German Network for Bioinformatics Infrastructure: Difference between revisions

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{{Infobox institute

{{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]]}}

| 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]] until 2021<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

{{Infobox institute|name=de.NBI -___location 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 supportedinitiated by the [[Federal Ministry of Education and Research]] providingfunding 2015-2021. 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.<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> From 2022, the network will be integrated into [[Forschungszentrum Jülich]].<ref>{{Cite journal |last=Pühler |first=A. |date=2021 |title=Verstetigung des de.NBI-Netzwerks |url=https://doi.org/10.11576/biuz-4634 |journal=Biologie in unserer Zeit |volume=51 |issue=3 |pages=221–222|doi=10.11576/biuz-4634 }}</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 name="autogenerated2" /> In additionAugust 2016, theGermany joined [[ELIXIR]], Nodethe inEuropean Germanylife-sciences Infrastructure for biological Information, with the German [[ELIXIR]] Node (ELIXIR-DE Germany) isbeing run by de.NBI partners 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 de.NBI project was [[Alfred Pühler]] until 2021. The head of the German ELIXIR Node is Andreas Tauch.<ref>{{Cite web|last=|first=|date=|title=de.NBI Quarterly Newsletter 2/20|url=https://www.denbi.de/images/Downloads/Newsletter/quarterly_newsletter_20.pdf|archive-url=|archive-date=|access-date=2020-06-15|website=de.NBI}}</ref>

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

== Organisation ==

Since November 2016, theThe de.NBI network consists of the eight interconnected centers includingand nearlyone coordination unit including 40 research, service and infrastructure groups with about 250 bioinformaticians involved.<ref>[https://www.gesundheitsindustrie-bw.de/de/fachbeitrag/aktuell/denbi-netzwerk-fuer-bioinformatik-infrastruktur-wird-weiter-ausgebaut de.NBI – Netzwerk für Bioinformatik-Infrastruktur wird weiter ausgebaut by Oliver Kohlbacher]</ref> In addition, it is possible to apply for an associated partnership as Service and Training Partner or as Training Partner within de.NBI.

*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]], [[Microscopy|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:{{cite journal| pmid=28606611 | doi=10.1016//wwwj.ncbijbiotec.nlm2017.nih06.gov/pubmed/28606611005 | volume=261 | title=BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication by| year=2017 | journal=J Biotechnol | pages=116–125 | last1 = Turewicz et| al.,first1 2017]= M | last2 = Kohl | first2 = M | last3 = Ahrens | first3 = M | last4 = Mayer | first4 = G | last5 = Uszkoreit | first5 = J | last6 = Naboulsi | first6 = W | last7 = Bracht | first7 = T | last8 = Megger | first8 = DA | last9 = Sitek | first9 = B | last10 = Marcus | first10 = K | last11 = Eisenacher | first11 = M| doi-access = free }}</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]]

**TopicsTopic: [[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]], [[Microscopy|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]],

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*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]]

**TopicsTopic: [[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]]

**TopicsTopic: [[Systems Biology]] and [[Data management]]

=== Associated Partners ===

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 ([[University of Kiel]], [[University of Jena]], [[German Cancer Research Center|DKFZ]], [[European Molecular Biology Laboratory|EMBL]] Heidelberg, [[Robert Koch Institute|RKI]] Werningerode, [[German National Library of Medicine|ZB MED]], [[Heidelberg University]], [[Federal Institute for Materials Research and Testing]]) and two Associated Training Partners ([[University Medical Center Hamburg-Eppendorf]], [[LeibnizUniversity Instituteof for Baltic Sea ResearchTübingen]]). These partners cover topics in [[Metabolomics]], [[Phylogenetics]], human bioinformatics, eukaryotic genomics, metaproteomics, [[DNA sequencing|NGS]], 16S rRNA [[amplicon]] and [[single-cell analysis]] as well as the general IT topics [[Linux]] and [[Scripting language|scripting languages]].

