German Network for Bioinformatics Infrastructure: Difference between revisions

Revision as of 05:18, 25 October 2019

Revision as of 15:19, 5 March 2020

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== 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 addition, the [[ELIXIR]] Node in Germany (ELIXIR-DE) is 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 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.<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)

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**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

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]]) and two Associated Training Partners ([[University Medical Center Hamburg-Eppendorf]], [[Leibniz Institute for Baltic Sea Research]]). 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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=== 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> 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 Authorization Infrastructure (ELIXIR AAI). ItThe de.NBI cloud comprises more than 1527,000 computecomputing cores and 541 PBpetabytes of storage capacity in(as April 2018. During 2018, the storage capacity was increased to 38 PB (Statusof February 20192020).

== 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. In 2017, online [[hackathons]] for different software packages and [[webinars]] have been established by the centers RBC and CIBI.

InA 2015,total of 17 training courses with 329 participants were organizedorganised by de.NBI in 2015. In 2016, the network has organizedorganised 40 training courses with 882 participants. For 2017, the network couldwas able to further increase the number of courses and participants (69 training coursestrainings with 1489 participants). In 2018, the de.NBI training program reached the1520 plateau phaseparticipants with 77 trainings. In 2019, de.NBI offered 79 training courses andwith 15201586 participants.

=== de.NBI Summer Schools===

Next to the training courses de.NBI offers an annual Summer School 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>, 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>, 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>. The de.NBI Summer School 2020 will be organized by BiGi and cover the topic of metagenomics.<ref>{{Cite web|url=https://www.denbi.de/training/735-de-nbi-summer-school-2020-metagenomics|title=de.NBI Summer School 2020 - Metagenomics|last=|first=|date=|website=|url-status=live|archive-url=|archive-date=|access-date=March 3, 2020}}</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>[https://www.denbi.de/training-archive-sorted-according-by-date/2015/142-de-nbi-late-summer-school-2015 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>[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 "Computational genomics and RNA biology".<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>

*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>. For pupils interested in bioinformatics, the BioBYTE summer school at the University of Halle, also supported by de.NBI, 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==