German Network for Bioinformatics Infrastructure

de.NBI - German Network for Bioinformatics Infrastructure

Established| 2015
Mission| Big Data Exploitation in Life Science
Coordinator| Alfred Pühler until 2021[1]
Members| 250
Location|

Bielefeld, Berlin, Bochum, Borstel (Sülfeld) (de), Braunschweig, Bremen, Dortmund, Dresden, Freiburg, Gatersleben, Gießen, Halle (Saale), Hamburg, Heidelberg, Jena, Jülich, Konstanz, Leipzig, Magdeburg, Munich, Rostock, Saarbrücken, Tübingen

Website| www.denbi.de

The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national, academic and non-profit infrastructure initiated by the Federal Ministry of Education and Research funding 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.[2] From 2022, the network will be integrated into Forschungszentrum Jülich.[3]

## Contents

* 1 History
* 2 Organisation
* 2.1 Associated Partners
* 3 Bioinformatics resources
* 3.1 Databases
* 3.2 Tools
* 3.3 Hardware
* 4 Training
* 4.1 de.NBI Summer Schools
* 4.2 Additional de.NBI Schools
* 5 References
* 6 External links

## 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.[2] In August 2016, Germany joined ELIXIR, the European life-sciences Infrastructure for biological Information, with the German ELIXIR Node (ELIXIR Germany) being run by de.NBI partners.[4][5][6]

The first coordinator of the de.NBI project was Alfred Pühler until 2021. The head of the German ELIXIR Node is Andreas Tauch.[7]

## Organisation

The de.NBI network consists of the eight interconnected centers and one coordination unit including 40 research, service and infrastructure groups with about 250 bioinformaticians involved.[8] 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 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):[9]
* 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
* Topic: 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 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
* Topic: 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
* Topic: 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, DKFZ, EMBL Heidelberg, RKI Werningerode, 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, NGS, 16S rRNA amplicon and single-cell analysis as well as the general IT topics Linux and scripting languages.

## Bioinformatics resources

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

### Databases

de.NBI develops and maintains the five large databases SILVA,[10] PANGAEA,[11] BacDive,[12] ProteinsPlus[13] and BRENDA.[14] 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),[15] EDGAR (Comparative Genome Analyses Plattform),[16] KNIME (Workflow engine),[17] OpenMS (Open-source software C++ library for LC/MS data management and analyses),[18] SeqAN (Open source C++ library of efficient algorithms and data structures),[19] PIA (toolbox for MS based protein inference and identification analysis),[9] Fiji (Image processing package), MetFrag (in silico fragmenter combines compound database searching and fragmentation prediction for small molecule identification from tandem mass spectrometry data),[20] COPASI (open source software application for creating and solving mathematical models of biological processes),[21] SIAMCAT (Framework for the statistical inference of associations between microbial communities and host phenotypes), e!DAL - PGP (Open source software framework to publish and share research data), MGX (Metagenome analysis),[22] ASA³P (automated WGS analysis of bacterial cohorts),[23] Bakta[24] (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.[25] 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). The de.NBI cloud comprises more than 56,000 computing cores and 80 petabytes of storage capacity (as of November 2021).

## 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. Since 2017, online training formats like hackathons or webinars are offered by all service centers.

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).[26]

### de.NBI Summer Schools

Next to the training courses de.NBI offers annual 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.[27] 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),[28] Cloud Computing for Bioinformatics (2017),[29] Computational genomics and RNA biology (2017),[30] Metabolomics (2018),[31] Research Data Management (2018)[32] and (Bio)Data Science (2019).[33] 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,[34] 2) Microbial Community Analysis organized by BiGi and HD-HuB.[35]

### Additional de.NBI Schools

In addition, as an outreach activity de.NBI supported the Summer School BioByte 2019 at University of Halle addressed at high school students which offers an ideal opportunity to get to know the diversity of bioinformatics.[36]

