German Network for Bioinformatics Infrastructure

de.NBI - German Network for Bioinformatics Infrastructure

Established	2015
Mission	Big Data Exploitation in Life Science
Coordinator	Alfred Pühler
Members	250
Location	Bielefeld, Berlin, Bochum, Borstel, Braunschweig, Bremen, Dortmund, Dresden, Freiburg, Gatersleben, Gießen, Halle (Saale), Hamburg, Heidelberg, Jena, Jülich, Konstanz, Leipzig, Magdeburg, Munich, Rostock, Saarbrücken, Tübingen
Website	www.denbi.de

The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing bioinformatics services to users in life sciences research and biomedicine in Germany and Europe. The partners organize training events, courses and summer schools on tools, standards and compute services provided by de.NBI to assist researchers to more effectively exploit their data .

History

In May 2013, the announcement of funding guidelines for a German Network for Bioinformatics Infrastructure (de.NBI) was published by the German Federal Ministry of Education and Research (BMBF). The aim of this announcement was to establish an infrastructure in Germany that will provide solutions to the ‘Big Data Problem’ in life science by means of bioinformatics services and training. A second announcement of funding guidelines for de.NBI partner projects was published in November 2015. The de.NBI program was launched by the BMBF in March 2015, and the partner projects started their work in November 2016. In addition, the ELIXIR Node in Germany is run by de.NBI since August 2016 .

The first coordinator of the project and Head of the German ELIXIR Node is Alfred Pühler.

Organisation

Since November 2016, the de.NBI network consists of the eight interconnected centers including nearly 40 research, service and infrastructure groups with about 250 bioinformaticians . In addition, it is possible to apply for an associated partnership within de.NBI.

• Heidelberg Center for Human Bioinformatics (HD-HuB)
  • Members: The German Cancer Research Center (DKFZ, research groups Boutros, Brors, Buchhalter), European Molecular Biology Laboratory (EMBL, research groups Bork, Huber, Korbel), Heidelberg University (research groups Rohr, Russell, Erfle), Charité Berlin (Research groups Eils, Ishaque) and Saarland University (Research group Walter)
  • Topic: Human Bioinformatics, e.g. Exome, Genomics, Transcriptomics, Metagenomics, Phenotyping, Bioimaging, Epigenetics and Cloud Computing
  • Associated Partner: Division of Computational Genomics and System Genetics (Dr. Oliver Stegle, DKFZ)

• Bielefeld-Gießen Resource Center for Microbial Bioinformatics (BiGi):
  • Members: Bielefeld University, University of Gießen and Otto von Guericke University Magdeburg
  • Topic: Microbial Bioinformatics, e.g. Genomics, Transcriptomics, Metagenomics, Proteomics, Metaproteomics, Metabolomics and Cloud Computing

• Bioinformatics for Proteomics (BioInfra.Prot):
  • Members: Ruhr University Bochum ("Medical Bioinformatics" research unit of the Medizinisches Proteom-Center), Leibniz Institute for Analytical Sciences ISAS e.v. Dortmund ("Department of Bioanalytics"), Research Center Borstel and Max Planck Institute of Molecular Cell Biology and Genetics
  • Topics: Proteomics and Lipidomics

• Center for Integrative Bioinformatics (CIBI):
  • Members: Free University of Berlin, University of Tübingen, University of Konstanz, Leibniz Institute of Plant Biochemistry Halle (Saale) and Max Planck Institute of Molecular Cell Biology and Genetics
  • Topic: Bioinformatics workflow management system, e.g. for Genomics, Proteomics, Metabolomics, Bioimaging, Deep learning and Machine learning

• RNA Bioinformatics Center (RBC):
  • Members: University of Freiburg, University of Leipzig, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Leibniz-Institut für Alternsforschung Jena and University of Rostock,
  • Topic: RNA bioinformatics, e.g. Transcriptome analysis, RNA structure analysis, prediction of ncRNA targets, definition and classification of RNA transcripts and the analysis of protein-RNA interaction

• German Crop BioGreenformatics Network (GCBN):
  • Members: Leibniz Institute of Plant Genetics and Crop Plant Research at Gatersleben (IPK, BIT, Uwe Scholz), Helmholtz Zentrum München (HMGU, PGSB, Klaus Mayer) and Forschungszentrum Jülich (FZJ, IBG-2 Plant Sciences, Björn Usadel).
  • Topic: Plant Bioinformatics, e.g. Genomics, Genome annotation, Phenotyping, Plant Databases

