March 2021 Galactic News

Events, platform news, blog posts, videos, pubs, jobs and releases

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Galaxy News

If you have anything to include to next month's newsletter, then please send it to outreach@galaxyproject.org.


Event News

Despite COVID-19, there is still a lot going on, although online. We have updated our list of events to reflect what we know. Some highlights:

GCC2021 goes virtual

The 2021 Galaxy Community Conference will be virtual, affordable, and globally accessible.

Things are just too uncertain to continue to plan an in person event for early July. GCC2021 won't be in person, but it will be more accessible and affordable because of it:

  • GCC2021 events will be held twice each day, once in their original Ghent time zone (GCC EMEA/APO), and again 8 hours later in the Americas (GCC Americas).
  • Registration rates will be a fraction of the cost of an in person event, and will include a significant discount for students and researchers based in low and lower-middle income countries.

Other things are changing too. See the announcement for details.

Galaxy-ELIXIR webinar series

3, 10, 17, 24 March
Galaxy-ELIXIR webinars series: Advanced Features

With this series of four webinars chaired by Hans-Rudolf Hotz, the global Galaxy community will present advanced features that may have remain unknown due to the rapid developments in every Galaxy release. The series will touch upon workflows, data processing and management, interoperability and interactive tools, among others.

Advanced Galaxy workflow features, 3 March, watch the video

Processing thousands of datasets simultaneously, 10 March

Galaxy bridge to Jupyter notebooks and RStudio, 17 March

Speed up your data analysis with Galaxy: Features no one knows about, 24 March

Papercuts CoFest February

18 or 25 Mar?

UseGalaxy.NO

23 March, 7 April, or 13 April

ELIXIR Norway is pleased to announce the first online course on using the Norwegian e-infrastructure for Life Science (NeLS) and the nationally supported usegalaxy.no. There are 3 identical events. Please register for only one of them.

Galaxy Developer Roundtable

There next roundtable meetup will be:

March 18: Bringing GPU support to Galaxy, Jashwant Raj, Gulsum Gudukbay will discuss the integration of GPU Resources in Galaxy for accelerating tool executions.

Biohackathon Europe

Deadline: 1 April

Galaxy has always had a strong presence at Biohackathon Europe. We hope this tradition will continue in November 2021. Get your proposals in now.

Galaxy Platforms News

The Galaxy Platform Directory lists resources for easily running your analysis on Galaxy, including publicly available servers, cloud services, and containers and VMs that run Galaxy. Here's the recent platform news we know about:

ASaiM integrates and hierarchically organizes metagenomic and metatranscriptomic tools to orient user choice toward the best tool for a given task. It now has a new publication and new functionality and the update is now available as its own Docker image, and on UseGalaxy.eu too.

ASaiM paper, figure 1, showing workflow

A one-stop resource offering a wide range of computational analyses from proteome-wide interactomes to structure of protein complexes. Includes shared workflows and supports anonymous use.

InteractoMIX is the result of the combined efforts of Structural Bioinformatics and Bioinsilico labs.

InteractoMIX visual abstract, from paper

UseGalaxy.*

Galactic Blog Activity

The Galaxy community has recorded different ways of joining us, with suggestions for newcomers.

GalaxyWorks logo.

GalaxyWorks is a company that offers commercial-grade support for Galaxy instances. They have started a blog highlighting aspects of Galaxy (and sometimes their offerings too). Two posts from the past month:

The ELIXIR Authentication and Authorisation Infrastructure (AAI) enables researchers to use their home organisation credentials or community or commercial identities (e.g. ORCID, LinkedIn, Google) to sign in and access Galaxy.

ELIXIR

By Mali Salmon-Divon.

Mali shares the feedback of two workshops run using TIaaS: one or graduate students and another one for medical doctors.

TIaaS

Doc, Hub, and Training Updates

GTN Smörgåsbord

This week-long workshop on how to use Galaxy was online, global, and free. The program covers a general introduction to the Galaxy platform, NGS Analysis (DNA-seq and RNA-seq), Proteomics, and also features a Choose your own adventure day (!?).

