Skill UI

A powerful Python library that extends pandas to enable complex spatial operations on vector geometric data. It supports reading and writing diverse formats, including Shapefile, GeoJSON, and GeoPackage. Users can perform advanced GIS tasks such as spatial joins, buffering, overlay analysis, calculating areas, managing Coordinate Reference Systems (CRS), and generating interactive choropleth maps, making it essential for geographic data science projects.

This skill proactively detects and reports comprehensive system resources, including CPU cores, GPU types (NVIDIA, AMD, Apple Silicon), available memory, and disk space. It generates a detailed JSON report with strategic, context-aware recommendations for optimizing scientific computing workflows, such as recommending parallel processing libraries (Dask, joblib), out-of-core methods (Zarr), or appropriate GPU acceleration backends (Metal, ROCm). Use this before any large-scale data analysis, model training, or computationally intensive simulation to make informed architectural decisions.

gget is a comprehensive command-line tool and Python package offering unified access to over 20 genomic databases. It facilitates quick lookups for gene information, sequence analysis (BLAST), protein structures, and expression data, supporting both interactive CLI use and advanced programmatic Python workflows for biological research.

This skill provides comprehensive tools to analyze and engineer protein glycosylation patterns. It scans amino acid sequences for canonical N-glycosylation sequons (N-X-S/T) and predicts O-glycosylation hotspots. Use cases include optimizing therapeutic antibodies, designing vaccine antigens, and characterizing biosimilars by rationally modifying glycan structures for improved stability, function, or immune evasion.

Gtars is a high-performance toolkit written in Rust with Python bindings, designed for comprehensive analysis of genomic interval data. It provides specialized modules for overlap detection, generating coverage tracks (WIG/BigWig), tokenization for Machine Learning models, and detailed fragment analysis in single-cell genomics. Use it for robust bioinformatics pipelines and computational genomics research.

Histolab is a specialized Python library for digital pathology research, enabling robust processing of Whole Slide Images (WSI). It automates complex workflows including tissue detection, sophisticated segmentation, and flexible tile extraction from various formats (SVS, TIFF). This tool is crucial for preparing structured, high-quality datasets required for deep learning models and advanced computational pathology analysis.

Hypogenic is an advanced framework that uses Large Language Models (LLMs) to systematically generate and test hypotheses on complex tabular datasets. It supports three powerful modes: data-driven generation (HypoGeniC), literature-grounded refinement (HypoRefine), and combined union methods. This tool is essential for accelerating scientific discovery in fields such as predictive modeling, content analysis, and deception detection by combining empirical data insights with theoretical knowledge.

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 skill provides comprehensive integration with the LabArchives Electronic Lab Notebook (ELN) platform via its REST API. It allows users to programmatically manage notebooks, retrieve user data, automate entry creation, upload diverse attachments (PDF, CSV, images), perform full notebook backups, and generate detailed usage reports. Ideal for automating scientific workflows and integrating ELN data with tools like Jupyter or REDCap.

LaminDB is an open-source, lineage-native lakehouse specifically designed for complex biological datasets and models. It provides unified capabilities for querying, tracking data lineage, validating schemas, and ensuring FAIR compliance across diverse data types (e.g., AnnData, Parquet, Zarr). Use this skill when managing multi-modal genomic data, tracking computational workflows (like Nextflow/Snakemake), or building robust, reproducible data infrastructure in bioinformatics.

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.

This advanced skill generates comprehensive, professional-grade market research reports (50+ pages) modeled after top consulting firm deliverables (McKinsey, BCG). It supports deep data analysis using research-lookup, multi-framework strategic assessment (PESTLE, SWOT, Porter's Five Forces), and extensive visual generation using scientific schematics and image generation tools. The output is in professional LaTeX format, compiled to PDF, suitable for strategic planning, investment decisions, and thought leadership.