Zaoqu-Liu
163 verified skills7,172 total stars
fda-database
Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
development44
adaptyv
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
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chembl-search
Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search.
data-ai44
arxiv-search
Search arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic search.
testing44
astropy
Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing.
development44
longevity-scholar
This skill should be used when users explicitly request academic papers, recent research, most cited research, or scholarly articles about longevity, aging, lifespan extension, or related topics. Triggers on phrases like "find papers on", "latest research about", "most cited studies on", or "academic literature about" in the context of longevity.
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bioservices
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 analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.
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polars
Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow backend. Best for 1-100GB datasets, ETL pipelines, faster pandas replacement. For larger-than-RAM data use dask or vaex.
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browser-automation
Browser automation for accessing scientific databases that lack REST APIs. Uses the browser-use Python framework (81k+ GitHub stars) to control a real browser via LLM vision. Enables data extraction from web-only databases like GEPIA2, GeneCards advanced features, COSMIC public data, and journal full-text access. Use as a fallback when curl-based API access fails or when the target database has no programmatic API. Requires pip install browser-use and a Chromium browser.
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cirq
Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.
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citation-management
Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.
development44
clinical-decision-support
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug development, clinical research, and evidence synthesis.
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clinical-reports
Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.
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clinicaltrials-database
Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.
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clinical-trials-search
Search ClinicalTrials.gov with natural language queries. Find clinical trials, enrollment, and outcomes using Valyu semantic search.
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clinpgx-database
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
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content-engine
Create platform-native content systems for X, LinkedIn, TikTok, YouTube, newsletters, and repurposed multi-platform campaigns. Use when the user wants social posts, threads, scripts, content calendars, or one source asset adapted cleanly across platforms.
testing44
cobrapy
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
data-ai44
datacommons-client
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 statistics, environmental data, or any public datasets available through Data Commons. Applicable for querying population statistics, GDP figures, unemployment rates, disease prevalence, geographic entity resolution, and exploring relationships between statistical entities.
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datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
development44
denario
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.
development44
devtu-auto-discover-apis
Automatically discover life science APIs online, create ToolUniverse tools, validate them, and prepare integration PRs. Performs gap analysis to identify missing tool categories, web searches for APIs, automated tool creation using devtu-create-tool patterns, validation with devtu-fix-tool, and git workflow management. Use when expanding ToolUniverse coverage, adding new API integrations, or systematically discovering scientific resources.
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devtu-create-tool
Create new scientific tools for ToolUniverse framework with proper structure, validation, and testing. Use when users need to add tools to ToolUniverse, implement new API integrations, create tool wrappers for scientific databases/services, expand ToolUniverse capabilities, or follow ToolUniverse contribution guidelines. Supports creating tool classes, JSON configurations, validation, error handling, and test examples.
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devtu-fix-tool
Fix failing ToolUniverse tools by diagnosing test failures, identifying root causes, implementing fixes, and validating solutions. Use when ToolUniverse tools fail tests, return errors, have schema validation issues, or when asked to debug or fix tools in the ToolUniverse framework.
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devtu-github
GitHub workflow for ToolUniverse - push code safely by moving temp files, activating pre-commit hooks, running tests, and cleaning staged files. Use when pushing to GitHub, fixing CI failures, or cleaning up before commits.
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devtu-optimize-descriptions
Optimize tool descriptions in ToolUniverse JSON configs for clarity and usability. Reviews descriptions for missing prerequisites, unexpanded abbreviations, unclear parameters, and missing usage guidance. Use when reviewing tool descriptions, improving API documentation, or when user asks to check if tools are easy to understand.
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devtu-optimize-skills
Optimize ToolUniverse skills for better report quality, evidence handling, and user experience. Apply patterns like tool verification, foundation data layers, disambiguation-first, evidence grading, quantified completeness, and report-only output. Use when reviewing skills, improving existing skills, or creating new ToolUniverse research skills.
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drugbank-database
Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.
development44
drugbank-search
Search DrugBank comprehensive drug database with natural language queries. Drug mechanisms, interactions, and safety data powered by Valyu.
data-ai44
drug-labels-search
Search FDA drug labels with natural language queries. Official drug information, indications, and safety data via Valyu.
development44
exploratory-data-analysis
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.
