Skill UI

A systematic tool for scientific inquiry, guiding users through the entire research process. It helps formulate testable, mechanistic hypotheses from raw observations or preliminary data, following the established scientific method. The workflow includes comprehensive literature review, evidence synthesis, generating competing explanations, and designing experiments, all while mandating the creation of scientific schematics for visualization.

This comprehensive tool guides the systematic creation of detailed technical specifications. It orchestrates the entire design lifecycle, including context loading, deep discovery and analysis (tailored for new features, extensions, or simple additions), synthesis using established design principles, and generating a boundary-first, structured design draft. Ensures all requirements are mapped to explicit technical components.

Latch is a robust Python framework designed for building, deploying, and managing complex, scalable bioinformatics workflows as serverless pipelines. It supports integrating multiple analysis tools (like Nextflow/Snakemake) and handles cloud data management (LatchFile/LatchDir) and detailed resource configuration (GPU, CPU, memory). Ideal for running large-scale analyses such as RNA-seq, AlphaFold, and single-cell analysis in a reproducible, production-ready environment.

MarkItDown is a powerful tool designed to convert a wide array of file types—including PDF, DOCX, images, audio, and structured data (JSON/XML)—into clean, token-efficient Markdown format. It supports advanced features like OCR for scanned documents, transcription for audio, and AI-enhanced descriptions, making diverse content readily consumable and structured for modern Language Models and AI pipelines.

NeuroKit2 is a comprehensive Python toolkit designed for processing and analyzing diverse physiological biosignals. It covers multiple domains including cardiovascular (ECG, PPG), neural (EEG), autonomic (EDA), respiratory (RSP), and muscular (EMG) signals. Use this skill for advanced psychophysiology research, complex pattern detection, and real-time clinical monitoring applications.

An end-to-end toolkit designed for analyzing high-density Neuropixels electrophysiology recordings. It implements best practices using SpikeInterface, covering the entire workflow: data loading (SpikeGLX, NWB), preprocessing, motion/drift correction, advanced spike sorting (Kilosort4), quality metric computation, and unit curation (including AI-assisted review). Ideal for neuroscience research.

PathML is a comprehensive Python framework designed for computational pathology workflows. It supports end-to-end analysis of Whole Slide Images (WSI), including loading 160+ proprietary formats, performing advanced stain normalization and tissue segmentation, constructing spatial cell graphs, and training deep learning models (e.g., HoVer-Net) for multiplex immunofluorescence and spatial proteomics. Ideal for large-scale biomedical image analysis.

Polars is a lightning-fast DataFrame library built on Apache Arrow for Python. It provides an expression-based API, lazy query optimization, and parallel computation capabilities for efficient data manipulation, analytics, and ETL pipelines. It is designed to handle large, memory-intensive datasets, making it an ideal alternative for migrating from pandas or optimizing complex data workflows.

PyHealth is a comprehensive Python toolkit designed for building deep-learning pipelines in the clinical and healthcare domains. It supports diverse data modalities, including EHR records, physiological signals, and medical images. The framework follows a stable 5-stage pipeline (Dataset → Task → Model → Trainer → Metrics), enabling users to perform complex tasks like predicting mortality, optimizing drug recommendations, staging sleep, or cross-mapping medical codes (ICD/ATC/RxNorm) on datasets like MIMIC-III/IV and OMOP.

Pymatgen is a comprehensive Python toolkit designed for computational materials science. It enables users to create, analyze, and manipulate complex crystal structures, calculate electronic properties (DOS, band structures), simulate phase transitions, and interact with large material databases like the Materials Project. Ideal for solid-state physics, chemistry, and advanced materials research.

Pymoo is a comprehensive Python framework designed for solving both single-objective and multi-objective optimization problems. It implements state-of-the-art evolutionary algorithms (like NSGA-II, NSGA-III, MOEA/D) and is specialized in identifying Pareto-optimal fronts. This tool is essential for engineering design and scientific problems requiring the analysis of trade-offs among multiple conflicting objectives.

QuTiP is a powerful Python library designed for simulating and analyzing quantum mechanical systems. It provides comprehensive tools to model both closed (unitary) and open (dissipative) quantum dynamics. Users can study complex phenomena like decoherence, quantum optics, and master equations. The library supports various time evolution solvers, calculating entanglement, entropy, and visualizing quantum states on the Bloch sphere or in phase space. Ideal for theoretical physics research and academic simulations.