Galaxy Community Hub

Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational research.

  • Accessible: programming experience is not required to easily upload data, run complex tools and workflows, and visualize results.
  • Reproducible: Galaxy captures information so that you don't have to; any user can repeat and understand a complete computational analysis, from tool parameters to the dependency tree.
  • Transparent: Users share and publish their histories, workflows, and visualisations via the web.
  • Community centered: Our inclusive and diverse users (developers, educators, researchers, clinicians, etc.) are empowered to share their findings.

Welcome to the Galaxy Community Hub, where you'll find community curated documentation of all things Galaxy.


  News

Two New Teaching Papers using Galaxy – Two hand-in-hand teaching papers have been published this week using Galaxy as a teaching platform.

COVID updates: B.1.617.2 detected in COG-UK data from the beginning of April – We checked the COG-UK data to see if we’d find representative samples of B.1.617.2 (one of the Indian lineages, and a Variant of Concern).

Exploring and monitoring COVID-19 variants with Galaxy – Galaxy Europe has developed a pipeline to automatically create COVID-19 variant information and statistics from raw sequencing data generated by COVID-19 Genomics UK Consortium (COG-UK).

GCC2021 Conference Fellowships in honor of James Taylor – Apply by May 17

GCC2021 Abstract and Fellowship Submission, and Early Registration Deadlines Extended – Talks & Fellowships due 17 May; Poster/Demos due 14 June

  Events

Galaxy @ 2021 Biology of Genomes- May 11.

Galaxy Training Network CoFest- May 20. Connect with the Galaxy Training Community!

Galaxy Papercuts CoFest Day: May 20- May 20. A community contribution day

Variant calling in humans, animals and plants with Galaxy- May 25. Hands on guidance on performing variant calling in polyploid organisms including humans, plants and animals. Apply by 12 May.

9th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis- May 25. Theoretical and practical aspects of using next generation sequencing (NGS) data for analyzing repeat composition of plant genomes.

  @galaxyproject


  Recent Videos

Customizeable welcome and introduction page for new Galaxy users - Galaxy Developer Round Table call

Webinar: Galaxy Resources for Tool Developers - Galaxy resources for getting your tools used.

Webinar: Building a bioinformatics platform: Lessons learned from immuneML - immuneML is a platform for the analysis of adaptive immune receptors through machine learning

Webinar: Galaxy Resources for Educators and Trainers - Resources for teaching with Galaxy

Tools for Applied Data Science Using Cloud-Based Platform - How to launch and use Galaxy within AnVIL

  Blog

Galaxy Helm chart v4.0 – From dev to testing to production on the same stack.

Plant Transcriptomics Workshop: A Summary – New platform, new learners, new paradigms.

Monitoring of raw open data for SARS-CoV-2 genome surveillance – UseGalaxy.eu is now automatically collecting, and analyzing raw sequencing data published by the COVID-19 Genomics UK Consortium (COG-UK).

Tips and tricks for Galaxy – "a useful bag of tricks and tools"

GTN Smörgåsbord: A Global Galaxy Course – A report on the largest Galaxy event ever.

  Careers

Bioinformatic Engineer – Institut Pasteur de Lille, Lille, France . Apply by Jun 1.

Ingénieur de Recherche Bioinformatique – Institut Pasteur de Lille, Lille, France . Apply by Sep 1.

Computational Biologist – GalaxyWorks, Baltimore (or remote), Maryland, United States

Postdoctoral Fellowships – Blankenberg Lab, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States

Research Associate in Biomedical Data Science – Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore. Maryland, United States


  New Platforms

SHAMAN - A user-friendly website for metataxonomic analysis from raw reads to statistical analysis.

IPK Blast - BLAST for barley, wheat, and rye. Part of IPK Crop Analysis Tools Suite (CATS).

immuneML - Machine learning-based analysis and classification of adaptive immune receptors and repertoires (AIRR).

ASaiM Docker Image - Tools for metagenomic and metatranscriptomic studies, hierarchically organized to orient user choice toward the best tool for a given task.

InteractoMIX - One-stop resource offering a wide range of computational analyses from proteome-wide interactomes to structure of protein complexes.

  Recent Pubs

Fostering accessible online education using Galaxy as an e-learning platform - Serrano-Solano, B., Föll, M. C., Gallardo-Alba, C., Erxleben, A., Rasche, H., Hiltemann, S., Fahrner, M., Dunning, M. J., Schulz, M. H., Scholtz, B., Clements, D., Nekrutenko, A., Batut, B., & Grüning, B. A. (2021). PLOS Computational Biology, 17(5), e1008923.

A constructivist-based proposal for bioinformatics teaching practices during lockdown - Gallardo-Alba, C., Grüning, B., & Serrano-Solano, B. (2021). PLOS Computational Biology, 17(5), e1008922.

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19) - Rajczewski, A. T., Mehta, S., Nguyen, D. D. A., Grüning, B., Johnson, J. E., McGowan, T., Griffin, T. J., & Jagtap, P. D. (2021). Clinical Proteomics, 18(1), 15.

SHAMAN: A user-friendly website for metataxonomic analysis from raw reads to statistical analysis - Volant, S., Lechat, P., Woringer, P., Motreff, L., Campagne, P., Malabat, C., Kennedy, S., & Ghozlane, A. (2020). BMC Bioinformatics, 21(1), 345.

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL). - Schatz, M. C., Philippakis, A. A., Afgan, E., Banks, E., Carey, V. J., Carroll, R. J., Culotti, A., Ellrott, K., Goecks, J., Grossman, R. L., Hall, I., Hansen, K. D., Lawson, J., Leek, J. T., Luria, A. O., Mosher, S., Morgan, M., Nekrutenko, A., O’Connor, B. D., … Team, A. (2021). BioRxiv, 2021.04.22.436044.