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export-docx
Export research project reports to Word (.docx) format with embedded figures and formatted references. Use when user says "导出 Word", "/export word", "转 docx", "生成 Word 报告", "export to Word", or wants a Word document from project results.
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figure-pipeline
Five-step figure generation pipeline inspired by PaperVizAgent (Google Research, 2026). Orchestrates Retriever → Planner → Stylist → Visualizer → Critic stages for publication-quality scientific figures. Retrieves reference figures from literature, plans layout and composition, applies journal-specific styling, generates the figure, then critiques and refines. Use when the user needs high-quality figures for papers/presentations and wants a more deliberate, reference-driven approach than direct code generation. Especially useful for multi-panel figures and complex data visualizations.
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frontend-slides
Create HTML-based presentations that run in a browser. Use ONLY when the user explicitly asks for an HTML presentation or web-based slides. For PowerPoint (.pptx) generation, use the pptx-generation skill instead.
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gene-database
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
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get-available-resources
This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.
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hmdb-database
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
data-ai44
latex-posters
Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication.
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skills/literature
# Literature Search & Review ## Overview Comprehensive academic literature search and synthesis across 15+ sources. ## Capabilities - Multi-database parallel search (PubMed, arXiv, bioRxiv, medRxiv, OpenAlex, Semantic Scholar, Crossref, DBLP, CORE, DOAJ, Europe PMC) - Web search via Agent-Reach (Exa semantic search, Jina Reader for any URL/PDF) - Social academic search (Twitter/X threads, YouTube talks, GitHub repos) - Structured literature reviews with citation networks - Knowledge gap identi
development44
literature-review
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).
development44
literature-search
Comprehensive scientific literature search across PubMed, arXiv, bioRxiv, medRxiv. Natural language queries powered by Valyu semantic search.
testing44
market-research
Conduct market research, competitive analysis, investor due diligence, and industry intelligence with source attribution and decision-oriented summaries. Use when the user wants market sizing, competitor comparisons, fund research, technology scans, or research that informs business decisions.
testing44
market-research-reports
Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scientific-schematics and generate-image, deep integration with research-lookup for data gathering, and multi-framework strategic analysis including Porter Five Forces, PESTLE, SWOT, TAM/SAM/SOM, and BCG Matrix.
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markitdown
Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.
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matlab
MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processing, differential equations, optimization, statistics, or creating scientific visualizations. Also use when the user needs help with MATLAB syntax, functions, or wants to convert between MATLAB and Python code. Scripts can be executed with MATLAB or the open-source GNU Octave interpreter.
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biomed-dispatch
Dispatch biomedical research and data analysis tasks to Claude Code with K-Dense Scientific Skills. Use this skill when the user asks to run any bioinformatics, genomics, drug discovery, clinical data analysis, proteomics, multi-omics, medical imaging, or scientific computation task. Also use for literature search (PubMed, bioRxiv), pathway analysis, protein structure prediction, or scientific writing tasks.
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feishu-rich-card
Send rich interactive cards with embedded images in Feishu group chats. Use when reporting progress, sharing analysis results, or presenting any content that benefits from mixed text+image layout in Feishu. Combines SVG UI templates (or matplotlib/PIL charts) with Feishu Card Kit API.
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svg-ui-templates
Generate professional SVG UI panels for structured information display. Use when presenting lists, task checklists, pipeline/dependency status diagrams, or rich-text report layouts as SVG images. Covers four templates - list-panel, checklist-panel, pipeline-status, richtext-layout. Style is professional, business-oriented, academic-grade with Material Design color palette.
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molfeat
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
data-ai44
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.
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offer-k-dense-web
Optional integration with K-Dense Web for end-to-end multi-agent research workflows. Use when the user asks about K-Dense or needs complex research orchestration beyond single-agent capability.
