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{{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|access-date=2019-02-07}}</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
== 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 name="autogenerated2" />
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
*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|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):<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>
▲*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]]
*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 [[Primary transcript|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
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=== Databases ===
de.NBI develops and maintains the five large databases [[SILVA]],<ref>[https://www.ncbi.nlm.nih.gov/pubmed/28648396 25 years of serving the community with ribosomal RNA gene reference databases and tools by Glöckner et al., 2017]</ref>
=== 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>
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.<ref>[https://www.nature.com/articles/nrg.2017.113 Cloud computing for genomic data analysis and collaboration by Ben Langmead & Abhinav Nellore, 2018]</ref>
== Training ==
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=== 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
*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.<ref>[https://www.denbi.de/training-archive-sorted-according-by-date/2016/180-de-nbi-summer-school-2016-from-big-data-to-big-insights de.NBI Summer School 2016]</ref>
*September 2017: The third de.NBI summer school was organized by all RBC partners. It focused on
*September 2018: The fourth summer school was organized on "Riding the Data Life Cycle" by BioData, GCBN and de.NBI-SysBio.<ref>[https://www.denbi.de/training-archive-sorted-according-by-date/2018/122-de-nbi-summer-school-2018-riding-the-data-life-cycle de.NBI Summer School 2018]</ref>
*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 <ref>{{Cite web|url=https://www.denbi.de/training/528-de-nbi-summer-school-2019-bio-data-science|title=de.NBI Summer School 2019 - (Bio)Data Science|website=www.denbi.de|access-date=2019-01-24}}</ref>
===Additional de.NBI Schools ===
In addition, de.NBI organized the first cloud summer school in June 2017<ref>[https://www.denbi.de/training-archive-sorted-according-by-date/2017/219-de-nbi-summer-school-on-cloud-computing-for-bioinformatics de.NBI Cloud Summer School 2017]</ref> and supported a winter school on metabolics in March 2018.<ref>[https://www.denbi.de/training-archive-sorted-according-by-date/2018/87-de-nbi-winter-school-on-computational-metabolomics de.NBI Winter School 2018]</ref>
==References==
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* {{Official website|http://www.denbi.de/}}
* [https://twitter.com/denbiOffice Official Twitter channel]
* [https://www.youtube.com/channel/UCgZ5PU3CyD4c8yxxzJi130g Official Youtube channel]
{{Bioinformatics}}
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