German Network for Bioinformatics Infrastructure: Difference between revisions

Revision as of 16:05, 7 February 2019

Latest revision as of 05:01, 10 September 2024

(43 intermediate revisions by 23 users not shown)

Line 1:

{{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|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|___location=[[Bielefeld]],

| name = de.NBI - German Network for Bioinformatics Infrastructure

[[Berlin]],

| image = [[File:De.NBI_Logo.svg|de.NBI - German Network for Bioinformatic Infrastructure|240px]]

[[Bochum]],

| established = 2015

[[Borstel]],

| website = {{URL|https://www.denbi.de}}

[[Braunschweig]],

| 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>

[[Bremen]],

| head_label = Coordinator

[[Dortmund]],

| mission = Big Data Exploitation in Life Science

[[Dresden]],

| num_members = 250

[[Freiburg]],

| ___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]]

[[Gießen]],

}}

[[Halle (Saale)]],

[[Hamburg]],

[[Heidelberg]],

[[Jena]],

[[Jülich]],

[[Konstanz]],

[[Gatersleben]],

[[Magdeburg]],

[[Leipzig]],

[[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>[https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbx040/3738742 Bioinformaticsname="autogenerated2" in/> Germany:In towardAugust a2016, national-levelGermany infrastructurejoined by[[ELIXIR]], Andreasthe TauchEuropean &life-sciences ArwaInfrastructure Al-Dilaimi]</ref>.for Inbiological additionInformation, with the German [[ELIXIR]] Node in(ELIXIR Germany) isbeing run by de.NBI since August 2016 partners.<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 150250 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 RusselBoutros, SchlesnerBrors, BoutrosBuchhalter), [[European Molecular Biology Laboratory]] (EMBL, research groups Bork, Huber, Korbel), [[Heidelberg University]] (research groups Eils/Rohr, Russell, Erfle/Reymann), [[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">{{cite journal| pmid=28606611 | doi=10.1016/j.jbiotec.2017.06.005 | volume=261 | title=BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication | year=2017 | journal=J Biotechnol | pages=116–125 | last1 = Turewicz | first1 = 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>

*Bioinformatics for Proteomics (BioInfra.Prot)<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., 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]]

**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]],

**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]]

**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: [[University of Kiel]], [[University of Jena]]===

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]], [[University of Tübingen]]). 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]].

**Topics: [[Metabolomics]], [[Phylogenetics]], Human Bioinformatics, Genomics for Eukaryotes

== Bioinformatics resources ==

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

=== 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| alfirst1 = 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 = 21.,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]</ref>,= PIAK (toolbox| forlast2 MS= basedDadi protein| inferencefirst2 and= identificationTH analysis)<ref>[https://www.ncbi.nlm.nih.gov/pubmed/28606611| BioInfra.Prot:last3 A= comprehensiveEhrhardt proteomics| workflowfirst3 including= dataM standardization,| proteinlast4 inference,= expressionHauswedell analysis| andfirst4 data= publicationH by| Turewiczlast5 et= al.,Mehringer 2017]| 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). ItThe de.NBI cloud comprises more than 1556,000 computecomputing cores and 580 PBpetabytes of storage capacity in(as April 2018. During 2018, the storage capacity was increased to 38 PB (Statusof FebruaryNovember 20192021).

== 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>

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). In 2018, the de.NBI training program reached the plateau phase with 77 training courses and 1520 participants.

=== de.NBI Summer Schools===

Next to the training courses de.NBI offers annual [[Summer school|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> Two de.NBI Summer Schools took place in 2021. 1) Analysis of mass spectrometry data in proteomics, lipidomics and Metabolomics organized by BioInfra.Prot, CIBI 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/1150-de-nbi-summer-school-2021-proteomics-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 2021 - 2 |url=https://www.denbi.de/training-archive-sorted-according-by-date/1269-de-nbi-summer-school-2021-part-2-microbial-community-analysis |access-date=2022-03-23}}</ref>

*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<ref>[http://www.denbi.de/events/45-lss2015 de.NBI Summer School 2015]</ref>.

*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>[http://www.denbi.de/events/206-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 “Computational genomics and RNA biology”<ref>[http://www.denbi.de/events/331-lss2017 de.NBI Summer School 2017]</ref>.

*September 2018: The fourth summer school was organized on "Riding the Data Life Cycle" by BioData, GCBN and de.NBI-SysBio<ref>[http://www.denbi.de/events/534-lss2018 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, as an outreach activity de.NBI supported the Summer School BioByte 2019 at [[Martin Luther University of Halle-Wittenberg|University of Halle]] addressed at high school students 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|archive-url=|archive-date=|access-date=March 3, 2020}}</ref>

In addition, de.NBI organized the first cloud summer school in June 2017<ref>[http://www.denbi.de/events/332-cloud1 de.NBI Cloud Summer School 2017]</ref> and supported a winter school on metabolics in March 2018<ref>[http://www.denbi.de/events/468-de-nbi-winter-school-on-computational-metabolomics de.NBI Winter School 2018]</ref>.

==References==

Line 104 ⟶ 81:

* {{Official website|http://www.denbi.de/}}

* [https://twitter.com/denbiOffice Official Twitter channel]

* [https://www.youtube.com/channel/UCgZ5PU3CyD4c8yxxzJi130g Official Youtube channel]

{{Bioinformatics}}

[[Category:Bioinformatics]]

[[Category:Biology organisations based in Germany]]

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

[[Category:Genetics in Germany]]