• Center for Biological Data (BioData):
  • Members: Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig University of Technology, Jacobs University Bremen, University of Bremen, University of Hamburg
  • Topics: Databases

• de.NBI Systems Biology Service Center (de.NBI-SysBio):
  • Members: Heidelberg Institute for Theoretical Studies, Heidelberg University, University of Rostock and Max Planck Institute for Dynamics of Complex Technical Systems
  • Topics: Systems Biology and Data management

• Associated Partners: University of Kiel, University of Jena
  • Topics: Metabolomics, Phylogenetics, Human Bioinformatics, Genomics for Eukaryotes

Bioinformatics resources

The de.NBI network offers a large portfolio of resources for the German and international life science community. It mainly includes databases, bioinformatics tools and hardware based on a federated cloud system.

Databases

de.NBI develops and maintains the five large databases SILVA, PANGAEA, BacDive, ProteinPlus and BRENDA. They provide access to ribosomal RNA genes from all three domains of life (SILVA), georeferenced data from earth system research (PANGAEA), strain-linked information on the different aspects of bacterial and archaeal biodiversity (BacDive), protein structures (ProteinPlus) and to comprehensive enzyme information (BRENDA).

Tools

de.NBI develops and supplies about 100 bioinformatics tools for the German and global life sciences community, e.g. Galaxy (computational biology)/useGalaxy.eu (Workflow engine for all Freiburg RNA Tools), EDGAR (Comparative Genome Analyses Plattform), KNIME (Workflow engine), OpenMS (Open-source software C++ library for LC/MS data management and analyses), SeqAN (Open source C++ library of efficient algorithms and data structures), PIA (toolbox for MS based protein inference and identification analysis), Fiji (software) (Image processing package), MetFrag (in silico fragmenter combines compound database searching and fragmentation prediction for small molecule identification from tandem mass spectrometry data), COPASI (Open source software application for creating and solving mathematical models of biological processes), SIAMCAT (Framework for the statistical inference of associations between microbial communities and host phenotypes), e!DAL - PGP (Open source software framework to publish and share research data), MGX (Metagenome analysis) and many more.

de.NBI tools are also registered and searchable in the ELIXIR Tools and Data Services Registry that provides more information in a standardized format.

Hardware

de.NBI develops and maintains a cloud system (de.NBI cloud) started in 2016. It is a collaboration project between the universities of Bielefeld, Freiburg, Gießen, Heidelberg and Tübingen. The whole system is accessible through a single sign-on (SSO) via the central de.NBI Cloud Portal and is based on the ELIXIR Authentication and Authorization Infrastructure (ELIXIR AAI). It comprises more than 15,000 compute cores and 5 PB of storage capacity in April 2018. During 2018, the storage capacity was increased to 38 PB (Status February 2019).

Training

Different types of training activities are supported and organized by de.NBI. First of all, the summer schools provide training courses for undergraduate and graduate students in specific topics related to one or several de.NBI centers. The respective centers organize tool-specific training. These trainings are attached to existing conferences or organized independently. In addition, online training was introduced on the de.NBI website in 2016. In 2017, online hackathons for different software packages and webinars have been established by the centers RBC and CIBI.

In 2015, 17 training courses with 329 participants were organized by de.NBI. In 2016, the network has organized 40 training courses with 882 participants. For 2017, the network could further increase the number of courses and participants (69 training courses with 1489 participants). In 2018, the de.NBI training program reached the plateau phase with 77 training courses and 1520 participants.

de.NBI Summer Schools

• September 2015: The first de.NBI Summer School was organized by the Bielefeld-Gießen (BiGi) Center for Microbial Bioinformatics, RBC and de.NBI-SysBio. This de.NBI Late Summer School was focused on the workflow from genome assembly to genome and transcriptome analysis.
• September 2016: The second de.NBI summer school was organized by BioInfraProt, CIBI and BiGi at Dagstuhl and focused on proteomics and the analysis of mass spectrometry data.
• September 2017: The third de.NBI summer school was organized by all RBC partners. It focused on “Computational genomics and RNA biology”.
• September 2018: The fourth summer school was organized on "Riding the Data Life Cycle" by BioData, GCBN and de.NBI-SysBio.
• September 2019: The fifth summer school will be organized by the service centers GCBN, BioData, de.NBI-SysBio and BioInfra.Prot. The topic will be "(Bio)Data Science" and it will take place in Gatersleben

Additional de.NBI Schools

In addition, de.NBI organized the first cloud summer school in June 2017 and supported a winter school on metabolics in March 2018.

External links

• Official website
• Official Twitter channel
• Official Youtube channel