Skill UI

A comprehensive guide to MATLAB and GNU Octave, covering core scientific computing tasks. This skill details capabilities in matrix operations, linear algebra, data visualization (2D/3D), statistical analysis, signal processing, and solving differential equations. It is ideal for users requiring complex numerical simulation, data modeling, and scientific scripting.

Matplotlib is Python's foundational library for creating highly customizable static, animated, and interactive visualizations. It supports various plot types (line, scatter, heatmap, 3D) and offers both pyplot and object-oriented interfaces. Ideal for generating publication-quality scientific charts, complex multi-panel figures, and integrating into notebooks.

Perform comprehensive molecular dynamics (MD) simulations using high-performance engines like OpenMM and analysis tools like MDAnalysis. This skill allows users to model the time evolution of biological systems, covering system preparation (solvation, force field assignment), energy minimization, NVT equilibration, and advanced analysis (RMSD, free energy surfaces). Ideal for structural biology, drug binding studies, and biophysics research.

Molfeat is a comprehensive Python library designed for molecular featurization. It converts chemical structures (SMILES/RDKit) into numerical feature vectors, supporting over 100 featurizers like ECFP, MACCS, and deep embeddings (ChemBERTa). It unifies featurization pipelines, making it ideal for QSAR modeling, virtual screening, and integrating into deep learning ML workflows.

NetworkX is a powerful Python library used for creating, manipulating, and analyzing complex networks and graphs. It supports graph structures (directed/undirected, multi-edges) and provides extensive algorithms for tasks such as finding shortest paths, calculating centrality measures (e.g., PageRank), detecting communities, and simulating various network types (e.g., scale-free, small-world). Ideal for social science, biology, and transportation network modeling.

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.

This skill provides a comprehensive Python API integration for the OMERO platform, an open-source solution for managing and analyzing large-scale microscopy datasets. Users can programmatically access images, retrieve structured data, analyze raw pixel data, manage complex annotations (ROIs), and execute batch processing workflows essential for high-content screening and advanced biological 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.

This comprehensive skill provides a standardized pipeline for reconstructing the evolutionary history of biological sequences (genes, proteins, genomes). It guides users through essential steps, including multiple sequence alignment using MAFFT, maximum likelihood tree inference with IQ-TREE 2, and visualization with ETE3. Ideal for research in viral phylodynamics, molecular clock studies, and large-scale comparative genomics.

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.

A high-performance library built on Polars for advanced genomic interval operations and bioinformatics file I/O. It provides robust support for core interval arithmetic (overlap, merge, complement) and reading/writing major formats like VCF, BAM, BED, and GFF. Features include out-of-core streaming, cloud-native I/O (S3, GCS, Azure), and a powerful SQL interface, making it ideal for large-scale genomic research.

This skill provides programmatic access to the PrimeKG, a comprehensive knowledge graph integrating over 20 primary databases. It facilitates multiscale biological research by mapping complex relationships between genes, drugs, diseases, and phenotypes. Use it for drug repurposing, identifying novel disease targets, and analyzing molecular mechanisms across various biological scales.