| 7.8 | skills.sh | cobrapy cobrapy enables constraint-based metabolic modeling through flux balance analysis, gene knockouts, flux sampling, and minimal media calculations. supports sbml, json, yaml model formats and provides context managers for safe temporary modifications. |
| 6.8 | skills.sh | transformers transformers covers loading and inference with hugging face pre-trained models across nlp, vision, and audio domains via pipelines, manual model loading, and fine-tuning workflows. |
| 6.2 | skills.sh | xlsx xlsx covers creation, editing, and analysis of spreadsheet files with detailed formatting and formula standards for financial models, including color-coding conventions, number formatting rules, and error prevention practices. |
| 5.8 | skills.sh | scanpy scanpy covers standard single-cell rna-seq workflows from quality control through trajectory analysis, but lacks step-by-step procedure detail and omits edge cases entirely. |
| 5.5 | skills.sh | bioservices bioservices wraps 40+ bioinformatics databases (uniprot, kegg, chembl, reactome) behind a unified python interface for cross-resource queries and identifier mapping. covers sequence retrieval, pathway analysis, and compound search. |
| 5.4 | skills.sh | market-research-reports generates 50+ page market research reports modeled on consulting firm deliverables using LaTeX, frameworks like porter's five forces and swot, and research-lookup integration for data. output contract and error handling both underspecified. |
| 5.3 | skills.sh | pyzotero pyzotero wraps the zotero api v3 for programmatic library management. covers reading, creating, updating items, collections, tags, and citation export but lacks procedural depth and error handling specifics. |
| 4.8 | skills.sh | matplotlib matplotlib covers low-level plotting with full element customization. useful for scientific visualizations, multi-panel figures, and format exports. typical choice when fine-grained control over plot appearance matters. |
| 4.3 | skills.sh | biopython biopython is a python toolkit for molecular biology tasks including sequence manipulation, file parsing, and database access. the provided skill documentation is incomplete and does not specify concrete trigger patterns, procedures, decision logic, or error handling. |
| 4.3 | skills.sh | latex-posters latex-posters provides high-level context for creating conference and academic research posters using beamerposter, tikzposter, or baposter, but lacks procedural depth and concrete workflow steps for execution. |
| 4.2 | skills.sh | polars-bio polars-bio wraps interval operations and file i/o for genomic data atop polars, claiming 6-38x speedup over bioframe. no runnable procedures provided. |
| — | skills.sh | scikit-learn Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering,… |
| — | skills.sh | matchms Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and… |
| — | skills.sh | neurokit2 Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when… |
| — | skills.sh | scientific-schematics Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.1 Pro Preview for quality review. Only… |
| — | skills.sh | 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,… |
| — | skills.sh | molecular-dynamics Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization… |
| — | skills.sh | aeon This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection,… |
| — | skills.sh | histolab Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best… |
| — | skills.sh | rdkit Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D… |
| — | skills.sh | pptx Use this skill any time a .pptx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations;… |
| — | skills.sh | citation-management Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and… |
| — | skills.sh | scikit-survival Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival… |
| — | skills.sh | optimize-for-gpu GPU-accelerate Python code using CuPy, Numba CUDA, Warp, cuDF, cuML, cuGraph, KvikIO, cuCIM, cuxfilter, cuVS, cuSpatial, and RAFT. Use whenever the user… |
| — | skills.sh | 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… |
| — | skills.sh | stable-baselines3 Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick… |
| — | skills.sh | 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… |
| — | skills.sh | markdown-mermaid-writing Comprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishes text-based… |
| — | skills.sh | shap Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions,… |
| — | skills.sh | arboreto Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk… |
| — | skills.sh | imaging-data-commons Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and… |
| — | skills.sh | pyopenms Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex… |
| — | skills.sh | zarr-python Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing… |
| — | skills.sh | modal Cloud computing platform for running Python on GPUs and serverless infrastructure. Use when deploying AI/ML models, running GPU-accelerated workloads, serving… |
| — | skills.sh | simpy Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and… |
| — | skills.sh | geopandas Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial… |
| — | skills.sh | geomaster Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains.… |
| — | skills.sh | 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… |
| — | skills.sh | generate-image Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation including photos, illustrations, artwork, visual… |
| — | skills.sh | qutip Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED.… |
| — | skills.sh | geniml This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec,… |
| — | skills.sh | cirq Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization… |
| — | skills.sh | pdf Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple… |
| — | skills.sh | usfiscaldata Query the U.S. Treasury Fiscal Data API for federal financial data including national debt, government spending, revenue, interest rates, exchange rates, and… |
| — | skills.sh | 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… |
| — | skills.sh | pennylane Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical… |
| — | skills.sh | umap-learn UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for… |
| — | skills.sh | phylogenetics Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or… |
| — | skills.sh | torch-geometric Guide for building Graph Neural Networks with PyTorch Geometric (PyG). Use this skill whenever the user asks about graph neural networks, GNNs, node… |
| — | skills.sh | matlab MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts… |
| — | skills.sh | dnanexus-integration DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline… |
| — | skills.sh | rowan Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and… |
| — | skills.sh | dhdna-profiler Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how someone thinks, understand cognitive… |
| — | skills.sh | astropy Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates,… |
| — | skills.sh | molfeat Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular… |
| — | skills.sh | diffdock Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design.… |
| — | skills.sh | scvelo RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and… |
