Skill UI

Self-hosted open-source alternative to NotebookLM for organizing research, ingesting diverse sources, generating AI notes, running context-aware chats, performing vector search, producing multi-speaker podcasts, and automating workflows via a REST API.

Accelerates CPU-bound Python workflows by translating NumPy, pandas, ML, graph, image, simulation, and IO code into NVIDIA GPU kernels using CuPy, Numba CUDA, Warp, cuDF/cuML/cuGraph, KvikIO, cuSpatial, and RAFT for dramatic speedups.

PathML is a Python toolkit for computational pathology workflows, loading 160+ slide formats, preprocessing H&E images, constructing spatial graphs, training HoVer-Net/HACTNet models, and analyzing multiplex imaging for ML-ready pathology data.

A comprehensive toolkit for reconstructing and analyzing the evolutionary history of biological sequences (genes, proteins, genomes). The standard workflow includes multiple sequence alignment using MAFFT, robust maximum likelihood tree inference with IQ-TREE 2 and FastTree, and advanced visualization/manipulation using ETE3. This skill is essential for studies in viral phylodynamics, microbial genomics, protein family evolution, and molecular clock dating.

This skill provides complete, programmatic integration with the protocols.io API v3, enabling advanced management of scientific protocols. Use it for the entire protocol lifecycle, including discovery by DOI or keywords, creating new protocols, managing steps and materials, coordinating collaborative development, organizing workspaces, and tracking experiments. It covers authentication, file handling, and discussion management, making it ideal for automated lab workflows and scientific documentation systems.

PyDESeq2 brings the DESeq2 differential expression workflow to Python, letting users load bulk RNA-seq counts, specify design formulas, fit DESeq2 models, run Wald tests with FDR correction, optionally apply apeGLM shrinkage, and export gene-level statistics within pandas/AnnData pipelines.

Pydicom is a Python toolkit for reading, writing, and manipulating DICOM medical imaging files, helping teams extract pixel data, manage metadata, anonymize records, convert to standard formats, and integrate with PACS workflows in healthcare research and radiology applications.

PyLabRobot is a vendor-agnostic, pure Python SDK designed for autonomous and automated laboratory workflows. It provides a unified interface to control a wide array of laboratory equipment, including liquid handling robots (Hamilton, Opentrons, Tecan), plate readers, pumps, shakers, and incubators. Ideal for developing complex, multi-device, reproducible protocols and simulating experiments before physical execution.

A Python materials science library for constructing, analyzing, and converting crystal structures, computing phase diagrams and electronic properties, and integrating with the Materials Project API for high-throughput workflows.

PyMC is a powerful Python library for probabilistic programming and advanced Bayesian inference. This comprehensive guide details the full workflow for building, fitting, and validating complex Bayesian models. Learn to implement hierarchical structures, perform MCMC sampling (NUTS), conduct posterior predictive checks (PPC), and effectively quantify uncertainty using industry best practices.

PyOpenMS provides Python bindings for OpenMS to drive complete mass spectrometry workflows, covering data IO, spectral processing, feature/peptide-protein identification, quantitation, and metabolomics pipelines.

PyTorch Lightning Toolkit streamlines PyTorch model training by organizing LightningModules, LightningDataModules, Trainer configs, callbacks, logging, and distributed strategies for scalable multi-GPU/TPU runs in research or production workflows.