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openalex-database
Query and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for academic papers, analyzing research trends, finding works by authors or institutions, tracking citations, discovering open access publications, or conducting bibliometric analysis across 240M+ scholarly works. Use for literature searches, research output analysis, citation analysis, and academic database queries.
testing44
opentargets-database
Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
testing44
skills/patent-drafting
# Patent Drafting — Intellectual Property Protection for Research ## Overview Draft patent applications for scientific inventions, covering claims, specification, and prior art analysis. ## Patent Application Structure ### 1. Title - Descriptive but not limiting - Include key technical terms ### 2. Abstract (150 words max) - Technical problem, solution, key advantage - Independent claim in prose form ### 3. Background / Field of Invention - Technical field - Prior art and its limitations -
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patents-search
Search global patents with natural language queries. Prior art, patent landscapes, and innovation tracking via Valyu.
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pennylane
Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with PyTorch/JAX/TensorFlow. For hardware-specific optimizations use qiskit (IBM) or cirq (Google); for open quantum systems use qutip.
development44
perplexity-search
Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when conducting web searches for current information, finding recent scientific literature, getting grounded answers with source citations, or accessing information beyond the model knowledge cutoff. Provides access to multiple Perplexity models including Sonar Pro, Sonar Pro Search (advanced agentic search), and Sonar Reasoning Pro through a single OpenRouter API key.
development44
pptx-generation
Generate academic PowerPoint presentations (.pptx) using python-pptx. Use this skill for making PPT, slides, presentations, 生成PPT, 做PPT, 写PPT, 幻灯片. Provides complete helper functions and templates. Preferred over scientific-slides and frontend-slides for all PPTX generation.
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data-analysis
Load, analyze, and visualize datasets using pandas with AG Grid display
data-ai44
jupyter
Create and execute Jupyter notebooks for interactive data analysis using jupyter_execute and jupyter_notebook tools
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ml-experiment
Design and run machine learning experiments with proper evaluation using jupyter_execute, including training, benchmarking, and ablation studies
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skills/protocol-writing
# Protocol Writing — Reproducible Lab Protocols & SOPs ## Overview Write clear, reproducible experimental protocols and Standard Operating Procedures (SOPs) for any scientific discipline. ## Structure 1. **Title and Version** — Protocol name, version number, date, author 2. **Purpose** — What this protocol achieves and when to use it 3. **Safety** — Hazards, PPE requirements, waste disposal 4. **Materials** — Exact reagents (catalog numbers, lot numbers), equipment, consumables 5. **Preparatio
testing44
pubchem-database
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
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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.
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pufferlib
High-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems, or integration with game environments (Atari, Procgen, NetHack). Achieves 2-10x speedups over standard implementations. For quick prototyping or standard algorithm implementations with extensive documentation, use stable-baselines3 instead.
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pydicom
Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.
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pylabrobot
Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation. For Opentrons-only protocols with official API, opentrons-integration may be simpler.
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pymatgen
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.
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pymc-bayesian-modeling
Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.
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article-writing
Write articles, guides, blog posts, tutorials, newsletter issues, and other long-form content in a distinctive voice derived from supplied examples or brand guidance. Use when the user wants polished written content longer than a paragraph, especially when voice consistency, structure, and credibility matter.
testing44
kegg-database
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.
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humanizer-zh
去除文本中的 AI 生成痕迹。适用于编辑或审阅文本，使其听起来更自然、更像人类书写。 基于维基百科的"AI 写作特征"综合指南。检测并修复以下模式：夸大的象征意义、 宣传性语言、以 -ing 结尾的肤浅分析、模糊的归因、破折号过度使用、三段式法则、 AI 词汇、否定式排比、过多的连接性短语。
data-ai44
investor-materials
Create and update pitch decks, one-pagers, investor memos, accelerator applications, financial models, and fundraising materials. Use when the user needs investor-facing documents, projections, use-of-funds tables, milestone plans, or materials that must stay internally consistent across multiple fundraising assets.
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ena-database
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
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histolab
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 preparation, quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.
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pathml
Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler.
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labarchive-integration
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
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aeon
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.
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biorxiv-search
Search bioRxiv biology preprints with natural language queries. Semantic search powered by Valyu.
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biopython
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.
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deepchem
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.