== Bioinformatics resources ==

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=== Databases ===

de.NBI develops and maintains the five large databases [[SILVA ribosomal RNA database|SILVA]],<ref>[https:{{cite journal| pmid=28648396 | doi=10.1016//wwwj.ncbijbiotec.nlm2017.nih06.gov/pubmed/286483961198 | volume=261 | title=25 years of serving the community with ribosomal RNA gene reference databases and tools by| year=2017 | journal=J Biotechnol | pages=169–176 | last1 = Glöckner et| first1 = FO | last2 = Yilmaz | first2 = P | last3 = Quast | first3 = C | last4 = Gerken | first4 = J | last5 = Beccati | first5 = A | last6 = Ciuprina | first6 = A | last7 = Bruns | first7 = G | last8 = Yarza | first8 = P | last9 = Peplies | first9 = J | last10 = Westram | first10 = R | last11 = Ludwig | first11 = W| doi-access = free | hdl = al21.,11116/0000-0001-C16A-E 2017]| hdl-access = free }}</ref> [[PANGAEA]],<ref>[https:/{{cite journal| pmid=28743591 | doi=10.1016/wwwj.ncbijbiotec.nlm2017.nih07.gov/pubmed/28743591016 | volume=261 | title=Terminology supported archiving and publication of environmental science data in PANGAEA by| year=2017 | journal=J Biotechnol | pages=177–186 | last1 = Diepenbroek et| al.,first1 2017]= M | last2 = Schindler | first2 = U | last3 = Huber | first3 = R | last4 = Pesant | first4 = S | last5 = Stocker | first5 = M | last6 = Felden | first6 = J | last7 = Buss | first7 = M | last8 = Weinrebe | first8 = M| doi-access = free }}</ref> [[BacDive]],<ref>[https:{{cite journal| pmid=28487186 | doi=10.1016//wwwj.ncbijbiotec.nlm2017.nih05.gov/pubmed/28487186004 | volume=261 | title=Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase. by| year=2017 | journal=J Biotechnol | pages=187–193 | last1 = Reimer et| al.,first1 2017]= LC | last2 = Söhngen | first2 = C | last3 = Vetcininova | first3 = A | last4 = Overmann | first4 = J| doi-access = free }}</ref> [[ProteinPlus|ProteinsPlus]]<ref>[https:{{cite journal| pmid=28610996 | doi=10.1016//wwwj.ncbijbiotec.nlm2017.nih06.gov/pubmed/28610996004 | volume=261 | title=From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library by| year=2017 | journal=J Biotechnol | pages=207–214 | last1 = Bietz et| al.,first1 2017]= S | last2 = Inhester | first2 = T | last3 = Lauck | first3 = F | last4 = Sommer | first4 = K | last5 = von Behren | first5 = MM | last6 = Fährrolfes | first6 = R | last7 = Flachsenberg | first7 = F | last8 = Meyder | first8 = A | last9 = Nittinger | first9 = E | last10 = Otto | first10 = T | last11 = Hilbig | first11 = M | last12 = Schomburg | first12 = KT | last13 = Volkamer | first13 = A | last14 = Rarey | first14 = M| doi-access = free }}</ref> and [[BRENDA]].<ref>[https:{{cite journal| pmid=28438579 | doi=10.1016//wwwj.ncbijbiotec.nlm2017.nih04.gov/pubmed/28438579020 | volume=261 | title=The BRENDA enzyme information system-From a database to an expert system. by| year=2017 | journal=J Biotechnol | pages=194–206 | last1 = Schomburg et| al.,first1 2017]= I | last2 = Jeske | first2 = L | last3 = Ulbrich | first3 = M | last4 = Placzek | first4 = S | last5 = Chang | first5 = A | last6 = Schomburg | first6 = D| doi-access = free }}</ref> 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 ===

