We have a growing list of confirmed speakers and topics for GCC2021 (and we expect to have them placed in the schedule by the end of this week). Topics are wide-ranging, and reflect the breadth and depth of the Galaxy community and ecosystem.

Some highlights from the confirmed presentations list so far:

• Galaxy Training Network (GTN) Community Update

  • Saskia Hiltemann

• Introducing the Intergalactic Workflow Commission

  • Marius van den Beek

• Bridging Natural Language Processing and Biomedical Data Analysis

  • Nancy Ide

• Galaxy Language Server - Develop high-quality Galaxy tool wrappers at intergalactic speed

  • David López

• Analysis of Microscopy Data in Galaxy

  • Beatriz Serrano-Solano

• Open Life Science: An Open Research mentoring and training program

  • Muhammet Celik

• Using the Galaxy (Australia) Database to Aid an Undergraduate Investigation of RNF43 Mutations as Biomarkers for ctDNA Surveillance of Colorectal Cancer

  • Jordon Lima

• Designing a comprehensive workflow for detection and functional annotation of lncRNA

  • Bianca Pasat

• MaxQuant and MSstats in Galaxy enable reproducible quantitative high-throughput proteomics for everyone

  • Melanie Föll

• Modernizing the Galaxy Backend - Typing and the API

  • David López

• Modernizing the Galaxy Backend - Data Model

  • Sergey Golitsynskiy

• Fostering Public Health Bioinformatics and Collaboration with GalaxyTrakr

  • Justin Payne

• Updates from the Single-Cell Community

  • Mehmet Tekman

• Galaxy Australia - the influx state of a national eResearch service

  • Gareth Price

• Community engagement and how it influences Galaxy Australia Innovation

  • Johan Gustafsson

• The “ARIES Genomics” Italian public health surveillance system

  • Arnold Knijn
• ...

See the GCC2021 schedule for the most current list of confirmed presenters.

Publish your research fast and openly in F1000Research's Galaxy Gateway, an open platform dedicated to the Galaxy project.

Maximise the impact of your research, publishing a range of outputs such as a new Galaxy workflow or an update to an existing method or software tool. F1000Research is an Open Research publishing platform for scientists, scholars and clinicians offering rapid publication of articles and other research outputs without editorial bias.

BGI's Open Access Publishing division GigaScience Press is offering discounts to GCC2021 presenters in our two journals:

• GigaScience: 15% APC discount for the GigaScience Galaxy series.
• GigaByte: Less-complex workflow driven work is eligible for a free-APC discount.

We also publish data, software, and other research objects via our database, GigaDB, and Galaxy workflows via GigaGalaxy.net.

Plant tomorrow’s ideas.

We strive for new, fresh ideas and pioneering perspectives. We foster entrepreneurial spirit to set standards in our market and to create sustainable solutions for today’s and future challenges of our planet. We use Galaxy to support our research and breeding.

The Galaxy Resources webinar series wrapped up in May (see the blog post below. All webinars are available as videos. As of press time, there is only one webinar scheduled for June:

Analyzing your own data in VectorBase, June 10

Keep your eyes open for new webinars as they are scheduled.

11 June, Online

As part of the 2021 OME Community Meeting, Beatriz Serrano-Solano will give a talk on Imaging in Galaxy on day 4 (June 11) of the meeting. Conference registration is free.

The next roundtable meetups will be:

June 10: TBD:

June 24: TBD

We still need volunteers to lead discussions on a topic of interest on June 10 and 24.

21-25 June, Online

Gallantries is hosting a Galaxy training workshop at Belgrade Bioinformatics Conference 2021. This course will familiarise participants with the Galaxy Platform. Register now.

2 juillet

Ce module comprendra un exposé théorique avec des démonstrations pratiques complétées par quelques applications sur la manipulation de données de régions génomiques et sur l’analyse de jeux de données de type NGS (détection de SNP, analyse de données RNA-seq et ChIP-seq).

1-4 June, Online

As the 2021 Galaxy Community Conference (GCC2021) draws near (training starts June 28) the instructors behind the Galaxy Admin Track (and Galaxy Admin Training events) would like to gather to address some lingering issues before GCC.

17 June, Online, Global

The June Papercuts CoFest Day is now the GCC2021 CoFest Prep Day for participants to plan work (collaborative work, dang it) for the GCC2021 CoFest being held July 9-10, right after the 3-day GCC2021 meeting. We will have 3 calls, spread throughout the global day, and communicate via Gitter and (video as needed) between calls.

If you are participating in the GCC2021 CoFest^* then please join us June 17.

^* And if you aren't participating, then we urge you to reconsider your life choices! Participation is free but you need to register by June 25.