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skills/devtu-docs-quality
--- name: devtu-docs-quality description: TOP PRIORITY skill — find and immediately fix or remove every piece of wrong, outdated, or redundant information in ToolUniverse docs. Wrong code, broken links, incorrect counts, and overlapping instructions must be fixed or removed — never left in place. Runs five phases: (D) static method scan, (C) live code execution, (A) automated validation, (B) ToolUniverse audit, (E) less-is-more simplification. Core philosophy: each concept appears exactly once;
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export-latex
Export research project findings to a LaTeX manuscript draft with figures, references, and methods. Supports Nature, Cell, Lancet, and generic article formats. Use when user says "导出 LaTeX", "/export latex", "写论文初稿", "export to LaTeX", "generate manuscript", or wants a paper draft from project results. Builds on venue-templates skill.
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skills/fair-data
# FAIR Data Principles — Findable, Accessible, Interoperable, Reusable ## Overview Guidelines for making scientific data FAIR: Findable, Accessible, Interoperable, and Reusable. ## Findable - Assign globally unique persistent identifiers (DOIs) to datasets - Rich metadata describing the dataset (title, authors, description, keywords, dates) - Metadata registered in searchable resources (DataCite, re3data, FAIRsharing) - Data indexed in domain-specific repositories ## Accessible - Data retriev
testing44
matplotlib
Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for publication-ready multi-panel figures with journal styling, use scientific-visualization.
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molecular-dynamics
Autonomous molecular dynamics simulation pipeline inspired by DynaMate (2026). Designs, executes, and analyzes complete MD workflows for protein and protein-ligand systems. Covers structure retrieval, system preparation, minimization, equilibration, production, and trajectory analysis (RMSD, RMSF, hydrogen bonds, binding free energy). Uses OpenMM as the primary engine with AmberTools for preparation. Self-correcting — detects and fixes common simulation failures. Use when users ask for MD simulations, protein stability analysis, binding free energy calculations, or "跑个分子动力学模拟". Requires OpenMM and optionally AmberTools.
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neuropixels-analysis
Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.
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nutrient-document-processing
Process, convert, OCR, extract, redact, sign, and fill documents using the Nutrient DWS API. Works with PDFs, DOCX, XLSX, PPTX, HTML, and images.
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paper-2-web
This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.
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plotly
Interactive visualization library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashboards, exploratory analysis, and presentations. For static publication figures use matplotlib or scientific-visualization.
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pptx-posters
Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based poster design with responsive layouts and easy visual integration.
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theorem-proving
Construct and verify mathematical proofs using LaTeX typesetting and computational verification via jupyter_execute
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protocolsio-integration
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.
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pyhealth
Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).
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pydeseq2
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
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pyopenms
Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.
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pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
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clinvar-database
Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
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etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
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flowio
Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
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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.
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geo-database
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
data-ai44
skills/medge-dashboard
# Local Research Dashboard Skill ## 概述 每次科研任务开始时，生成一个临时的本地 dashboard，动态展示任务关键信息和产物预览。 ## 组件 - `state.json`：数据协议，openclaw 负责写入和更新 - `dashboard.html`：本地单文件页面，轮询 state.json 并渲染 - `dashboard_serve.py`：静态文件服务器，serve 任务根目录 所有文件放在**任务独立目录**中（如 `data/<task_name>/dashboard/`）。 --- ## state.json Schema ```json { "title": "任务标题", "updated_at": "2024-01-01 12:00:00", "panels": [ { "type": "progress|text|list|code|table|image|files|step", "label": "面板标题（可折叠的标识）", "content":
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medchem
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
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modal
Run Python code in the cloud with serverless containers, GPUs, and autoscaling. Use when deploying ML models, running batch processing jobs, scheduling compute-intensive tasks, or serving APIs that require GPU acceleration or dynamic scaling.
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open-targets-search
Search Open Targets drug-disease associations with natural language queries. Target validation powered by Valyu semantic search.
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pdb-database
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
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latex-writing
Create, edit, and compile LaTeX documents for academic papers using latex_compile, update_latex, and send_ui_directive tools
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gtars
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
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alphafold-database
Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
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brenda-database
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
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ensembl-database
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
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metabolomics-workbench-database
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
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biomni
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.
