German Network for Bioinformatics Infrastructure - de.NBI

de.NBI - German Network for Bioinformatics Infrastructure
Category:	Bioinformatics
Carrier:	BMBF
Facility location:	Bielefeld , Berlin , Bochum , Borstel , Braunschweig , Bremen , Dortmund , Dresden , Freiburg im Breisgau , Gatersleben , Gießen , Halle (Saale) , Hamburg , Heidelberg , Jena , Jülich , Konstanz , Leipzig , Magdeburg , Munich , Rostock , Saarbrücken , Tübingen
Management:	Alfred Puhler
Employee:	250
Homepage:	https://www.denbi.de/

German Network for Bioinformatics Infrastructure - de.NBI is a national academic network that offers bioinformatics services for the life sciences and biomedicine in Germany and Europe. De.NBI is financed by the Federal Ministry of Education and Research (BMBF). The de.NBI partners organize training events, courses and summer schools on software tools and standards, and offer computing capacity in the form of a cloud to help researchers use their data more effectively.

Emergence

In May 2013, the Federal Ministry of Education and Research (BMBF) announced the creation of funding guidelines for a German network for bioinformatics infrastructure (de.NBI). The aim of this announcement was to build an infrastructure in Germany that would offer solutions to the " big data problem" in the life sciences with the help of bioinformatics services and training . In November 2015, de.NBI published a second announcement of funding guidelines for partner projects. de.NBI was started by the BMBF in March 2015, while the partner projects started their work in November 2016. In addition, the ELIXIR node in Germany (ELIXIR-DE) has been operated by de.NBI partners since August 2016.

The first de.NBI coordinator is Alfred Pühler . The German ELIXIR node has been managed by Andreas Tauch since June 1, 2020.

organization

Since November 2016, the de.NBI network has consisted of the interconnected centers, which include almost 40 research, service and infrastructure groups with around 250 bioinformaticians. It is also possible to apply for an associated partnership within de.NBI as a “service and training partner” or just as a training partner. The eight de.NBI centers as well as the associated service and training partners and associated training partners are listed below.

• Heidelberg Center for Human Bioinformatics (HD-HuB)
  • Members: The German Cancer Research Center (DKFZ, research groups Boutros, Brors, accountants), European Laboratory for Molecular Biology (EMBL, research groups Bork, Huber, Korbel), Heidelberg University (research groups Rohr, Russell, Erfle), Charité Berlin (research groups Eils, Ishaque) and Saarland University (Walter research group)
  • Topics: human bioinformatics, e.g. B. Exome , Genomics , Transcriptomics , Metagenomics , Phenotyping , Bioimaging , Epigenetics and Cloud Computing
  • Associated partner: Department for Computational Genomics and System Genetics (Dr. Oliver Stegle, DKFZ)
• Bielefeld-Giessen Resource Center for Microbial Bioinformatics (BiGi)
  • Members: University of Bielefeld , University of Giessen and Otto-von-Guericke University Magdeburg
  • Topics: microbial bioinformatics, e.g. B. Genomics , Transcriptomics, Metagenomics, Proteomics , Metaproteomics , Metabolomics and Cloud Computing
• Bioinformatics for Proteomics (BioInfra.Prot)
  • Members: Ruhr University Bochum ("Medical Bioinformatics" research unit of the Medical Proteome Center), Leibniz Institute for Analytical Sciences ISAS ev Dortmund ("Department for Bioanalytics"), Research Center Borstel and Max Planck Institute for 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 for Plant Biochemistry Halle (Saale) and Max Planck Institute for Molecular Cell Biology and Genetics
  • Topics: bioinformatics workflow management system, e.g. B. 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 Institute for Aging Research Jena and University of Rostock
  • Topics: RNA bioinformatics, e.g. B. transcriptome analysis, RNA structure analysis, prediction of ncRNA binding sites, definition and classification of RNA transcripts and analysis of protein-RNA interaction
• German Crop BioGreenformatics Network (GCBN)
  • Members: Leibniz Institute for Plant Genetics and Crop Plant Research in Gatersleben (IPK, BIT, Uwe Scholz), Helmholtz Center Munich (HMGU, PGSB, Klaus Mayer) and Research Center Jülich (FZJ, IBG-2 Plant Sciences, Björn Usadel)
  • Topics: plant bioinformatics, e.g. B. Genomics, genome annotation, phenotyping, plant databases
• Center for Biological Data (BioData)
  • Members: German Collection of Microorganisms and Cell Cultures (DSMZ), Technical University of Braunschweig , Jacobs University of 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, Rostock University and Max Planck Institute for Dynamics of Complex Technical Systems
  • Topics: systems biology and data management
• Associated service and training partners: University of Kiel , University of Jena , German Cancer Research Center , EMBL Heidelberg, Robert Koch Institute Werningerode, ZB MED - Information Center Life Sciences
  • Topics: metabolomics, phylogenetics , human bioinformatics, genomics for eukaryotes , metaproteomics, single cell analysis
• Associated training partners: University Medical Center Hamburg-Eppendorf , Leibniz Institute for Baltic Sea Research
  • Topics: next generation sequencing , Linux, script languages , 16S rRNA amplicon analyzes