| — | skills.sh | 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… |
| — | skills.sh | scvi-tools Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with… |
| — | skills.sh | datamol Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization,… |
| — | skills.sh | depmap Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for… |
| — | skills.sh | 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.… |
| — | skills.sh | deeptools NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq… |
| — | skills.sh | latchbio-integration Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir,… |
| — | skills.sh | tiledbvcf Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel… |
| — | skills.sh | qiskit IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization… |
| — | skills.sh | labarchive-integration Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for… |
| — | skills.sh | adaptyv How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user… |
| — | skills.sh | pytdc Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and… |
| — | skills.sh | ginkgo-cloud-lab Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation… |
| — | skills.sh | medchem Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and… |
| — | skills.sh | 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… |
| — | skills.sh | benchling-integration Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for… |
| — | skills.sh | 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… |
| — | skills.sh | consciousness-council Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill whenever the user wants diverse viewpoints,… |
| — | skills.sh | glycoengineering Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated… |
| — | skills.sh | fluidsim Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D),… |
| — | skills.sh | neuropixels-analysis Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL… |
| — | skills.sh | scikit-bio Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick… |
| — | skills.sh | etetoolkit Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for… |
| — | skills.sh | pysam Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing… |
| — | skills.sh | pylabrobot Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified… |
| — | skills.sh | iso-13485-certification Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO… |
| — | skills.sh | pymatgen Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for… |
| — | skills.sh | omero-integration Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content… |
| — | skills.sh | 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… |
| — | skills.sh | esm Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C… |
| — | skills.sh | 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… |
| — | skills.sh | 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… |
| — | skills.sh | primekg Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more. |
| — | skills.sh | gget Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for… |
| — | skills.sh | gtars High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap… |
| — | skills.sh | timesfm-forecasting Zero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) without… |
| — | skills.sh | treatment-plans Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment,… |
| — | skills.sh | pydicom Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical… |
| — | skills.sh | pufferlib High-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent… |
| — | skills.sh | clinical-reports Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3,… |
| — | skills.sh | pathml Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation,… |
| — | skills.sh | clinical-decision-support Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses… |
| — | skills.sh | sympy Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations… |
| — | skills.sh | pyhealth Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14,… |
| — | skills.sh | vaex Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame… |
| — | skills.sh | pymoo Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and… |
| — | skills.sh | torchdrug PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge… |
| — | skills.sh | what-if-oracle Run structured What-If scenario analysis with multi-branch possibility exploration. Use this skill when the user asks speculative questions like "what if...",… |
| — | skills.sh | hypogenic Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical… |
| — | skills.sh | pytorch-lightning Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines,… |
| — | skills.sh | venue-templates Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE,… |
| — | skills.sh | research-grants Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader… |
| — | skills.sh | 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,… |
| — | skills.sh | pymc Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic… |
| — | skills.sh | networkx networkx — an installable skill for AI agents, published by k-dense-ai/scientific-agent-skills. |
| — | skills.sh | infographics Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Integrates research-lookup and… |
| — | skills.sh | paperzilla Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for recent project recommendations, canonical… |
| — | skills.sh | open-notebook Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organizing research materials into notebooks,… |
| — | skills.sh | scholar-evaluation Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem… |
| — | skills.sh | database-lookup database-lookup — an installable skill for AI agents, published by k-dense-ai/scientific-agent-skills. |
| — | skills.sh | parallel-web All-in-one web toolkit powered by parallel-cli, with a strong emphasis on academic and scientific sources. Use this skill whenever the user needs to search the… |
| — | skills.sh | seaborn Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive… |
| — | skills.sh | docx docx — an installable skill for AI agents, published by k-dense-ai/scientific-agent-skills. |
| — | skills.sh | statsmodels Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and… |
| — | skills.sh | markitdown Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP,… |
| — | skills.sh | bgpt-paper-search Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper… |
| — | skills.sh | hypothesis-generation Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with… |
| — | skills.sh | statistical-analysis Guided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for your data, assumption checking, power… |
| — | skills.sh | scientific-slides Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations,… |
| — | skills.sh | literature-review Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be… |
| — | skills.sh | scientific-brainstorming Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or… |
| — | skills.sh | scientific-visualization Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars,… |
| — | skills.sh | peer-review Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment,… |
| — | skills.sh | scientific-critical-thinking Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading… |
| — | skills.sh | scientific-writing Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1)… |
| — | skills.sh | paper-lookup Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles. Covers PubMed, PMC (full text), bioRxiv, medRxiv,… |
