Skill UI

ETE is a comprehensive toolkit for phylogenomic research, designed to handle and analyze hierarchical tree structures. It supports various tree formats (Newick, NHX) and provides advanced functionalities such as detecting evolutionary events (duplication/speciation), identifying orthologs/paralogs, integrating with NCBI taxonomy for lineage tracking, and generating publication-quality visualizations in PDF/SVG.

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.

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.

scikit-bio is a comprehensive Python library designed for advanced bioinformatics and biological data analysis. It provides robust capabilities for sequence manipulation (DNA, RNA, Protein), performing complex sequence alignments (pairwise and multiple), constructing and analyzing phylogenetic trees, and calculating diverse ecological metrics. It is essential for microbiome analysis, evolutionary studies, and general biological data processing, supporting standard formats like FASTA, Newick, and BIOM.

scVelo is a powerful Python package designed for RNA velocity analysis using single-cell RNA-seq data. It estimates cell state transitions by modeling the kinetics of mRNA splicing—specifically using the ratio of unspliced to spliced mRNA abundances. This allows researchers to reconstruct developmental trajectories and predict cell fates, even when only snapshot data is available, making it a vital complement to standard trajectory inference tools like Scanpy.

SimPy is a powerful, process-based discrete-event simulation framework written in Python. It enables users to model complex systems involving processes, shared resources, queues, and time-based interactions. It is ideal for analyzing manufacturing lines, network traffic, logistics, or service operations where resource contention and irregular, time-based events are key factors.

TorchDrug is a comprehensive PyTorch-based ML toolbox designed for molecular and protein science. It leverages Graph Neural Networks (GNNs) to tackle complex tasks including molecular property prediction, protein structure modeling, drug-target binding prediction, knowledge graph reasoning, and de novo molecular generation. It provides robust capabilities for accelerating drug discovery research.

Access a comprehensive network of 78 public databases across scientific, biomedical, environmental, and physical domains. This skill enables deterministic and reproducible data retrieval through documented REST APIs. It manages complex workflows including exhaustive pagination, cross-referencing identifiers across sources (e.g., PubChem, UniProt), and generating full provenance logs, ensuring results are auditable for high-stakes scientific research.

This comprehensive guide details best practices for securing a ClickHouse deployment. It covers essential security measures including role-based access control (RBAC) for granular user permissions, implementing row-level security for multi-tenancy, configuring network IP restrictions, enabling TLS encryption, and setting up detailed audit logging. Use this when hardening a production ClickHouse instance or enforcing strict data governance.

This guide details how to set up and execute large-scale, distributed GPU training jobs on the CoreWeave platform. It covers both single-node multi-GPU setups and multi-node training utilizing PyTorch DDP and Kubernetes resources (A100/H100). This workflow is ideal for fine-tuning large language models (LLMs) or running complex deep learning models that require high-performance, shared-storage compute clusters.

This guide demonstrates how to deploy GPU workloads on the CoreWeave platform using Kubernetes (kubectl). It covers deploying vLLM inference services for large language model (LLM) testing and running batch CUDA jobs for benchmarking. This is ideal for users running their first GPU workloads, testing inference pipelines, or verifying cluster access on bare-metal GPU nodes (A100, H100).