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 was published by the German Federal Ministry of Education and Research. 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 partners since August 2016. The first coordinator of the de.NBI project is Alfred Pühler. The head of the German ELIXIR Node is Andreas Tauch.
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 as Service and Training Partner or as Training Partner within de.NBI.
The de.NBI network is open for further partners which like to take part in the network. These partners are called Associated Partners and are divided into two groups: Associated Service and Training Partners or Associated Training Partners. Associated Service und Training Partners offer at least one service and training course while Associated Training Partners only provide at least one training course to the de.NBI network. As of February 2020 the de.NBI network has six Associated Service and Training Partners and two Associated Training Partners. These partners cover topics in Metabolomics, Phylogenetics, human bioinformatics, eukaryotic genomics, metaproteomics, NGS, 16S rRNA amplicon and single-cell analysis as well as the general IT topics Linux and scripting languages.
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, georeferenced data from earth system research, strain-linked information on the different aspects of bacterial and archaeal biodiversity, protein structures and to comprehensive enzyme information.
Tools
de.NBI develops and supplies about 100 bioinformatics tools for the German and global life sciences community, e.g. Galaxy /useGalaxy.eu, EDGAR, KNIME, OpenMS, SeqAN, PIA, Fiji , MetFrag, COPASI, SIAMCAT, e!DAL - PGP, MGX 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 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 via the central de.NBI Cloud Portal and is based on the ELIXIR Authentication and Authorization Infrastructure. The de.NBI cloud comprises more than 27,000 computing cores and 41 petabytes of storage capacity.
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. A total of 17 training courses with 329 participants were organised by de.NBI in 2015. In 2016 the network organised 40 training courses with 882 participants. For 2017, the network was able to further increase the number of courses and participants. In 2018, the de.NBI training program reached 1520 participants with 77 trainings. In 2019, de.NBI offered 79 training courses with 1586 participants.
de.NBI Summer Schools
Next to the training courses de.NBI offers an annual Summer School to cover a distinct topic in more detail. The first Summer School was held in 2015 by the Service Centers Bielefeld-Gießen Center for Microbial Bioinformatics, RBC and de.NBI-SysBio and was focused in the workflow from genome assembly to genome and transcriptome analysis. In the following years the Summer Schools were organized by the Service Centers BioInfraProt, CIBI and BiGi as well as BioData, GCBN and de.NBI-SysBio and held at different locations throughout Germany. The Summer Schools covered the topics proteomics and mass spectrometry data, Computational genomics and RNA biology, Research Data Management and Data Science. The de.NBI Summer School 2020 will be organized by BiGi and cover the topic of metagenomics.
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. For pupils interested in bioinformatics, the BioBYTE summer school at the University of Halle, also supported by de.NBI, offers an ideal opportunity to get to know the diversity of bioinformatics.