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:{{cite journal| pmid=28554830 | doi=10.1016//wwwj.ncbijbiotec.nlm2017.nih05.gov/pubmed/28554830019 | volume=261 | title=RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation by| year=2017 | journal=J Biotechnol | pages=76–84 | last1 = Backofen et| al.,first1 2017]= R | last2 = Engelhardt | first2 = J | last3 = Erxleben | first3 = A | last4 = Fallmann | first4 = J | last5 = Grüning | first5 = B | last6 = Ohler | first6 = U | last7 = Rajewsky | first7 = N | last8 = Stadler | first8 = PF| doi-access = free }}</ref> EDGAR (Comparative Genome Analyses Plattform),<ref>[https:/{{cite journal| pmid=28705636 | doi=10.1016/wwwj.ncbijbiotec.nlm2017.nih07.gov/pubmed/28705636010 | volume=261 | title=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| year=2017 | journal=J Biotechnol | pages=2–9 | last1 = Yu et| al.,first1 2017]= J | last2 = Blom | first2 = J | last3 = Glaeser | first3 = SP | last4 = Jaenicke | first4 = S | last5 = Juhre | first5 = T | last6 = Rupp | first6 = O | last7 = Schwengers | first7 = O | last8 = Spänig | first8 = S | last9 = Goesmann | first9 = A| doi-access = free }}</ref> [[KNIME]] (Workflow engine),<ref>[https:{{cite journal| pmid=28757290 | doi=10.1016//wwwj.ncbijbiotec.nlm2017.nih07.gov/pubmed/28757290028 | volume=261 | title=KNIME for reproducible cross-___domain analysis of life science data by| year=2017 | journal=J Biotechnol | pages=149–156 | last1 = Fillbrunn et| al.,first1 2017]= A | last2 = Dietz | first2 = C | last3 = Pfeuffer | first3 = J | last4 = Rahn | first4 = R | last5 = Landrum | first5 = GA | last6 = Berthold | first6 = MR| doi-access = free }}</ref> [[OpenMS]] (Open-source software C++ library for LC/MS data management and analyses),<ref>[https:{{cite journal| pmid=28559010 | doi=10.1016//wwwj.ncbijbiotec.nlm2017.nih05.gov/pubmed/28559010016 | volume=261 | title=OpenMS - A platform for reproducible analysis of mass spectrometry data by| year=2017 | journal=J Biotechnol | pages=142–148 | last1 = Pfeuffer et| al.,first1 2017]= J | last2 = Sachsenberg | first2 = T | last3 = Alka | first3 = O | last4 = Walzer | first4 = M | last5 = Fillbrunn | first5 = A | last6 = Nilse | first6 = L | last7 = Schilling | first7 = O | last8 = Reinert | first8 = K | last9 = Kohlbacher | first9 = O| doi-access = free }}</ref> [[SeqAN]] (Open source [[C++]] library of efficient algorithms and data structures),<ref>[https:{{cite journal| pmid=28888961 | doi=10.1016//wwwj.ncbijbiotec.nlm2017.nih07.gov/pubmed/28888961017 | volume=261 | title=The SeqAn C++ template library for efficient sequence analysis: A resource for programmers by| year=2017 | journal=J Biotechnol | pages=157–168 | last1 = Reinert et| al.,first1 2017]= K | last2 = Dadi | first2 = TH | last3 = Ehrhardt | first3 = M | last4 = Hauswedell | first4 = H | last5 = Mehringer | first5 = S | last6 = Rahn | first6 = R | last7 = Kim | first7 = J | last8 = Pockrandt | first8 = C | last9 = Winkler | first9 = J | last10 = Siragusa | first10 = E | last11 = Urgese | first11 = G | last12 = Weese | first12 = D| doi-access = free }}</ref> PIA (toolbox for MS based protein inference and identification analysis),<ref name="autogenerated1" /> [[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:{{cite journal| pmid=28554829 | doi=10.1016//wwwj.ncbijbiotec.nlm2017.nih05.gov/pubmed/28554829018 | volume=261 | title=Bioinformatics can boost metabolomics research by| year=2017 | journal=J Biotechnol | pages=137–141 | last1 = Meier et| al.,first1 2017]= R | last2 = Ruttkies | first2 = C | last3 = Treutler | first3 = H | last4 = Neumann | first4 = S| doi-access = free }}</ref> [[COPASI]] ([[Open-source software|Openopen source]] software application for creating and solving [[mathematical models]] of [[biological processes]]),<ref>[https:/{{cite journal| pmid=28655634 | doi=10.1016/wwwj.ncbijbiotec.nlm2017.nih06.gov/pubmed/286556341200 | pmc=5623632 | volume=261 | title=COPASI and its applications in biotechnology. | year=2017 | journal=J Biotechnol | pages=215–220 | last1 = Bergmann et| al.,first1 2017]= FT | last2 = Hoops | first2 = S | last3 = Klahn | first3 = B | last4 = Kummer | first4 = U | last5 = Mendes | first5 = P | last6 = Pahle | first6 = J | last7 = Sahle | first7 = S}}</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{{cite journal| pmid=29690922 | doi=10.gov1186/pubmed/29690922s40168-018-0460-1 | pmc=5937802 | volume=6 | title=Flexible metagenome analysis using the MGX framework. | year=2018 | journal=Microbiome | page=76 | last1 = Jaenicke et| al.first1 = S | last2 = Albaum | first2 = SP | last3 = Blumenkamp | first3 = P | last4 = Linke | first4 = B | last5 = Stoye | first5 = J | last6 = Goesmann | first6 = A| issue=1 | doi-access=free }}</ref> ASA³P (automated WGS analysis of bacterial cohorts),<ref>{{cite 2018]journal |title=ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates |date=2020-03-05 |journal=PLOS Computational Biology |volume=16 |issue=3 |at=pp.&nbsp;e1007134 |language=German |bibcode=2020PLSCB..16E7134S |doi=10.1371/journal.pcbi.1007134 |issn=1553-7358 |pmc=7077848 |pmid=32134915 |last1=Schwengers |first1=Oliver |last2=Hoek |first2=Andreas |last3=Fritzenwanker |first3=Moritz |last4=Falgenhauer |first4=Linda |last5=Hain |first5=Torsten |last6=Chakraborty |first6=Trinad |last7=Goesmann |first7=Alexander |doi-access=free }}</ref> Bakta<ref>{{Cite journal |last1=Schwengers |first1=Oliver |last2=Jelonek |first2=Lukas |last3=Dieckmann |first3=Marius Alfred |last4=Beyvers |first4=Sebastian |last5=Blom |first5=Jochen |last6=Goesmann |first6=Alexander |date=2021-11-05 |title=Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification |journal=Microbial Genomics |volume=7 |issue=11 |page=000685 |doi=10.1099/mgen.0.000685 |doi-access=free |issn=2057-5858 |pmc=8743544 |pmid=34739369}}</ref> (annotation of bacterial genomes and plasmids) 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 (de.NBI cloud) started in 2016.<ref>[https://www.nature{{cite journal | doi=10.com/articles1038/nrg.2017.113 | title=Cloud computing for genomic data analysis and collaboration by| Benyear=2018 | last1=Langmead &| Abhinavfirst1=Ben | last2=Nellore, 2018]| first2=Abhinav | journal=Nature Reviews Genetics | volume=19 | issue=4 | pages=208–219 | pmid=29379135 | pmc=6452449 }}</ref> 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 Authorizationauthorization Infrastructureinfrastructure]] (ELIXIR AAI). The de.NBI cloud comprises more than 2756,000 computing cores and 4180 petabytes of storage capacity (as of FebruaryNovember 20202021).