## References

1. ↑ "de.NBI Coordinator". https://www.denbi.de/organisation/de-nbi-coordinator.
2. ↑ 2.0 2.1 Bioinformatics in Germany: toward a national-level infrastructure by Andreas Tauch & Arwa Al-Dilaimi
3. ↑ Pühler, A. (2021). "Verstetigung des de.NBI-Netzwerks". Biologie in unserer Zeit 51 (3): 221–222. doi:10.11576/biuz-4634. https://doi.org/10.11576/biuz-4634.
4. ↑ ELIXIR Board Meeting Spring 2016
5. ↑ Germany joins ELIXIR
6. ↑ ELIXIR Germany
7. ↑ "de.NBI Quarterly Newsletter 2/20". https://www.denbi.de/images/Downloads/Newsletter/quarterly_newsletter_20.pdf.
8. ↑ de.NBI – Netzwerk für Bioinformatik-Infrastruktur wird weiter ausgebaut by Oliver Kohlbacher
9. ↑ 9.0 9.1 Turewicz, M; Kohl, M; Ahrens, M; Mayer, G; Uszkoreit, J; Naboulsi, W; Bracht, T; Megger, DA et al. (2017). "BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication". J Biotechnol 261: 116–125. doi:10.1016/j.jbiotec.2017.06.005. PMID 28606611.
10. ↑ Glöckner, FO; Yilmaz, P; Quast, C; Gerken, J; Beccati, A; Ciuprina, A; Bruns, G; Yarza, P et al. (2017). "25 years of serving the community with ribosomal RNA gene reference databases and tools". J Biotechnol 261: 169–176. doi:10.1016/j.jbiotec.2017.06.1198. PMID 28648396.
11. ↑ Diepenbroek, M; Schindler, U; Huber, R; Pesant, S; Stocker, M; Felden, J; Buss, M; Weinrebe, M (2017). "Terminology supported archiving and publication of environmental science data in PANGAEA". J Biotechnol 261: 177–186. doi:10.1016/j.jbiotec.2017.07.016. PMID 28743591.
12. ↑ Reimer, LC; Söhngen, C; Vetcininova, A; Overmann, J (2017). "Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase". J Biotechnol 261: 187–193. doi:10.1016/j.jbiotec.2017.05.004. PMID 28487186.
13. ↑ Bietz, S; Inhester, T; Lauck, F; Sommer, K; von Behren, MM; Fährrolfes, R; Flachsenberg, F; Meyder, A et al. (2017). "From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library". J Biotechnol 261: 207–214. doi:10.1016/j.jbiotec.2017.06.004. PMID 28610996.
14. ↑ Schomburg, I; Jeske, L; Ulbrich, M; Placzek, S; Chang, A; Schomburg, D (2017). "The BRENDA enzyme information system-From a database to an expert system". J Biotechnol 261: 194–206. doi:10.1016/j.jbiotec.2017.04.020. PMID 28438579.
15. ↑ Backofen, R; Engelhardt, J; Erxleben, A; Fallmann, J; Grüning, B; Ohler, U; Rajewsky, N; Stadler, PF (2017). "RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation". J Biotechnol 261: 76–84. doi:10.1016/j.jbiotec.2017.05.019. PMID 28554830.
16. ↑ Yu, J; Blom, J; Glaeser, SP; Jaenicke, S; Juhre, T; Rupp, O; Schwengers, O; Spänig, S et al. (2017). "A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies". J Biotechnol 261: 2–9. doi:10.1016/j.jbiotec.2017.07.010. PMID 28705636.
17. ↑ Fillbrunn, A; Dietz, C; Pfeuffer, J; Rahn, R; Landrum, GA; Berthold, MR (2017). "KNIME for reproducible cross-domain analysis of life science data". J Biotechnol 261: 149–156. doi:10.1016/j.jbiotec.2017.07.028. PMID 28757290.
18. ↑ Pfeuffer, J; Sachsenberg, T; Alka, O; Walzer, M; Fillbrunn, A; Nilse, L; Schilling, O; Reinert, K et al. (2017). "OpenMS - A platform for reproducible analysis of mass spectrometry data". J Biotechnol 261: 142–148. doi:10.1016/j.jbiotec.2017.05.016. PMID 28559010.
19. ↑ Reinert, K; Dadi, TH; Ehrhardt, M; Hauswedell, H; Mehringer, S; Rahn, R; Kim, J; Pockrandt, C et al. (2017). "The SeqAn C++ template library for efficient sequence analysis: A resource for programmers". J Biotechnol 261: 157–168. doi:10.1016/j.jbiotec.2017.07.017. PMID 28888961.
20. ↑ Meier, R; Ruttkies, C; Treutler, H; Neumann, S (2017). "Bioinformatics can boost metabolomics research". J Biotechnol 261: 137–141. doi:10.1016/j.jbiotec.2017.05.018. PMID 28554829.
21. ↑ Bergmann, FT; Hoops, S; Klahn, B; Kummer, U; Mendes, P; Pahle, J; Sahle, S (2017). "COPASI and its applications in biotechnology". J Biotechnol 261: 215–220. doi:10.1016/j.jbiotec.2017.06.1200. PMID 28655634.
22. ↑ Jaenicke, S; Albaum, SP; Blumenkamp, P; Linke, B; Stoye, J; Goesmann, A (2018). "Flexible metagenome analysis using the MGX framework". Microbiome 6 (1): 76. doi:10.1186/s40168-018-0460-1. PMID 29690922.
23. ↑ Schwengers, Oliver; Hoek, Andreas; Fritzenwanker, Moritz; Falgenhauer, Linda; Hain, Torsten; Chakraborty, Trinad; Goesmann, Alexander (2020-03-05). "ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates" (in German). PLOS Computational Biology 16 (3): pp. e1007134. doi:10.1371/journal.pcbi.1007134. ISSN 1553-7358. PMID 32134915. Bibcode: 2020PLSCB..16E7134S.
24. ↑ Schwengers, Oliver; Jelonek, Lukas; Dieckmann, Marius Alfred; Beyvers, Sebastian; Blom, Jochen; Goesmann, Alexander (2021-11-05). "Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification". Microbial Genomics 7 (11): 000685. doi:10.1099/mgen.0.000685. ISSN 2057-5858. PMID 34739369.
25. ↑ Langmead, Ben; Nellore, Abhinav (2018). "Cloud computing for genomic data analysis and collaboration". Nature Reviews Genetics 19 (4): 208–219. doi:10.1038/nrg.2017.113. PMID 29379135.
26. ↑ "de.NBI Quarterly Newsletter 01/22". 2022-02-24. https://www.denbi.de/downloads/21-about/1362-newsletter-27.
27. ↑ de.NBI Summer School 2015
28. ↑ de.NBI Summer School 2016
29. ↑ "de.NBI Summer School 2017 -2". 2017-04-01. https://www.denbi.de/training-archive-sorted-according-by-date/2017/219-de-nbi-summer-school-on-cloud-computing-for-bioinformatics.
30. ↑ de.NBI Summer School 2017
31. ↑ "de.NBI Winterschool 2018". 2017-11-02. https://www.denbi.de/training-archive-sorted-according-by-date/2018/87-de-nbi-winter-school-on-computational-metabolomics.
32. ↑ de.NBI Summer School 2018
33. ↑ "de.NBI Summer School 2019 - (Bio)Data Science". https://www.denbi.de/training/528-de-nbi-summer-school-2019-bio-data-science.
34. ↑ "de.NBI Summer School 2021 - 1". https://www.denbi.de/training-archive-sorted-according-by-date/1150-de-nbi-summer-school-2021-proteomics-lipidomics.
35. ↑ "de.NBI Summer School 2021 - 2". https://www.denbi.de/training-archive-sorted-according-by-date/1269-de-nbi-summer-school-2021-part-2-microbial-community-analysis.
36. ↑ "Sommerschule für neugierige Schülerinnen und Schüler, die die Naturwissenschaft der Zukunft entdecken möchten." (in de). https://biobyte.uni-halle.de/.

