tools

Introducing the Zip Explorer: Import individual files from ZIP archives

Preview the contents of local or remote ZIP archives, explore rich RO-Crate metadata, and import only the files you need directly from the Galaxy interface.

Secure Your Tools with Galaxy’s New Credentials System

Galaxy 25.1 introduces a powerful new credentials system that lets tools securely access external APIs and services with encrypted secret storage and a streamlined user experience.

Integration of the Hugging Face Hub with Galaxy

Galaxy users can now browse the Hugging Face Hub as a repository source, import models straight into their histories, and feed them into tools. A step-by-step example shows how to pull models from the Hugging Face Hub into Galaxy and then using the existing DocLayout-YOLO tool for document layout segmentation.

Using Claude AI for Literature Searches

LLMs for literature search produce 'interesting' results: It is almost useful

Galaxy Tool Wrapping: Introducing the New Tool Developers SIG

Join the newly formed Tool Developers Special Interest Group (SIG) to collaborate on high-quality tool maintenance and standardize best practices across the Galaxy ecosystem. This initiative offers a dedicated space for mentorship, peer review, and community-driven development for developers of all experience levels.

Freiburg Galaxy Team’s Internal Tool Development Workshop

Know more about the recent Tool Development workshop organized at Freiburg Galaxy Team

New Interactive Tools Panel in Galaxy 25.0

New panel allocated for interactive tools on Galaxy

🔬 QuPath-Galaxy: Bringing digital pathology image analysis to your browser.

Explore whole slide images and run powerful tissue analysis directly in your browser with the QuPath-Galaxy interactive tool.

nb2workflow: Turning Annotated Jupyter Notebooks into Galaxy Tools

Convert your scientific notebooks into reusable Galaxy tools with just a tag.

From text mining to astronomical sources distance estimation on Galaxy

Estimating redshifts of optical counter parts of sources detected in astronomy texts with a Galaxy Workflow

Topic extraction from Astrophysical Reports and follow-up analysis tool suggestions in Galaxy

Matching short scientific texts to relevant analysis pipelines using AI

Voronoi segmentation for Astronomy

Dividing the sky images in regions that include individual astronomical objects.

JupyterGIS: Collaborative Geospatial Analysis in the Cloud

Explore how JupyterGIS supports collaborative geospatial analysis in climate adaptation research.

Vizgen Postprocessing Tool (VPT) now available in Galaxy

Reprocess and refine the single-cell results of MERSCOPE experiments

BellaVista interactive tool now available in Galaxy

Open-Source Visualization for Imaging-Based Spatial Transcriptomics

CellxGene-VIP scRNA-seq, spatial transcriptomics, and multiome data visualization

CELLxGENE-VIP is a frontend plugin of CELLxGENE, enabling users to generate multiple QC plots in high-resolution SVG or PNG format. It can also visualize spatial transcriptomics and 10X multiome.

TabPFN: Foundation Model for Tabular Data in Galaxy

Fast machine learning method for making predictions on any tabular data

ColabFold: GPU-accelerated protein structure prediction comes to UseGalaxy.org

Optimized AlphaFold2-based protein structure prediction now available for all

The AquaINFRA Virtual Research Environment

Design rationale for using the Galaxy platform

Annual Report 2023 of the Freiburg Galaxy Team

Report about activities and achievements

The first Galaxy Tool Development Workshop in Freiburg, Germany

Learn to build and publish Galaxy tools in our first hands-on workshop in Freiburg.

Galaxy Community Call: Automatic updates of Galaxy tools and workflows

A forum to share updates and discuss community-wide topics

The ELIXIR Tools Platform - solutions for COVID-19 research