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benchling-integration
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
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skills/bioinformatics
# Bioinformatics Analysis ## Overview Computational biology and genomics analysis pipelines. GENERAL: not locked to any specific tool — use Scanpy, Seurat, DESeq2, or any appropriate package. ## Common Workflows ### RNA-seq Analysis 1. Quality control (FastQC, MultiQC) 2. Alignment (STAR, HISAT2) or pseudo-alignment (Salmon, kallisto) 3. Quantification (featureCounts, Salmon quant) 4. Normalization (DESeq2 vst/rlog, edgeR TMM) 5. Differential expression (DESeq2, edgeR, limma-voom) 6. Visualiz
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cosmic-database
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
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chembl-database
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
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deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
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hypogenic
Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis). Combines literature insights with data-driven hypothesis testing. For manual hypothesis formulation use hypothesis-generation; for creative ideation use scientific-brainstorming.
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gget
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
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lamindb
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
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geniml
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.
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latchbio-integration
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
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matchms
Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.
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opentrons-integration
Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons protocols, official API compatibility. For multi-vendor automation or broader equipment control use pylabrobot.
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dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
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arboreto
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
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cellxgene-census
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.
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biomedical-search
Complete biomedical information search combining PubMed, preprints, clinical trials, and FDA drug labels. Powered by Valyu semantic search.
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esm
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.
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pytdc
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
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pubmed-search
Search PubMed biomedical literature with natural language queries powered by Valyu semantic search. Full-text access, integrate into your AI projects.
data-ai44
quant-analysis
Quantitative finance analysis including portfolio optimization, risk modeling, and time series econometrics using jupyter_execute
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peer-review
Conduct thorough academic peer reviews with structured feedback using load_pdf and arxiv_to_prompt
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paper-search
Search and discover academic papers from arXiv and web sources using arxiv_to_prompt and web search
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neurokit2
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.
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medrxiv-search
Search medRxiv medical preprints with natural language queries. Powered by Valyu semantic search.
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cjk-viz
CJK (中日韩) 字体检测与 matplotlib 配置。任何涉及中文标签、标题、图例的 可视化任务启动前必须先执行本 skill 的字体检测流程，确保不会出现方块乱码。 适用于 matplotlib / seaborn / plotly 静态导出等场景。
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manuscript-review-revise
AI-powered manuscript review and revision system inspired by APRES (ICLR 2026). Evaluates scientific manuscripts using ScholarEval 8-dimension rubric plus citation-predictive heuristics, then performs targeted revisions while preserving core scientific claims. Outputs before/after comparison with improvement metrics. Use when the user says "/review", "帮我审一下", "review my manuscript", "improve this paper", "polish this draft", or provides a manuscript for quality improvement. Also triggered by "审稿", "修改论文", "润色".
testing44
skills/materials
# Materials Science ## Overview Computational materials science, simulation, and property prediction. ## Key Tools - **VASP**: Density functional theory (DFT) calculations - **Gaussian**: Quantum chemistry - **LAMMPS**: Molecular dynamics - **Pymatgen**: Python materials genomics - **ASE**: Atomic simulation environment - **Materials Project API**: Materials property database ## Common Workflows ### DFT Property Calculation 1. Structure optimization (VASP/Gaussian) 2. Electronic structure (b
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iso-13485-certification
Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conducting gap analysis of existing documentation, (2) creating Quality Manuals, (3) developing required procedures and work instructions, (4) preparing Medical Device Files, (5) understanding ISO 13485 requirements, or (6) identifying missing documentation for medical device certification. Also use when users mention medical device regulations, QMS certification, FDA QMSR, EU MDR, or need help with quality system documentation.
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generate-image
Generate or edit images using AI models (FLUX, Gemini). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that is not a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the scientific-schematics skill instead.
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evolving-memory
Evolving memory system inspired by EvoScientist. Extends ScienceClaw's research memory with four record types (finding, ideation, strategy, pitfall) to enable learning from past research sessions. Recall relevant strategies and pitfalls before recipe execution, extract and persist new lessons after completion. Use at the start and end of every research recipe, and when the user asks to recall past experience or improve workflows.