## External links

* Official website
* Official Twitter channel
* Official Youtube channel

* v
* t
* e

Bioinformatics

Databases|

* Sequence databases: GenBank, European Nucleotide Archive and DNA Data Bank of Japan
* Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information Resource
* Other databases: Protein Data Bank, Ensembl and InterPro
* Specialised genomic databases: BOLD, Saccharomyces Genome Database, FlyBase]], VectorBase]], WormBase, PHI-base, Arabidopsis Information Resource and Zebrafish Information Network

Software|

* BLAST
* Bowtie
* Clustal
* HMMER
* MUSCLE
* SAMtools
* TopHat

Other|

* Server: ExPASy
* Ontology: Gene Ontology
* Rosalind (education platform)

Institutions|

* Broad Institute
* Computational Biology Department (CBD)
* Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI)
* Database Center for Life Science (DBCLS)
* DNA Data Bank of Japan (DDBJ)
* European Bioinformatics Institute (EMBL-EBI)
* European Molecular Biology Laboratory (EMBL)
* Flatiron Institute
* J. Craig Venter Institute (JCVI)
* Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
* US National Center for Biotechnology Information (NCBI)
* Japanese Institute of Genetics
* Netherlands Bioinformatics Centre (NBIC)
* Philippine Genome Center (PGC)
* Scripps Research
* Swiss Institute of Bioinformatics (SIB)
* Wellcome Sanger Institute
* Whitehead Institute

Organizations|

* African Society for Bioinformatics and Computational Biology (ASBCB)
* Australia Bioinformatics Resource (EMBL-AR)
* European Molecular Biology network (EMBnet)
* International Nucleotide Sequence Database Collaboration (INSDC)
* International Society for Biocuration (ISB)
* International Society for Computational Biology (ISCB)
* Student Council (ISCB-SC)
* Institute of Genomics and Integrative Biology (CSIR-IGIB)
* Japanese Society for Bioinformatics (JSBi)

Meetings|

* Basel Computational Biology Conference‎ ([BC2])
* European Conference on Computational Biology (ECCB)
* Intelligent Systems for Molecular Biology (ISMB)
* International Conference on Bioinformatics (InCoB)
* ISCB Africa ASBCB Conference on Bioinformatics
* Pacific Symposium on Biocomputing (PSB)
* Research in Computational Molecular Biology (RECOMB)

File formats|

* CRAM format
* FASTA format
* FASTQ format
* NeXML format
* Nexus format
* Pileup format
* SAM format
* Stockholm format

Related topics|

* Computational biology
* List of biological databases
* Molecular phylogenetics
* Sequencing
* Sequence database
* Sequence alignment

* Category
* Commons

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