Bioinformatics resources

The de.NBI network offers a broad portfolio of resources for the German and international life sciences community. This mainly includes databases, bioinformatics software and the provision of computing capacity through a network cloud system.

Databases

de.NBI develops and maintains the five large databases SILVA, PANGEA, BacDive, ProteinPlus and BRENDA. These databases provide access to ribosomal RNA genes from all three areas of life (SILVA), geo-referenced data from Earth system research (PANGEA), strain-related information on the biodiversity of bacteria and archaea (BacDive), protein structures (ProteinPlus) and comprehensive enzyme information (BRENDA) .

Tools

de.NBI develops and delivers around 100 bioinformatics programs for the German and global life science community, e.g. B. Galaxy (Computational Biology) / useGalaxy.eu (workflow engine for all Freiburg RNA tools), EDGAR (comparative genome analysis platform), KNIME (workflow engine), OpenMS (open source C ++ library for LC / MS Data management and analysis), SeqAN (open source C ++ library for efficient algorithms and data structures), PIA (toolbox for MS-based protein inference and identification analysis), Fiji (software) (image processing package), MetFrag (in silico fragmenter combines components Database search and fragmentation prediction for the identification of small molecules from tandem mass spectrometry data), COPASI (open source software application for creating and solving mathematical models of biological processes), SIAMCAT (framework for the statistical inference of associations between microbial communities and host phenotypes), e! DAL-PGP (open source framework for publishing and sharing research data), MGX ( metagenome analysis) and many m honest.

The de.NBI tools are also registered and searchable in the ELIXIR Tools and Data Services registry, which provides further information in a standardized format.

hardware

de.NBI has been developing and operating a network cloud system (de.NBI-Cloud) since 2016. The cloud is provided in a collaboration project between the universities of Bielefeld, Freiburg, Gießen, Heidelberg, Tübingen and Charité Berlin. The entire system is accessible via the central de.NBI cloud portal via Single Sign-On (SSO) and is based on the ELIXIR authentication and authorization infrastructure (ELIXIR AAI). The de.NBI cloud comprises more than 27,000 computing cores and 41 petabytes of storage capacity (as of February 2020).

training

Different types of training activities are supported and organized by de.NBI. The de.NBI summer schools offer courses for students and doctoral candidates on specific topics that relate to one or more de.NBI centers. The respective centers organize specific training courses for the bioinformatics software on offer. These training courses take place at existing conferences or are organized independently of them. In addition, online training courses were introduced on the de.NBI website in 2016. Since 2017, online hackathons have been set up for various software packages and webinars by the “RNA Bioinformatics Center” (RBC) and “Center for integrative Bioinformatics” (CIBI).

