German Network for Bioinformatics Infrastructure

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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 [1].

History[edit]

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[2]. In addition, the ELIXIR Node in Germany is run by de.NBI since August 2016 [3][4][5].

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

Organisation[edit]

Since November 2016, the de.NBI network consists of the eight interconnected centers including nearly 40 research, service and infrastructure groups with about 150 bioinformaticians [6]. In addition, it is possible to apply for an associated partnership within de.NBI.

Bioinformatics resources[edit]

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

Databases[edit]

de.NBI develops and maintains the five large databases SILVA[8], PANGAEA[9], BacDive[10], ProteinPlus[11] and BRENDA[12]. 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[edit]

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)[13], EDGAR (Comparative Genome Analyses Plattform)[14], KNIME (Workflow engine)[15], OpenMS (Open-source software C++ library for LC/MS data management and analyses)[16], SeqAN (Open source C++ library of efficient algorithms and data structures)[17], PIA (toolbox for MS based protein inference and identification analysis)[18], 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)[19], COPASI (Open source software application for creating and solving mathematical models of biological processes)[20], SIAMCAT (Framework for the statistical inference of associations between microbial communities and host phenotypes), e!DAL - PGP (Open source software framework for publishing and sharing research data), MGX (Metagenome analysis)[21] 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[edit]

de.NBI develops and maintains a cloud system (de.NBI cloud) started in 2016[22]. 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 (Status April 2018).

Training[edit]

Different types of training activities are supported and organzied 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 introducted 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).

de.NBI Summer Schools[edit]

  • 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[23].
  • 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[24].
  • September 2017: The third de.NBI summer school was organized by all RBC partners. It focused on “Computational genomics and RNA biology”[25].
  • September 2018: A fourth summer school will be organized on "Riding the Data Life Cycle" by BioData, GCBN and de.NBI-SysBio[26].

Additional de.NBI Schools[edit]

In addition, de.NBI organized the first cloud summer school in June 2017[27] and supported a winter school on metabolics in March 2018[28].

References[edit]

  1. ^ Bioinformatics in Germany: toward a national-level infrastructure by Andreas Tauch & Arwa Al-Dilaimi
  2. ^ Bioinformatics in Germany: toward a national-level infrastructure by Andreas Tauch & Arwa Al-Dilaimi
  3. ^ ELIXIR Board Meeting Spring 2016
  4. ^ Germany joins ELIXIR
  5. ^ ELIXIR Germany
  6. ^ de.NBI – Netzwerk für Bioinformatik-Infrastruktur wird weiter ausgebaut by Oliver Kohlbacher
  7. ^ BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication by Turewicz et al., 2017
  8. ^ 25 years of serving the community with ribosomal RNA gene reference databases and tools by Glöckner et al., 2017
  9. ^ Terminology supported archiving and publication of environmental science data in PANGAEA by Diepenbroek et al., 2017
  10. ^ Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase. by Reimer et al., 2017
  11. ^ From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library by Bietz et al., 2017
  12. ^ The BRENDA enzyme information system-From a database to an expert system. by Schomburg et al., 2017
  13. ^ RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation by Backofen et al., 2017
  14. ^ A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies by Yu et al., 2017
  15. ^ KNIME for reproducible cross-domain analysis of life science data by Fillbrunn et al., 2017
  16. ^ OpenMS - A platform for reproducible analysis of mass spectrometry data by Pfeuffer et al., 2017
  17. ^ The SeqAn C++ template library for efficient sequence analysis: A resource for programmers by Reinert et al., 2017
  18. ^ BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication by Turewicz et al., 2017
  19. ^ Bioinformatics can boost metabolomics research by Meier et al., 2017
  20. ^ COPASI and its applications in biotechnology. Bergmann et al., 2017
  21. ^ Flexible metagenome analysis using the MGX framework. Jaenicke et al., 2018
  22. ^ Cloud computing for genomic data analysis and collaboration by Ben Langmead & Abhinav Nellore, 2018
  23. ^ de.NBI Summer School 2015
  24. ^ de.NBI Summer School 2016
  25. ^ de.NBI Summer School 2017
  26. ^ de.NBI Summer School 2018
  27. ^ de.NBI Cloud Summer School 2017
  28. ^ de.NBI Winter School 2018

External links[edit]