== 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. InSince 2017, online training formats like [[hackathonshackathon]]s for different software packages andor [[webinars]] haveare been establishedoffered by theall service centers RBC and CIBI.

The de.NBI training program started in 2015 with 17 f2f training courses with 329 participants, steadily increasing to 79 courses with 1586 Participants in 2019. In 2020 and 2021, the practical delivery of training was significantly affected by the COVID-19 pandemic, but the development of online training and materials (40 courses with 1,149 participants in 2020) enabled 2,128 training participants to be upskilled in 49 courses in 2021. A total of 9,076 scientists have been trained in 371 courses through our bioinformatics network to date (as of January 2022).<ref>{{Cite web |date=2022-02-24 |title=de.NBI Quarterly Newsletter 01/22 |url=https://www.denbi.de/downloads/21-about/1362-newsletter-27 |access-date=2022-03-22}}</ref>

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 (69 trainings with 1489 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 Schoolschool|summer schools]] to cover a distinct topic in more detail. The first Summer School was held in 2015 by the Service Centers Bielefeld-Gießen (BiGi) Center for Microbial Bioinformatics, RBC and de.NBI-SysBio and was focused in the workflow from genome assembly to genome and transcriptome analysis.<ref>[https://www.denbi.de/training-archive-sorted-according-by-date/2015/142-de-nbi-late-summer-school-2015 de.NBI Summer School 2015]</ref> 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 (2016),<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> Cloud Computing for Bioinformatics (2017),<ref>{{Cite web |date=2017-04-01 |title=de.NBI Summer School 2017 -2 |url=https://www.denbi.de/training-archive-sorted-according-by-date/2017/219-de-nbi-summer-school-on-cloud-computing-for-bioinformatics |access-date=2022-03-22}}</ref> Computational genomics and RNA biology (2017),<ref>[https://www.denbi.de/training-archive-sorted-according-by-date/2017/242-de-nbi-late-summer-school-2017-computational-genomics-and-rna-biology de.NBI Summer School 2017]</ref> Metabolomics (2018),<ref>{{Cite web |date=2017-11-02 |title=de.NBI Winterschool 2018 |url=https://www.denbi.de/training-archive-sorted-according-by-date/2018/87-de-nbi-winter-school-on-computational-metabolomics |access-date=2022-03-22}}</ref> Research Data Management (2018)<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> and (Bio)Data Science (2019).<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>. TheTwo de.NBI Summer SchoolSchools 2020took willplace bein organized2021. by1) BiGiAnalysis of mass spectrometry data in proteomics, lipidomics and coverMetabolomics theorganized topicby ofBioInfra.Prot, metagenomicsCIBI and de.NBI-SysBio,<ref>{{Cite web |title=de.NBI Summer School 2021 - 1 |url=https://www.denbi.de/training-archive-sorted-according-by-date/7351150-de-nbi-summer-school-20202021-metagenomicsproteomics-lipidomics |access-date=2022-03-23}}</ref> 2) Microbial Community Analysis organized by BiGi and HD-HuB.<ref>{{Cite web |title=de.NBI Summer School 20202021 - Metagenomics|last=|first=|date=|website=2 |url-status=live|archivehttps://www.denbi.de/training-url=|archive-sorted-according-by-date=/1269-de-nbi-summer-school-2021-part-2-microbial-community-analysis |access-date=March 3, 20202022-03-23}}</ref>

===Additional de.NBI Schools ===

In addition, de.NBIas organizedan theoutreach 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-bioinformaticsactivity de.NBI Cloudsupported the Summer School 2017]</ref>BioByte and2019 supportedat a[[Martin winterLuther schoolUniversity onof metabolics in March 2018<ref>[https://www.denbi.de/trainingHalle-archive-sorted-according-by-date/2018/87-de-nbi-winter-school-on-computational-metabolomicsWittenberg|University de.NBIof Winter School 2018Halle]]</ref>. Foraddressed pupilsat interested in bioinformatics, the BioBYTE summerhigh school atstudents the University of Halle, also supported by de.NBI,which offers an ideal opportunity to get to know the diversity of bioinformatics.<ref>{{Cite web|url=https://biobyte.uni-halle.de/|title=Sommerschule für neugierige Schülerinnen und Schüler, die die Naturwissenschaft der Zukunft entdecken möchten.|last=|first=|date=|website=|language=de|url-status=live|archive-url=|archive-date=|access-date=March 3, 2020}}</ref>.

==References==

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[[Category:Bioinformatics]]

[[Category:Biology organisations based in Germany]]

[[Category:European Union and science and technology]]

[[Category:Genetics in Germany]]