Skill UI

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.

Pysam is a comprehensive Python toolkit for handling genomic data. It provides a Pythonic interface for reading, writing, and manipulating essential genomic formats, including SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences. It is critical for developing robust bioinformatics pipelines, performing coverage analysis, and analyzing genetic variations.

A powerful AI tool designed to transform complex scientific concepts into publication-quality visual schematics. Utilizing Nano Banana 2 AI for generation and Gemini 3.1 Pro Preview for rigorous quality review, the skill specializes in creating architectural diagrams, neural network structures, biological pathways, and complex flowcharts. It employs smart iterative refinement, ensuring the output meets predefined quality thresholds for academic journals, posters, and reports.

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.

PyTorch Geometric (PyG) is the definitive standard library for building Graph Neural Networks (GNNs) atop PyTorch. It provides specialized data structures for handling diverse graph types, including heterogeneous graphs. The library offers over 60 GNN layer implementations (such as GCN, GAT, GraphSAGE), full support for dataset loading (Planetoid, TUDataset, OGB), and necessary data transformations. It is essential for deep learning tasks involving node classification, graph classification, and link prediction.

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 tool generates a comprehensive debug bundle for troubleshooting Alchemy SDK issues. It collects crucial diagnostic evidence, including connectivity tests for core, enhanced, and NFT APIs, network status across multiple chains (Ethereum, Polygon, Arbitrum), SDK version, and environment details. Use it when encountering complex blockchain query failures or preparing detailed support tickets for reliable issue resolution.