Use the VVV Galaxy server to determine the composition of a viral population. Uses a novel bioinformatic tool for rapid and simple visualization of viral genetic diversity.

VVV is supported by Agence National de Sécurité Sanitaire, de l’environnement et du travail (ANSES) Laboratory of Ploufragan-Plouzané-Niort, Université Bretagne Loire (UBL), France.

SHAMAN is a user-friendly website for metataxonomic analysis from raw reads to statistical analysis. SHAMAN does not look like Galaxy, but it uses the Galaxy@Pasteur server for data analysis and workflow execution.

SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for targeted metagenomics, statistical analysis and results visualization with a large variety of plots (barplot, boxplot, heatmap, …).

The imaging flavor of Galaxy offers a set of training materials and tools that you can assemble into workflows to perform image analysis.

• New high memory servers for Galaxy Australia
• Lots of tool updates on UseGalaxy.eu and UseGalaxy.org.au.

The Galaxy ecosystem is very broad in scope and reaches many audiences, each one with different needs. To provide those different profiles with the resources available, four webinars have taken place during April and May for researchers, trainers & educators, tool developers and admins & infrastructure providers. You can watch them all now.

¿Hablas español?: The first curated tutorial in Spanish!

Galaxy has always had Google-translated tutorials, but we are now embarking on a project to assess the learning experience with human-translated, vs Google-translated, bioinformatics tutorials. We are aiming to survey usage and utility in a workshop for native Spanish speakers.

The project started with Anna Syme's A short introduction to Galaxy, and produced Breve introducción a Galaxy - en español. Many thanks to Wendi Bacon, Beatriz Serrano-Solano, Patricia Carvajal López, Alejandra Escobar-Zepeda, Saskia Hiltemann, and Helena Rasche for making this happen.

By Kaivan Kamali.

There is a new slide deck and video for the Deep Learning (Part 3) - Convolutional neural networks (CNN) tutorial.

Convolutional neural networks are specifically tailored to image and video processing tasks. This material explains what convolutional neural networks are, discusses their architecture, and solves an image classification problem using a CNN in Galaxy.

By Erik Schill and Simon Bray

BioBlend (Sloggett et al. 2013) is a Python library to enable simple interaction with Galaxy via the command line or scripts. This tutorial covers the basics behind BioBlend and the Galaxy API from a developer perspective, and demonstrates how to implement a simple method in BioBlend.

This is the 200th tutorial in the Galaxy Training Network Library.

Have you noticed a new emphasis on Galaxy Developer training? The new BioBlend tutorial is an example. So is the new Galaxy for Developers track at GCC2021. Reflecting these and other developments, the Development in Galaxy topic in the GTN now has subsections for areas from Core to Viz.

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. https://doi.org/10.1371/journal.pcbi.1008923

Gallardo-Alba, C., Grüning, B., & Serrano-Solano, B. (2021). PLOS Computational Biology, 17(5), e1008922. https://doi.org/10.1371/journal.pcbi.1008922

Volant, S., Lechat, P., Woringer, P., Motreff, L., Campagne, P., Malabat, C., Kennedy, S., & Ghozlane, A. (2020). BMC Bioinformatics, 21(1), 345. https://doi.org/10.1186/s12859-020-03666-4

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. https://doi.org/10.1186/s12014-021-09321-1

Mehta, S., Easterly, C. W., Sajulga, R., Millikin, R. J., Argentini, A., Eguinoa, I., Martens, L., Shortreed, M. R., Smith, L. M., McGowan, T., Kumar, P., Johnson, J. E., Griffin, T. J., & Jagtap, P. D. (2020). Proteomes, 8(3), 15. https://doi.org/10.3390/proteomes8030015

Sherafat, E., Force, J., & Măndoiu, I. I. (2020). BMC Bioinformatics, 21(18), 498. https://doi.org/10.1186/s12859-020-03813-x

Fahrner, M., Kook, L., Fröhlich, K., Biniossek, M. L., & Schilling, O. (2021). Proteomes, 9(2), 26. https://doi.org/10.3390/proteomes9020026

The Galaxy Helm chart automates the mechanics of deploying Galaxy into a single package. The same package can be used to deploy Galaxy for development, testing, or production. With v4, the chart also introduces improvements for managing Galaxy over time.

See this blog post by Alex Mahmoud, Nuwan Goonasekera, Keith Suderman, and Enis Afgan for details.

Nebulizer is a Python utility which provides a high-level interactive command-line interface to remotely administer Galaxy servers. It is built on top of the BioBlend library and offers an interface and range of functionality that complements the lower-level interfaces offered by Ephemeris and Parsec.