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
How does the GTN stay FAIR and Collaborative? – Find out how contributing simple markdown tutorials can result in fantastically FAIR training.
Omicron and SARS-CoV-2 genome surveillance – A first view of the Omicron lineage’s mutational pattern derived transparently and fully reproducibly from raw sequencing reads
GTN Video Library – Videos from online training events are now easier to find.
GTN API with OpenAPI 3 specification – Access data from the GTN in a more accessible, API based way.
Galaxy Release 21.09 – Tool Panel Views, Collections, Reports, Remote Data, FastAPI, SQLAlchemy & much more!
Events
Genome Assembly and Annotation 2021 – Dec 1. A 3-day training course on bioinformatics methods for de novo assembly and structural and functional annotation of genomes using short (Illumina) and long reads (PacBio / Oxford Nanopore) sequencing technologies (will be run in french).
RNA Sequencing (RNA-seq) and Differential Expression – Dec 6. Using Galaxy and the command line. Register by 29 November.
Using traefik to bridge cloud and local setups – Dec 9. Join the discsussion
VEuPathDB Workshop 2021 – Dec 13. A free 4-day virtual workshop
Galaxy Developer Roundtable – Jan 6. Volunteer to lead the discussion
Recent Videos
How Galaxy Imaging makes cloud-based image analysis possible – Presented at the Euro-BioImaging Virtual Pub
How to launch Galaxy workflows from Dockstore – Dockstore and Galaxy are now integrated
Galaxy 21.09 Release Highlights – New Toolbox; Change Datatype + DBkey; Remote Files Enhancements
Image analysis in Galaxy - pain points and lessons learnt – October 28 Galaxy Developer Round Table
Fast, scalable, free, & user-friendly Galaxy workflows for reference genome assembly – The latest version of VGP's pipeline has been ported to Galaxy.
Blog
Galaxy interactive tools and R Shiny apps – Some dreams, mixing synchronous and asynchronous workflows in Galaxy and adding high degree of interactivity into Galaxy thanks to R Shiny are ready to be reality
An overview and statistics on the Galaxy Help Forum – Galaxy Help, together with the different Gitter channels, is one of the primary meeting places where Galaxy users turn to searching for answers.
FORCeS eScience course report – Tools in Climate Science: Linking Observations with Modelling
Sunsetting the CloudLaunch service – There are now better alternatives to using Galaxy on the cloud
SARS-CoV-2 analysis training with Galaxy: a perspective from Africa – The switch to online bioinformatics training forced by the COVID-19 pandemic has opened spaces for collaboration in ways that were previously limited by geography.
Careers
UI/UX Engineer – University of Freiburg, Freiburg, Germany
Bioinformatics Software and Platforms Service Manager – QCIF, Brisbane, Queensland, Australia
Postdoctoral position: multidimensional integration of high throughput sequencing data – MeInBio, University of Freiburg, Freiburg, Germany
Sujet stage M2: Développement d’un workflow Galaxy d’analyse de promoteurs chez les plantes – Limagrain, Chappes, France
Scientific software developer – RECETOX, Brno, Czechia
New Platforms
miRGalaxy – NGS data analysis focusing on microRNAs and their sequence variants—isomiRs.
MitoLink – An integrated workflow system to facilitate understanding of genotype-phenotype correlations in cases of mitochondrial dysfunction.
Galaxy India – The Indian community server.
VVV – Determine the composition of a viral population.
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).
Recent Pubs
MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging – Schapiro, D., Sokolov, A., Yapp, C., Chen, Y.-A., Muhlich, J. L., Hess, J., Creason, A. L., Nirmal, A. J., Baker, G. J., Nariya, M. K., Lin, J.-R., Maliga, Z., Jacobson, C. A., Hodgman, M. W., Ruokonen, J., Farhi, S. L., Abbondanza, D., McKinley, E. T., Persson, D., … Sorger, P. K. (2021). Nature Methods, 1–5.
miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data – Glogovitis, I., Yahubyan, G., Würdinger, T., Koppers-Lalic, D., & Baev, V. (2021). Cancers, 13(22), 5663.
Laniakea@ReCaS: Exploring the potential of customisable Galaxy on-demand instances as a cloud-based service – Tangaro, M. A., Mandreoli, P., Chiara, M., Donvito, G., Antonacci, M., Parisi, A., Bianco, A., Romano, A., Bianchi, D. M., Cangelosi, D., Uva, P., Molineris, I., Nosi, V., Calogero, R. A., Alessandri, L., Pedrini, E., Mordenti, M., Bonetti, E., Sangiorgi, L., … Zambelli, F. (2021). BMC Bioinformatics, 22(15), 544.
Expanding the Galaxy’s reference data – VijayKrishna, N., Joshi, J., Coraor, N., Hillman-Jackson, J., Bouvier, D., Beek, M. van den, Eguinoa, I., Coppens, F., Golitsynskiy, S., Stolarczyk, M., Sheffield, N. C., Gladman, S., Cuccuru, G., Grüning, B., Soranzo, N., Rasche, H., Langhorst, B. W., Bernt, M., Fornika, D., … Blankenberg, D. (2021). BioRxiv, 2020.10.09.327114.
Ready-to-use public infrastructure for global SARS-CoV-2 monitoring – Maier, W., Bray, S., van den Beek, M., Bouvier, D., Coraor, N., Miladi, M., Singh, B., De Argila, J. R., Baker, D., Roach, N., Gladman, S., Coppens, F., Martin, D. P., Lonie, A., Grüning, B., Kosakovsky Pond, S. L., & Nekrutenko, A. (2021). Nature Biotechnology, 1–2.