Skill UI

FluidSim is an object-oriented Python framework for high-performance Computational Fluid Dynamics (CFD) simulations. It provides specialized solvers for complex equations like 2D/3D Navier-Stokes, shallow water, and stratified flows. Utilizing pseudospectral methods with FFT, the framework supports parallel computing (MPI) and offers a complete workflow, including parameter configuration, simulation execution, and advanced post-processing and visualization.

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.

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.

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.

An expert skill for transforming CPU-bound Python code into highly performant GPU-accelerated code using NVIDIA technologies. It specializes in optimizing scientific workflows, including machine learning (ML), physics simulations, geospatial analysis, and large-scale array computations. Utilize tools like CuPy for array operations, Numba CUDA for custom kernels, and Warp for spatial computing and differentiable simulations, achieving dramatic speedups (10x to 1000x). Use this when dealing with NumPy, pandas, SciPy, or complex computational loops that benefit from parallel processing on NVI...

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.

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.

A comprehensive Python wrapper for OpenMS, designed for sophisticated computational mass spectrometry workflows. It supports end-to-end analysis in proteomics and metabolomics, enabling feature detection, peptide/protein identification, quantitative analysis (label-free/isobaric), and adduct/accurate mass annotation. Ideal for researchers processing complex LC-MS/MS raw data and running high-level pipelines.

RDKit is a powerful, open-source cheminformatics library providing extensive Python APIs for molecular analysis and structural manipulation. It supports molecular I/O (SMILES, SDF, InChI), calculating physicochemical descriptors (MW, LogP), generating fingerprints, performing substructure searching, and analyzing stereochemistry. This toolkit is essential for advanced research in drug discovery, computational chemistry, and materials science.

This guide provides comprehensive guidelines for performing vertical scaling on Qdrant instances. Vertical scaling involves upgrading the computational resources (CPU, RAM, or disk) of existing nodes rather than adding new nodes. It is the recommended first step when single nodes experience resource exhaustion (e.g., RAM usage > 80%, CPU saturation). The guide covers sizing guidelines, best practices for cloud deployment, and clearly defines the thresholds when horizontal scaling becomes necessary.

A comprehensive tool for performing pathway and gene-set enrichment analysis (GSEA, ORA, ssGSEA, GSVA). Used in computational biology to determine which biological pathways or gene sets are significantly over-represented in a given list of genes or ranked gene data. Supports multiple databases (GO, KEGG, Reactome, MSigDB) and provides tools for result interpretation, visualization, and publication-ready reporting.