Skill UI

Geniml provides a robust framework for running machine learning and statistical workflows over genomic interval sets. It treats coordinates, assemblies, and model artifacts as explicit contracts, enabling users to validate data structures (like BED files) and plan complex runs (such as Region2Vec or scEmbed) locally. The tool emphasizes reproducibility, adherence to biological data standards, and running without unnecessary network calls.

This tool provides a conservative, resource-aware snapshot of the current process's environment, including CPU, memory, disk, and accelerator limits. It helps users plan workloads accurately by providing clear boundary constraints (cgroup, scheduler, host limits) without performing stressful tests or making assumptions about usability.

gget is a comprehensive command-line and Python package providing unified access to over 20 major bioinformatics databases. Users can perform deep analyses across genomics, proteomics, and disease associations. Key functions include gene information lookups, sequence alignment (BLAST), structural prediction (AlphaFold), single-cell analysis, and enrichment studies, supporting both interactive queries and automated pipelines.

A comprehensive toolkit for medical device manufacturers seeking ISO 13485 certification. This skill guides users through gap analysis, creating mandatory Quality Management System (QMS) documentation, and ensuring compliance with global medical device regulations (e.g., EU MDR, FDA QMSR). It provides templates, guidance, and structured processes for foundational QMS documents like Quality Manuals and CAPA procedures.

Provides secure, programmatic integration with the LabArchives ELN and Inventory APIs. This toolkit manages regional endpoint selection, handles complex signed-request authentication (HMAC-SHA-512), and facilitates user authorization flows for automated lab data management and record keeping. It is essential for developing robust, evidence-based science workflows.

Use terminal commands to discover, list, create, edit, move, copy, enable/disable, and delete AI agent skills across 11 tools, handling format conversions and scope overrides between global and project configurations.

NetworkX is a powerful Python library used for generating, manipulating, and analyzing complex networks and graphs. It provides comprehensive tools for running essential graph algorithms (e.g., shortest paths, centrality, community detection), modeling diverse structures (social, biological, transportation), and handling various data formats (GraphML, JSON, Pandas). Ideal for system modeling and scientific research.

A comprehensive research toolkit for building and auditing reproducible workflows for physiological time-series data. It specializes in preprocessing, event/interval analysis, multimodal alignment, and extracting variability and complexity features from signals like ECG and EDA. Designed strictly for academic and research use, emphasizing rigorous data contracts and method-aware validation, while strictly disclaiming any diagnostic or medical device validation role.

A comprehensive end-to-end toolkit for analyzing high-density Neuropixels extracellular recordings. It guides the user through the complete electrophysiology workflow, including data loading (SpikeGLX, NWB), robust preprocessing, motion/drift correction, advanced spike sorting (Kilosort4, etc.), quality metric calculation, and AI-assisted unit curation. Ideal for generating publication-ready results from large neural datasets.

PyHealth is a modular Python toolkit designed for developing deep learning pipelines in clinical and healthcare settings. It provides a standardized 5-stage framework (Dataset → Task → Model → Trainer → Metrics) to handle complex, multi-modal data, including EHR records, physiological signals, and medical imaging. Use cases include predicting mortality, readmission risks, recommending drugs, or performing medical code mapping (ICD/ATC).

PyMC is a powerful Python library designed for probabilistic programming and sophisticated Bayesian modeling. It enables users to build complex models, such as hierarchical structures and time series, and perform rigorous inference using methods like MCMC (NUTS) sampling and Variational Inference. Key features include model comparison (LOO, WAIC) and comprehensive diagnostic tools for uncertainty quantification.

Qiskit is a comprehensive SDK for developing quantum algorithms. It enables users to build, optimize, simulate, and execute quantum circuits using modern APIs (Qiskit 2.x). It supports local exact sampling, high-performance noisy simulation via Qiskit Aer, and direct execution on IBM Quantum hardware through the Runtime service, making it a powerful tool for quantum research and development.