Skill UI

Integrate with the DNAnexus cloud genomics platform to build apps/applets, manage FASTQ/BAM/VCF data, run workflows, and script automations via dxpy for biomedical pipelines.

Conduct rigorous, multi-database literature reviews with systematic workflows, verified citations in styles like APA or Nature, and AI-enhanced schematics for publication-ready markdown and PDF outputs in biomedical and technical domains.

TorchDrug is a PyTorch-native toolbox for building graph neural networks tailored to molecules, proteins, and biomedical knowledge graphs, covering property prediction, generation, retrosynthesis, and knowledge graph reasoning with curated datasets and models.

Leverages 78 public scientific, biomedical, materials, and economic REST APIs to find compounds, genes, pathways, clinical trials, patents, economic indicators, weather, and other structured data, returning raw JSON plus the databases/endpoints used.

Collection of battle-tested PyTorch training recipes covering architecture selection, optimizers, LR scheduling, precision tips, and debugging to train or fine-tune LLMs, vision, diffusion, and biomedical models with high GPU throughput.

A comprehensive toolkit for developing and executing genomics pipelines on the DNAnexus cloud platform. It provides capabilities for app/applet building, managing large biomedical datasets (FASTQ, BAM, VCF), orchestrating complex workflows, and interacting programmatically using the dxpy Python SDK.

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.

PyTDC (Therapeutics Data Commons) is an open-science platform providing comprehensive, AI-ready datasets and benchmarks for the entire drug discovery and development pipeline. It supports single-instance prediction (e.g., ADME, toxicity), multi-instance prediction (DTI, DDI, PPI), and novel molecule generation (MolGen). Use this skill for benchmarking machine learning models and predicting complex biomedical properties.

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 skill guides the systematic process of conducting comprehensive academic literature reviews. It allows users to search multiple biomedical, scientific, and technical databases (e.g., PubMed, arXiv, Semantic Scholar) to synthesize current knowledge. The output generates professionally formatted reports (Markdown/PDF) with verified citations, and mandatorily integrates AI-generated scientific schematics to enhance visualization and depth, suitable for research papers, meta-analyses, and state-of-the-art reports.

This guide provides a comprehensive workflow for searching and retrieving biomedical literature from PubMed and NCBI. It covers advanced query construction using MeSH terms and specific field tags, advanced filtering (date, publication type), and a repeatable programmatic workflow using NCBI E-utilities (esearch, efetch). Essential for researchers conducting systematic reviews and literature monitoring.

This skill provides comprehensive tools and methodologies for working with the Brain Imaging Data Structure (BIDS) standard. It is essential for organizing, validating, querying, and converting complex multi-modal neuroscience and biomedical datasets (including MRI, EEG, MEG, PET, etc.). Use this when setting up BIDS-compliant directory structures, ensuring data integrity before publication, or converting raw DICOM scans into standardized formats.