The network provides 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.
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.
[7] The de.NBI network consists of the eight interconnected centers and one coordination unit including 40 research, service and infrastructure groups with about 250 bioinformaticians involved.
The de.NBI network offers a large portfolio of resources for the German and international life science community.
[14] 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).
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),[15] EDGAR (Comparative Genome Analyses Plattform),[16] KNIME (Workflow engine),[17] OpenMS (Open-source software C++ library for LC/MS data management and analyses),[18] SeqAN (Open source C++ library of efficient algorithms and data structures),[19] PIA (toolbox for MS based protein inference and identification analysis),[9] 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),[20] COPASI (open source software application for creating and solving mathematical models of biological processes),[21] 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),[22] ASA³P (automated WGS analysis of bacterial cohorts),[23] Bakta[24] (annotation of bacterial genomes and plasmids) and many more.
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.
[27] 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.