Galaxy Interest Group

Galaxy is an open web-based platform for data-intensive biomedical research. The mission of the DTL Galaxy Interest Group is to build a community of users, developers, systems administrators, trainers, and compute providers who are interested in Galaxy and to streamline collaborative efforts.

• Find Galaxy servers and events at https://choosegalaxy.nl.
• Contact Saskia Hiltemann if you would like to join us or collaborate.

The DTL Galaxy Interest Group was established in 2016 as a specific community connecting various Dutch stakeholders developing and working with the Galaxy system. Three major focus areas are Tool Dissemination, Service & e-Infra Support, and Training & Education. Members of the DTL Galaxy Interest Group have active roles in multiple global, European, and Dutch collaboration projects on developing and using the Galaxy platform to support large-scale data analysis in the fields of NGS, proteomics, and metabolomics.

Open community
The Interest Group is currently chaired by Saskia Hiltemann from Erasmus MC, who is an active contributor to the Galaxy main project and the Galaxy training network. We are building this group as an open community and we invite interested parties from both academia and industry to join us. 

Reproducible research
Galaxy is an open source, web-based platform for data-intensive biomedical research. It is widely used by research groups to perform data analyses, and for the training of students and young scientists. Galaxy has been endorsed by multiple national and European bioinformatics initiatives (e.g., ELIXIR, DTL, TraIT, BBMRI-NL, Health-RI) as the recommended platform for sharing bioinformatics methods and workflows and promoting reproducible research. Many of the members of the DTL Galaxy Interest Group are also member of the ELIXIR Galaxy WG (see also below).

A key asset of Galaxy is the active developer and user community worldwide. There are more than 5000 tools available in the public Galaxy tool repository (toolshed), including a wide range of tools applied to genomics, proteomics, metabolomics, imaging, and statistics, which can easily be combined into workflows, making Galaxy an efficient data integration platform. With over 5000 citations, Galaxy has become an important component of biomedical research.

Choose your Galaxy!
Please visit our web page https://choosegalaxy.nl for further information about Galaxy activities within the Dutch community.

• Servers – There are a number of options for using Galaxy within The Netherlands, please visit the site to find the best fit for your project.
• Projects – Stay up to date on the latest Galaxy-related projects
• Events – Find Galaxy related training events, meetups, and more

Our projects:

There are several ongoing collaborative projects:

• Centralised Galaxy Server – hosted at the SURFsara HPC Cloud.
• Galaxy-launcher – using Ansible and Docker for provisioning of production Galaxy environments. This procedure is used both locally by groups running Galaxy on their servers or HPC infrastructure and centrally to provide a public Galaxy instance, currently maintained by DTL and SURFsara.
• Galaxy-as-a-service – Led by UMCs (Erasmus and Leiden) and service provider partners (Lygature/TraIT, SURFsara) we are piloting the possibility of offering Galaxy as a service for the general user community in the Netherlands for both academia and industry
• Training and Training materials – Several members of the group are involved in national Galaxy training activities and in the creation of a central global infrastructure for the sharing, dissemination and maintenance of a rich set of training materials to support education activities. In the Netherlands the Galaxy courses are coordinated by BioSB and ELIXIR-NL

Our posters and publications

• Publications
  • EGA-TraIT ELIXIR implementation study: Integration of EGA secure data access into Galaxy – Hoogstrate et al., F1000, 2016
  • EGA-TraIT ELIXIR implementation study: Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data – Chao Zhang et al., F1000, 2017
• Posters
  • BioSB Conference 2017 Poster: Collaborative building of the Galaxy eco-system in the Netherlands
  • Galaxy Training Poster ISMB 2017: Scaling Bioinformatics Training
  • ECCB 2016 Poster: Training efforts in the Netherlands: combining forces to provide data-related training for the life science research community

Collaborations with ELIXIR & Galaxy community 

• Contributions to the Galaxy code base and addition of tools to the Galaxy toolshed
• EGA-TraIT ELIXIR implementation study: Integration of EGA secure data access into Galaxy, Hoogstrate et al., F1000, 2016
• DTL and SURF organised a Focus meeting ‘Maintaining a Dutch Public Galaxy Server‘ on 15 April 2016
• EGA-TraIT ELIXIR implementation study: Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data, Chao Zhang et al., F1000, 2017
• Member of ELIXIR Galaxy Working Group
• Co-organizer of training workshops:
  • ELIXIR European  Galaxy Developer Workshop, Strasbourg, January 2017
  • ELIXIR/GOBLET/GTN hackathon for Galaxy material reuse, Cambridge, May 2017
• Members of the DTL Galaxy WG  contribute their  Galaxy expertise by acting as trainers in ELIXIR  Galaxy Training events and hackathons
• ELIXIR-NL will deliver a Galaxy course for ELIXIR in 2018
• ELIXIR-NL participates the Galaxy use case for ELIXIR 2018-2022 (ELIXIR use cases)

Galaxy Interest Group members

• Saskia Hiltemann – ErasmusMC
• Leon Mei – LUMC
• Cico Zhang – VU
• Andrew Stubbs – ErasmusMC
• David van Zessen – ErasmusMC
• Youri Hoogstrate – ErasmusMC
• Rita Azevedo – Lygature
• Celia van Gelder – DTL and BioSB
• Niek Bosch – SURFsara
• Johan den Dunnen – LUMC
• Ruben Vorderman – LUMC
• Rob Hooft – DTL
• Sanne Abeln – VU
• Ruud Ross – SURFsara
• Peter Horvatovich – University of Groningen
• Erikjan Bogaard – SURFsara
• Irene Nooren – SURFsara
• Christian Rausch – NKI
• Remond Fijneman – NKI