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Galaxy Europe / Freiburg

Our Services

The Freiburg Galaxy Team is offering several services to enable reproducible and accessible research for everyone:

The European Galaxy Server

Our flagship service is the European Galaxy server UseGalaxy.eu which is the biggest Galaxy instance in Europe, and one of the biggest worldwide.

With free registration to the UseGalaxy.eu server we provide you an easy access to:

  • Free compute and storage resources (250 GB per user)
  • Databases (e.g. EMBL-EBI ENA, NCBI SRA, Ensembl, UCSC, UniProt, and many organism-specific databases)
  • More than 2500 different, well-documented and constantly maintained scientific tools
  • Puplic HTS data analyis workflows
  • Reference genomes
  • Visualizations

This effort, combined with our community-maintained workflows and our in-depth Galaxy training material, makes up for a truly productive work experience. We believe in enabling everyone to perform reproducible science.

Simply upload your data from your computer or via FTP and get started with your data analysis! If you have one, you can log in with your ELIXIR AAI!

Galaxy Subcommunities

We want to encourage scientists to join forces and foster subcommunities by giving them a common place, a Galaxy subdomain page. Every subdomain comes with its own welcome page, specific tool box, example data, workflows, and training material. More information can be found on the https://galaxyproject.eu webpage.

Training

We are passionate about training! Our team wants to support researchers to take part in their own data analyses by educating them in e.g. big data analysis, programming, data management, and Galaxy server administration. We believe that sharing of knowledge and the open science movement are the key points in future.

Workshop picture Workshop picture Workshop picture

Galaxy Training Workshops

Locally in Freiburg, we offer twice per year a free full-week hands-on high-throughput sequencing (HTS) data analysis workshop. A typical workshop schedule for a week looks as follows:

  • Monday: Introduction to Galaxy and HTS data analysis
  • Tuesday: Quality control, IGV, ChIP-Seq data analysis
  • Wednesday: RNA-Seq data analysis
  • Thursday: HiC data analysis, Methyl-C data analysis
  • Friday: Bring your own data, exercises

We have more training material for various topics to teach, e.g. Transcriptomics, Metabolomics, Metagenomics, Proteomics, Genome Annotation, Variant Calling, among others. Topics usually are selected from desired topics of the applicants.

All workshops are announced on our events page. Registrations are possible through our website after the announcement.

We and other members of the Galaxy training network (GTN) are giving training courses around the world for data analysis, and for developers and administrators. Check the website of the main Galaxy project as well as the de.NBI website for de.NBI courses

Galaxy Training Material

The Freiburg Galaxy Team is a very active contributor to the community-driven development of GTN Galaxy training material. All of this material is online, and freely accessible for everyone at https://training.galaxyproject.org.

We provide more than 170 tutorials designed for both self-training and workshops for Galaxy users, developers, and administrators. Each tutorial comes with:

  • Introduction of the topic with information and theoretical background as slide show
  • Step-by-step instruction of the data analysis guiding through the analysis workflow
  • Real-world example data sets stored in our data library and on zenodo
  • Interactive tour

We also provide the technical support with tools, data, virtualized instances, … . So you can use this material on our Galaxy instance or you can spin up your own Galaxy server!

If you want to offer a training course to other researchers, we do maintain a set of material for “train the trainers” and we are happy to share our knowledge and experience in this area with you. We are also providing training material for Galaxy developers and admins, as well as the possibility to use iPython notebooks and jupyter directly in Galaxy. If you want to give a Galaxy training, you can request a TIaaS on our webpage to get dedicated resources for it.

Collaboration/Contribution Fests

Contribution fests (or hackathons) are short events (usually few days) where people join forces to develop new, or improving existing techniques, tools, training materials, etc.

We organize numerous hackathons per year on site or online, in close cooperation with de.NBI, ELIXIR, and the Galaxy community.

Training Infrastructure-as-a-Service (TIaaS)

We are very excited to offer a special service for Galaxy trainers: Training infrastructure as a Service!

If you have a training event planned, get in touch with us and we will allocate you completely dedicated compute resources for the duration of your training. Your users’ jobs on usegalaxy.eu will be directed to these resources and are free from the regular job queue. No setup, no queueing times, no hassle. Apply here.

Just drop us a mail and concentrate on the important things during your training.

Virtualization for Sensitive Data

For sensitive (biomedical) data and users with internet limitations, we offer virtualizations for Galaxy and many other tools. Our aim is to enable all researchers easy access to tools, wherever they need them.

Virtualized deployments

Spending valuable time in compilation hell or frustrating conversations with cluster admins because tools are not available should not be a problem nowadays.

Therefore, we are leading the Bioconda and BioContainers projects, which together form the best stack for reproducible science ever.

Virtualization of Galaxy and customized flavors

With the Galaxy Docker project, we offer a “Galaxy in a box”. It is a production-ready, scalable Galaxy instance, complete with all goodies included that makes Galaxy so popular.

To meet custom need, we also maintain and offer these Galaxy instance for download in a variety of different “flavors”. For example:

Data analysis

You don’t have time to analyse your data or have a very specialized question? Our team consists of experts in different fields (RNA-Seq, ChIP-Seq, Metagenomics, etc).

We are eager to assist you and solve your scientific question with you! We have a long track record of solving advance NGS analysis tasks in tight collaborations with world-wide community of experimental groups.

Tool integration

Do you have a scientific question and can’t find the appropriate tool for it? We will put ideas into code, and then the code into Galaxy, so everyone can use it!

"Tools available on usegalaxy.eu"

We are also maintaining, adapting and optimizing existing Galaxy tools in collaboration with the Galaxy community, for example as part of the Intergalactic Utilities Commission.

Scientific computing cloud

As part of the German Network for Bioinformatics Infrastructure de.NBI, we maintain a scientific cloud for our users.

If you have special needs or require a virtualized computing environment for your research, get in touch with us and we will work with you to develop a personalised solution.