A total of 17 training courses with 329 participants were organized by de.NBI in 2015. In 2016, the network organized 40 training courses with 882 participants. For 2017, the network was able to further increase the number of courses and participants (69 training courses with 1489 participants). In 2018, the de.NBI training program with 77 training sessions reached 1,520 participants. In 2019, de.NBI offered 79 training courses in which 1,586 people took part.

de.NBI summer schools

• September 2015: The first de.NBI summer school was organized by the service centers BiGi, RBC and de.NBI-SysBio. This de.NBI summer school focused on the processes from genome assembly to genome and transcriptome analysis.
• September 2016: The second de.NBI summer school was organized by BioInfraProt, CIBI and BiGi in Dagstuhl and focused on the field of proteomics and the analysis of mass spectrometry data.
• September 2017: The third de.NBI summer school was organized by all RBC partners. The focus was on “Computational Genomics and RNA Biology”.
• September 2018: The fourth summer school was organized by the BioData, GCBN and de.NBI-SysBio centers on the subject of "Riding the Data Life Cycle".
• September 2019: The fifth summer school was organized by the GCBN, BioData, de.NBI-SysBio and BioInfra.Prot service centers and took place in Gatersleben. The topic was about "(Bio) Data Science".
• September 2020: The sixth summer school with the topic "Metagenomics" is organized by the BiGi service center and takes place in Giessen.

Additional de.NBI courses

In addition to the annual summer schools, de.NBI organized the first cloud summer school in June 2017 and supported a winter school on the subject of metabolites in March 2018. For students interested in bioinformatics, the BioBYTE summer school at the University of Halle , which is also supported by de.NBI, offers an ideal opportunity to get to know the diversity of bioinformatics.

Industry forum

The de.NBI Industry Forum offers industrial companies assistance in solving bioinformatic issues. The forum is aimed at companies that are active in industrial biotechnology , as well as biodata and software companies that work with data and tools in the life sciences. The members of the de.NBI industry forum have access to training courses and are informed about developments in the network. The de.NBI industry forum also offers a platform for networking industry and science.

