German Network for Bioinformatics Infrastructure: Difference between revisions

Revision as of 15:51, 18 March 2019

Revision as of 10:28, 27 March 2019

Line 1:

{{Infobox institute|name=de.NBI - German Network for Bioinformatics Infrastructure|image=[[File:De.NBI_Logo.svg|de.NBI - German Network for Bioinformatic Infrastructure|240px]]|established=2015|website={{URL|https://www.denbi.de}}|head=[[Alfred Pühler]]<ref>{{Cite news|url=https://www.denbi.de/organisation/de-nbi-coordinator|title=de.NBI Coordinator|last=|first=|date=|work=|access-date=2019-02-07|archive-url=|archive-date=|dead-url=}}</ref>|head_label=Coordinator|mission=Big Data Exploitation in Life Science|num_members=250|___location=[[Bielefeld]], [[Berlin]], [[Bochum]], {{ill|Borstel (Sülfeld)|de|lt=Borstel}}, [[Braunschweig]], [[Bremen]], [[Dortmund]], [[Dresden]], [[Freiburg]], [[Gatersleben]], [[Gießen]], [[Halle (Saale)]], [[Hamburg]], [[Heidelberg]], [[Jena]], [[Jülich]], [[Konstanz]], [[Leipzig]], [[Magdeburg]], [[Munich]], [[Rostock]], [[Saarbrücken]], [[Tübingen]]}}

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 <ref name="autogenerated2">[https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbx040/3738742 Bioinformatics in Germany: toward a national-level infrastructure by Andreas Tauch & Arwa Al-Dilaimi]</ref>.

== 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<ref>[https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbx040/3738742 Bioinformatics in Germany: toward a national-level infrastructure by Andreas Tauch & Arwaname="autogenerated2" Al-Dilaimi]</ref>. In addition, the [[ELIXIR]] Node in Germany is run by de.NBI since August 2016 <ref>[https://www.elixir-europe.org/news/elixir-board-meeting-2016-spring-session ELIXIR Board Meeting Spring 2016]</ref><ref>[https://www.elixir-europe.org/news/germany-joins-elixir Germany joins ELIXIR]</ref><ref>[https://www.elixir-europe.org/about-us/who-we-are/nodes/germany. ELIXIR Germany]</ref>.

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

Line 20:

**Topic: Microbial Bioinformatics, e.g. [[Genomics]], [[Transcriptomics]], [[Metagenomics]], [[Proteomics]], [[Metaproteomics]], [[Metabolomics]] and [[Cloud Computing]]

*Bioinformatics for Proteomics (BioInfra.Prot)<ref name="autogenerated1">[https://www.ncbi.nlm.nih.gov/pubmed/28606611 BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication by Turewicz et al., 2017]</ref>:

**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]]

Line 54:

=== 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)<ref>[https://www.ncbi.nlm.nih.gov/pubmed/28554830 RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation by Backofen et al., 2017]</ref>, EDGAR (Comparative Genome Analyses Plattform)<ref>[https://www.ncbi.nlm.nih.gov/pubmed/28705636 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]</ref>, [[KNIME]] (Workflow engine)<ref>[https://www.ncbi.nlm.nih.gov/pubmed/28757290 KNIME for reproducible cross-___domain analysis of life science data by Fillbrunn et al., 2017]</ref>, [[OpenMS]] (Open-source software C++ library for LC/MS data management and analyses)<ref>[https://www.ncbi.nlm.nih.gov/pubmed/28559010 OpenMS - A platform for reproducible analysis of mass spectrometry data by Pfeuffer et al., 2017]</ref>, [[SeqAN]] (Open source [[C++]] library of efficient algorithms and data structures)<ref>[https://www.ncbi.nlm.nih.gov/pubmed/28888961 The SeqAn C++ template library for efficient sequence analysis: A resource for programmers by Reinert et al., 2017]</ref>, PIA (toolbox for MS based protein inference and identification analysis)<ref>[https://www.ncbi.nlm.nih.gov/pubmed/28606611 BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication by Turewicz et al.,name="autogenerated1" 2017]</ref>, [[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)<ref>[https://www.ncbi.nlm.nih.gov/pubmed/28554829 Bioinformatics can boost metabolomics research by Meier et al., 2017]</ref>, [[COPASI]] ([[Open-source software|Open source]] software application for creating and solving [[mathematical models]] of [[biological processes]])<ref>[https://www.ncbi.nlm.nih.gov/pubmed/28655634 COPASI and its applications in biotechnology. Bergmann et al., 2017]</ref>, [[SIAMCAT]] (Framework for the statistical inference of associations between [[microbial communities]] and host [[phenotypes]]), [[The e!DAL Plant Phenomics and Genomics Research Data Repository|e!DAL - PGP]] (Open source software framework to publish and share research data), MGX ([[Metagenome]] analysis)<ref>[https://www.ncbi.nlm.nih.gov/pubmed/29690922 Flexible metagenome analysis using the MGX framework. Jaenicke et al., 2018]</ref> 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.