After the success of the first ‘Galaxy-ELIXIR webinar series: FAIR data and Open Infrastructures to tackle the COVID-19 pandemic’ last spring, the Galaxy community has been running a second Galaxy-ELIXIR webinar series on ‘Open Data Infrastructures to tackle COVID-19 pandemic’.

In this second edition, and for six consecutive weeks, speakers from all around the globe have been describing the latest Galaxy developments for working with SARS-CoV-2 data. If you missed them, the recordings are now available osn the ELIXIR Europe YouTube channel.

Galaxy-ELIXIR webinar series

New GTN welcome video

Geert Bonamie (VIB Bioinformatics Core) has produced an astonishing video introduction to the GTN features.

Publications

Pub curation activities are on a semi-hiatus right now but a few publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library anyway. Here are the new open access Galactic and Stellar pubs:

Ostrovsky, A., Hillman‐Jackson, J., Bouvier, D., Clements, D., Afgan, E., Blankenberg, D., Schatz, M. C., Nekrutenko, A., Taylor, J., Team, the G., & Lariviere, D. (2021). Current Protocols, 1(2), e31. https://doi.org/10.1002/cpz1.31

Mehta, S., Crane, M., Leith, E., Batut, B., Hiltemann, S., Arntzen, M. Ø., Kunath, B. J., Delogu, F., Sajulga, R., Kumar, P., Johnson, J. E., Griffin, T. J., & Jagtap, P. D. (2021). F1000Research, 10, 103. https://doi.org/10.12688/f1000research.28608.1

Gangiredla, J., Rand, H., Benisatto, D., Payne, J., Strittmatter, C., Sanders, J., Wolfgang, W. J., Libuit, K., Herrick, J. B., Prarat, M., Toro, M., Farrell, T., & Strain, E. (2021). BMC Genomics, 22(1), 114. https://doi.org/10.1186/s12864-021-07405-8

Ramsey, J., Rasche, H., Maughmer, C., Criscione, A., Mijalis, E., Liu, M., Hu, J. C., Young, R., & Gill, J. J. (2020). PLOS Computational Biology, 16(11), e1008214. https://doi.org/10.1371/journal.pcbi.1008214

Pires, J. G., da Silva, G. F., Weyssow, T., Conforte, A. J., Pagnoncelli, D., da Silva, F. A. B., & Carels, N. (2021). Frontiers in Genetics, 12. https://doi.org/10.3389/fgene.2021.624259

Who's Hiring

Blankenberg Lab, Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States

Utilize high-throughput omics technologies, such as next generation sequencing, and data-intensive computing to explore biomedical research questions.

Cleveland Clinic

Galaxy-SynBioCAD team, MICALIS Institute, INRAE & AgroParisTech, Jouy-en-Josas, France

Design solutions to synthesize molecules in microorganisms & to implement the sesolutions on robotized workstations.

Apply by 1 March.

SynBioCAD

MEMO Group, Norwegian University of Life Science, Ås, Norway

Interested in host-microbiome interactions and multi-omic data? We have multiple positions starting in 2021. Projects have fun and interesting EU partners. Will be hiring after Christmas.

Norwegian University of Life Science

Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University.

Data science research and education focusing on genomics (AnVIL, Genomic Data Science Community Network), cancer (ITCR) or pain A2CPS.

Johns Hopkins

Johns Hopkins University, Baltimore, Maryland, United States.

Provide technical expertise and oversight for the AnVIL Project, which incorporates Galaxy, Bioconductor, Terra, Gen3, and Dockstore into a secure cloud-based software ecosystem for genomic data analysis.

AnVIL

The Schatz Lab at Johns Hopkins University is looking for:

  • Self-driven individuals that can work independently to fill multiple software development positions on the Galaxy Project.
  • Ambitious individuals to fill a programmer analyst position working on the Galaxy and AnVIL projects.

Johns Hopkins

The French Institute of Bioinformatics (IFB) is offering a 1-year position for a developer to work on usegalaxy.fr, focused on the contribution to the development, evolution, deployment and maintenance of the French infrastructure.

IFB

VIB-UGent Center for Plant Systems Biology has two open positions to work on the ELIXIR Belgium research data analysis team, both for an initial duration of 2 years.

Johns Hopkins

Releases

Other News