Galaxy and its community
The Freiburg Galaxy team is highly involved in many projects related to the global Galaxy community:
- Galaxy core development and maintenance.
- Lead of the European Galaxy Server with 2,700 bioinformatics tools and access to large compute infrastructures.
- Tool integration into Galaxy and their maintenance (update to newstes version and version tracking) through:
- Galaxy Training Material, a collection of Galaxy-related tutorials and its infrastructure, developed and maintained by the community.
- Galaxy Docker, to provide an easy distributable full-fledged Galaxy installation.
- Development and maintenance of different Galaxy flavours.
- Jupyter integration into Galaxy.
- GalaxyP, a Galaxy community dedicated to developing tools, workflows and training material for proteomic research.
- Galaxy Genome Annotation (GGA), a group of projects focused on supporting genome annotation inside Galaxy.
A successful Horizon grant from the European Commission allows us together with 15 European partners to leverage a federated open access computational infrastructure through Galaxy as a gateway for data resources, tools and applications by the FAIR principle. The project will start in summer 2022 and is the first time a direct funding for the European Galaxy community, which will provide more resources for users (via Galaxy and Coud APIs) to all users in Europe - national Galaxy servers included.
Bioconda and BioContainers
Spending valuable time in compilation/installation should not be a problem nowadays. Therefore, the Freiburg Galaxy team is leading the Bioconda and BioContainers projects, which together form the best stack for reproducible science ever.
Bioconda is a channel for the conda package manager specializing in bioinformatics with around 9,000 bioinformatics packages ready to use with
BioContainers is an open source and community-driven framework which provides system-agnostic executable environments for bioinformatics software, with around 70,000 containers ready to use.
The Freiburg Galaxy team is part of de.NBI, the German Network for Bioinformatics Infrastructure, through the RNA Bioinformatics Center. de.NBI is a national infrastructure project providing training, cooperations & cloud computing through the de.NBI cloud with substantial compute and storage resources for bioinformatic use-cases.
ELIXIR unites Europe’s leading life science organizations in managing and safeguarding the increasing volume of data being generated by publicly funded research. Via de.NBI, the Freiburg Galaxy team is also involved in ELIXIR, as technical coordinator for the German node.
The Freiburg Galaxy team is also co-leading the ELIXIR Galaxy Community, particularly with the maintenance of European Galaxy instance (usegalaxy.eu). Monthly meetings, webinars and various activities are organised around the ELIXIR Galaxy Community.
The team has participated in several ELIXIR Implementation Studies since 2018:
- ELIXIR Implementation Study - Galaxy Community, in 2018, with a focus on setting up the newly established ELIXIR Galaxy Community
- Expanding the Galaxy: meeting (the needs of) ELIXIR Communities, 2019
- Strengthen Data Management in Galaxy, 2021
- Reference hCNV datasets, use-case workflows and benchmarking, 2021
- Beacon and beyond — Implementation-driven standards and protocols for CNV discovery and data exchange, 2021
- Deploying Reproducible Containers and Workflows Across Cloud Environments, 2021
The European Open Science Cloud (EOSC), and EOSC-Life in particular, brings together the 13 Life Science ‘ESFRI’ research infrastructures to create an open, digital and collaborative space for biological and medical research. The project will publish ‘FAIR’ data and a catalog of services provided by participating RIs for the management, storage and reuse of data in the European Open Science Cloud.
AgroServ supports research and innovation by providing customized and integrated RI services in view of achieving a sustainable and resilient agriculture and supporting agroecological transitions. This aim will take place in line with the One-Health approach, with particular regard to threats and risks on agroecosystems and to enhance new agroecological practices and their socio-economic benefits. Through the AgroServ Data Portal, Galaxy tools and workflows will be provided. The project will start in 2022.
European Grid Infrastructure - Advanced Computing for EOSC (EGI-ACE) is a 30-month project coordinated by the EGI Foundation with a mission to empower researchers from all disciplines to collaborate in data- and compute-intensive research through free-at-point-of-use services.
The objective of the Horizon 2020 EU project HealthyCloud is to generate a number of guidelines, recommendations and specifications that will enable distributed health research across Europe in the form of a Ready-to-implement Roadmap.
The Pandemic Research Infrastructure (PaRI) project brings together the needs, interests and resources to create e-infrastructure to support research excellence in the Nordic region.
Data Management Projects
The aim of the project BioDATEN (Bioinformatics DATa ENvironment) is to provide the foundation of a Science Data Centre in close cooperation with the life science communities such as research groups and infrastructure providers such as libraries and computing centres.
The NFDI DataPLANT consortium provides services to complement existing infrastructures and focuses on supporting and easing the processes of complete and meaningful research metadata management in plant sciences.
ELIXIR-CONVERGE will deliver the provisioning, across Europe, of distributed local support for data management. This will be based on a toolkit for researchers that enables lifecycle management for their research data, in compliance with international standards.
The goal of the MIRACUM (Medical Informatics for Research and Care in University Medicine) project is to foster IT innovations for healthcare research and medical care. The project aims for accessibility and usability of clinical data, imaging data and data from molecular and genomics analyses at local and across different locations through a modular, scalable and federated data integration center. Taking advantage of digitalization in medicine, linking data and generating medical knowledge is required for a better, data-based healthcare delivery system. MIRACUM unites 10 university hospitals, 2 universities, and an industrial partner from 7 German federal states.
As part of the MTB (Molecular Tumor Board) use case, the Freiburg Galaxy team is developing and maintaining together with Melanie Börries the EXOM-seq pipeline in Galaxy.
The BeYond-COVID project aims to make COVID-19 data accessible to scientists in laboratories but also to anyone who can use it, such as medical staff in hospitals or government officials. Going beyond SARS-CoV-2 data, the project will provide a framework for making data from other infectious diseases open and accessible to everyone.
The Collaborative Research Centre 1425 - “Heterocellular Nature of Cardiac Lesions: Identities, Interactions, Implications” brings together scientists working in cardiac research.
As part of the Collaborative Research Centre 992 - “Medical Epigenetics”, the Freiburg Galaxy team is helping researchers to analyse their epigenetic data. In this framework, we are developing and maintaining deepTools and HiCExplorer together with the group of Thomas Make from MPI-IE.
COST Action CA16212
Plants are vital to human life and health and are essential to mitigate the effects of climate change. In this COST Action for Impact of Nuclear Domains On Gene Expression and Plant Traits, the Freiburg Galaxy team is helping to connect the European plant community and foster FAIR data principles.
HiCExplorer is a set of programs to process, normalize, analyze and visualize Hi-C data. It addresses the common tasks of Hi-C analysis from processing to visualization. The Freiburg Galaxy team is involved in the maintenance and new development of HiCExplorer. You can access HiCExplorer via https://hicexplorer.usegalaxy.eu.
deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. deepTools is the Swiss Army Knife of NGS processing and is cited more than 3,000 times. It is of course part of the European Galaxy server and was used more than 230,000 times.
Capacity Building Projects
The Gallantries project aims to increase bioinformatics and core data analysis skills in the field of life sciences across Europe.
Open Life Science
Open Life Science (OLS) is a 16-week long mentoring & training program for Open Science ambassadors. Currently the call for the 4th round - OLS-4 - is running.
In the Street Science community, we want to make science tangible & accessible by bringing it to the “street” via open science workshops. These workshops are an excuse to meet, discuss, educate and develop ideas in a neutral, open, noncompetitive and not-for-profit environment.