Galaxy Community Hub

GCC2021: June 28 - July 10

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

Galaxy Release 21.05 – Workflow Reports, Remote Files, Visualizations

New Paper: Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine – The Galaxy-ML platform provides all the tools necessary to define a learner, train it, evaluate it, and visualize its performance.

June 2021 Galactic News – GCC2021 starts this month; James Taylor Video; plus a whole lot more.

GCC2021 Early Registration Deadline moved to June 8 – Please join us at Galaxy's annual community gathering

GCC2021 Poster/Demo Abstracts due June 14 – Registration closes June 25

  Events

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

Strengthening the integration of Galaxy in the Tools Ecosystem- Jun 3. Latest developments and plans, and discussion of current and future collaborations within ELIXIR.

Galaxy for microbiome via ASaiM story - From a local project to a global effort to support microbiome data analysis- Jun 7. Register by 14 April

Galaxy Browser Dev Environment Update; plus Gitpod- Jun 10. Environments for Galaxy Development

Analyzing your own data in VectorBase- Jun 10. Analyze your own data in VectorBase

  @galaxyproject


  Recent Videos

Webinar: Galaxy Resources for System Administrators and Infrastructure Providers - Gianmaruo Cuccuru and Lucille Delisle wrap up the series

Happy 42nd Birthday James Taylor - James was one of the founders and principal investigators of the Galaxy Project. May 18 would have been his 42nd birthday.

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

  Blog

A Galaxy of tools at your fingertips – Galaxy is now available in all flavors of the Terra platform.

Galaxy Resources for ... Webinars Summary – Watch them now.

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).

  Careers

Research Data Manager – IrsiCaixa AIDS Research Institute, Barcelona, Spain . Apply by Jun 20.

Two-year bioinformatics freelance position – San Martino Hospital, Genoa, Italy . Apply by Jun 13.

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


  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.