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export-pptx
Export research project findings to a presentation (.pptx) with key findings, figures, and conclusions. Use when user says "导出 PPT", "/export pptx", "做个汇报", "生成 PPT", "export to PowerPoint", "make a presentation from results", or wants slides from project results. Builds on pptx-generation skill.
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drug-repurposing
Systematic drug repurposing analysis inspired by NovusAI. Evaluates existing drugs for new therapeutic indications through multi-dimensional evidence gathering across target networks, clinical trials (including failures), patent landscape, safety profiles, and off-label literature. Produces ranked repurposing candidates with evidence scores. Use when users ask about finding new uses for existing drugs, off-label potential, "老药新用", or "drug repurposing for X". Complements target-validation (which starts from a target) by starting from a drug.
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drug-discovery-search
End-to-end drug discovery platform combining ChEMBL compounds, DrugBank, targets, and FDA labels. Natural language powered by Valyu.
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diffdock
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
documentation44
create-tooluniverse-skill
Create high-quality ToolUniverse skills following test-driven, implementation-agnostic methodology. Integrates tools from ToolUniverse's 1,264+ tool library, creates missing tools when needed using devtu-create-tool, tests thoroughly, and produces skills with Python SDK + MCP support. Use when asked to create new ToolUniverse skills, build research workflows, or develop domain-specific analysis capabilities for biology, chemistry, or medicine.
tools44
skills/clinical
# Clinical Research ## Overview Clinical study design, statistical analysis, and regulatory compliance for medical research. ## Study Designs | Design | Level of Evidence | Best For | |--------|------------------|----------| | RCT | I | Treatment efficacy | | Cohort (prospective) | II | Risk factors, prognosis | | Cohort (retrospective) | III | Exposure-outcome associations | | Case-control | III | Rare diseases, risk factors | | Cross-sectional | IV | Prevalence, correlations | | Case report/
tools44
skills/chemistry
# Chemistry & Drug Discovery ## Overview Computational chemistry, cheminformatics, and drug discovery workflows. ## Key Tools - **RDKit**: Molecular manipulation, fingerprints, descriptors, substructure search - **PubChem**: Chemical compound database (100M+ compounds) - **ChEMBL**: Bioactivity database for drug-like molecules - **Open Babel**: Format conversion, 3D generation - **AutoDock Vina**: Molecular docking - **GROMACS/OpenMM**: Molecular dynamics simulations ## Common Workflows ###
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asta-corpus-search
Search Allen AI's Asta Scientific Corpus (225M+ papers, 12M+ full-text, 2.4B+ citations) via MCP endpoint. Provides paragraph-level semantic search across full-text publications, citation graph traversal, and author analysis. Use as a complement to PubMed/OpenAlex/Semantic Scholar for deeper literature discovery, especially when full-text search or citation network analysis is needed. Requires ASTA_API_KEY in .env (free registration at allenai.org/asta).
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anndata
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
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omero-integration
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
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gwas-database
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
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dask
Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars.
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geopandas
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.
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hypothesis-generation
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 experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.
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peer-review
Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating claims/evidence quality use scientific-critical-thinking; for quantitative scoring frameworks use scholar-evaluation.
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pymoo
Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
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skills/academic-literature-search
# Academic Literature Search — 学术文献检索与引用管理 Use this skill when the user asks to search for academic papers, retrieve literature, generate citations, format references, or any task involving PubMed, bioRxiv, arXiv, or academic reference management. Trigger keywords: "搜文献", "检索", "找论文", "参考文献", "引用", "citation", "search papers", "PubMed", "bioRxiv", "arXiv", "GB/T 7714", "PMID", "DOI", "批量引用". ## Core Principles 1. **MCP first, Python second**: PubMed operations → MCP tools (zero code). P
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biorxiv-database
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
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humanizer
Remove signs of AI-generated writing from text. Use when editing or reviewing text to make it sound more natural and human-written. Based on Wikipedia's comprehensive "Signs of AI writing" guide. Detects and fixes patterns including: inflated symbolism, promotional language, superficial -ing analyses, vague attributions, em dash overuse, rule of three, AI vocabulary words, negative parallelisms, and excessive conjunctive phrases.
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