw 571
nonlinear-solvers Select and configure nonlinear solvers for f(x)=0 or min F(x). Use for Newton methods, quasi-Newton (BFGS, L-BFGS), Broyden, Anderson acceleration, diagnosing convergence issues, choosing line search vs trust region, and analyzing Jacobian quality.
beita6969/ScienceClaw 571
latex-writing Write and format LaTeX documents for academic journals. Use when: user asks to write LaTeX code, format papers for specific journals (Nature/Science/IEEE/ACM), create equations, tables, or BibTeX entries. NOT for: non-LaTeX writing (use paper-writing), data analysis, or literature search.
beita6969/ScienceClaw 571
epidemiology Performs epidemiological analyses including disease modeling (SIR/SEIR), outbreak investigation, risk factor identification, incidence/prevalence estimation, and causal inference from observational data; trigger when users discuss disease spread, public health data, or population-level health patterns.
beita6969/ScienceClaw 571
wikidata-knowledge Query Wikidata for structured knowledge using SPARQL and entity search. Use when: (1) finding structured facts about entities (people, places, organizations), (2) querying relationships between entities, (3) cross-referencing external identifiers (Wikipedia, VIAF, GND, ORCID), (4) building knowledge graphs from linked data. NOT for: full-text article content (use Wikipedia API), scientific literature (use semantic-scholar), geospatial data (use OpenStreetMap).
beita6969/ScienceClaw 571
scienceclaw-discovery Identify research gaps, synthesize cross-disciplinary insights, and generate novel hypotheses. Use when: user asks about unexplored areas, cross-field connections, or new research directions. NOT for: routine literature review or data analysis.
beita6969/ScienceClaw 571
networkx 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, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.
beita6969/ScienceClaw 571
himalaya CLI to manage emails via IMAP/SMTP. Use `himalaya` to list, read, write, reply, forward, search, and organize emails from the terminal. Supports multiple accounts and message composition with MML (MIME Meta Language).
beita6969/ScienceClaw 571
energy-systems Analyzes energy systems including renewable energy resource assessment, power grid modeling, battery storage optimization, energy efficiency evaluation, and techno-economic analysis of energy technologies; trigger when users discuss solar, wind, grid integration, energy storage, or power system design.
beita6969/ScienceClaw 571
test-driven-development Use when implementing any feature or bugfix, before writing implementation code
beita6969/ScienceClaw 571
science-communication
beita6969/ScienceClaw 571
pdb-structure Query the RCSB PDB API for protein 3D structures, experimental metadata, and structure files. Use when the user needs crystal or cryo-EM structure data, PDB entries, resolution info, or structure file downloads. NOT for protein sequences/annotations (use UniProt), gene data (use NCBI), or pathway info (use KEGG).
beita6969/ScienceClaw 571
math-computation Mathematical computation including symbolic math, numerical methods, linear algebra, calculus, differential equations, optimization, and mathematical modeling. Uses Python with SymPy, NumPy, SciPy. Use when user asks to solve equations, compute integrals/derivatives, do matrix operations, solve ODEs/PDEs, optimize functions, or build mathematical models. Triggers on "solve equation", "integral", "derivative", "matrix", "eigenvalue", "differential equation", "optimization", "linear algebra", "symbolic math", "proof".
beita6969/ScienceClaw 571
fluidsim 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.
beita6969/ScienceClaw 571
data-stats-analysis Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
beita6969/ScienceClaw 571
quantum-espresso Use when working on first-principles materials calculations with Quantum ESPRESSO, especially SCF, band structures, DOS, phonons, electron-phonon coupling, Fermi surfaces, or charge-density analysis.
ZimoLiao/scholaraio 332
index Rebuild FTS5 full-text search index or FAISS semantic vector index. Use when the user wants to update or rebuild search indexes after metadata changes.
ZimoLiao/scholaraio 332
draw Generate diagrams and vector graphics. Supports Mermaid (flowcharts, sequence diagrams, ER diagrams, Gantt charts, mind maps) via mermaid-py, and custom vector graphics (shapes, text, gradients, layers) via cli-anything-inkscape. Outputs PNG/SVG/PDF to workspace/. Use when the user wants to visualize workflows, architecture, data relationships, research timelines, concept maps, or create polished figures for papers.
ZimoLiao/scholaraio 332
document Generate and inspect Office documents (DOCX, PPTX, XLSX). Generate by writing Python scripts that call python-docx, python-pptx, and openpyxl APIs directly. Inspect with `scholaraio document inspect` to verify layout, content, and catch issues (overflow, missing elements). Use when the user wants to create Word reports, PowerPoint presentations, Excel data sheets, or inspect any Office document.
ZimoLiao/scholaraio 332