Web links

• official website

Individual evidence

1. ^ ^{A b} Arwa Al-Dilaimi, Andreas Tauch: Bioinformatics in Germany: toward a national-level infrastructure . In: Briefings in Bioinformatics . April 18, 2017, doi : 10.1093 / bib / bbx040 .
2. ↑ ELIXIR Board meeting: 2016 Spring session | ELIXIR. Retrieved February 12, 2019 . 
3. ↑ Germany joins ELIXIR | ELIXIR. Retrieved February 12, 2019 . 
4. ↑ ELIXIR Nodes | ELIXIR. Retrieved February 12, 2019 . 
5. ↑ de.NBI: de.NBI Quarterly Newsletter Issue 2/20. de.NBI, May 29, 2020, accessed on June 15, 2020 (English). 
6. ↑ de.NBI - Network for bioinformatics infrastructure is being expanded - Health Industry BW. Retrieved February 12, 2019 . 
7. ↑ Michael Turewicz, Michael Kohl, Maike Ahrens, Gerhard Mayer, Julian Uszkoreit: BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication . In: Journal of Biotechnology . tape 261 , November 10, 2017, ISSN  1873-4863 , p. 116-125 , doi : 10.1016 / j.jbiotec.2017.06.005 , PMID 28606611 .
8. ↑ Frank Oliver Glöckner, Pelin Yilmaz, Christian Quast, Jan Gerken, Alan Beccati: 25 years of serving the community with ribosomal RNA gene reference databases and tools . In: Journal of Biotechnology . tape 261 , November 10, 2017, ISSN  1873-4863 , p. 169-176 , doi : 10.1016 / j.jbiotec.2017.06.1198 , PMID 28648396 .
9. ↑ Michael Diepenbroek, Uwe Schindler, Robert Huber, Stéphane Pesant, Markus Stocker: Terminology supported archiving and publication of environmental science data in PANGEA . In: Journal of Biotechnology . tape 261 , November 10, 2017, ISSN  1873-4863 , p. 177-186 , doi : 10.1016 / j.jbiotec.2017.07.016 , PMID 28743591 .
10. ↑ Lorenz C. Reimer, Carola Söhngen, Anna Vetcininova, Jörg Overmann: Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase . In: Journal of Biotechnology . tape 261 , November 10, 2017, ISSN  1873-4863 , p. 187-193 , doi : 10.1016 / j.jbiotec.2017.05.004 , PMID 28487186 .
11. ↑ Stefan Bietz, Therese Inhester, Florian Lauck, Kai Sommer, Mathias M. von Behren: From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library . In: Journal of Biotechnology . tape 261 , November 10, 2017, ISSN  1873-4863 , p. 207-214 , doi : 10.1016 / j.jbiotec.2017.06.004 , PMID 28610996 .
12. ^ I. Schomburg, L. Jeske, M. Ulbrich, S. Placzek, A. Chang: The BRENDA enzyme information system-From a database to an expert system . In: Journal of Biotechnology . tape 261 , November 10, 2017, ISSN  1873-4863 , p. 194-206 , doi : 10.1016 / j.jbiotec.2017.04.020 , PMID 28438579 .
13. ↑ Rolf Ofen, Jan Engelhardt, Anika Erxleben, Jörg Fallmann, Björn Grüning: RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation . In: Journal of Biotechnology . tape 261 , November 10, 2017, ISSN  1873-4863 , p. 76-84 , doi : 10.1016 / j.jbiotec.2017.05.019 , PMID 28554830 .
14. ↑ J. Yu, J. Blom, SP Glaeser, S. Jaenicke, T. Juhre: A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies . In: Journal of Biotechnology . tape 261 , November 10, 2017, ISSN  1873-4863 , p. 2-9 , doi : 10.1016 / j.jbiotec.2017.07.010 , PMID 28705636 .
15. ↑ Alexander Fillbrunn, Christian Dietz, Julianus Pfeuffer, René Rahn, Gregory A. Landrum: KNIME for reproducible cross-domain analysis of life science data . In: Journal of Biotechnology . tape 261 , November 10, 2017, ISSN  1873-4863 , p. 149–156 , doi : 10.1016 / j.jbiotec.2017.07.028 , PMID 28757290 .
16. ↑ Julianus Pfeuffer, Timo Sachsenberg, Oliver Alka, Mathias Walzer, Alexander Fillbrunn: OpenMS - A platform for reproducible analysis of mass spectrometry data . In: Journal of Biotechnology . tape 261 , November 10, 2017, ISSN  1873-4863 , p. 142-148 , doi : 10.1016 / j.jbiotec.2017.05.016 , PMID 28559010 .
17. ↑ Knut Reinert, Temesgen Hailemariam Dadi, Marcel Ehrhardt, Hannes Hauswedell, Svenja Mehringer: The SeqAn C ++ template library for efficient sequence analysis: A resource for programmers . In: Journal of Biotechnology . tape 261 , November 10, 2017, ISSN  1873-4863 , p. 157-168 , doi : 10.1016 / j.jbiotec.2017.07.017 , PMID 28888961 .
18. ↑ Michael Turewicz, Michael Kohl, Maike Ahrens, Gerhard Mayer, Julian Uszkoreit: BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication . In: Journal of Biotechnology . tape 261 , November 10, 2017, ISSN  1873-4863 , p. 116-125 , doi : 10.1016 / j.jbiotec.2017.06.005 , PMID 28606611 .
19. ^ René Meier, Christoph Ruttkies, Hendrik Treutler, Steffen Neumann: Bioinformatics can boost metabolomics research . In: Journal of Biotechnology . tape 261 , November 10, 2017, ISSN  1873-4863 , p. 137-141 , doi : 10.1016 / j.jbiotec.2017.05.018 , PMID 28554829 .
20. ^ Frank T. Bergmann, Stefan Hoops, Brian Klahn, Ursula Kummer, Pedro Mendes: COPASI and its applications in biotechnology . In: Journal of Biotechnology . tape 261 , November 10, 2017, ISSN  1873-4863 , p. 215–220 , doi : 10.1016 / j.jbiotec.2017.06.1200 , PMID 28655634 , PMC 5623632 (free full text).
21. ^ Sebastian Jaenicke, Stefan P. Albaum, Patrick Blumenkamp, ​​Burkhard Linke, Jens Stoye: Flexible metagenome analysis using the MGX framework . In: Microbiome . tape 6 , no. 1 , 2018, ISSN  2049-2618 , p. 76 , doi : 10.1186 / s40168-018-0460-1 , PMID 29690922 , PMC 5937802 (free full text).
22. ↑ Abhinav Nellore, Ben Langmead: Cloud computing for genomic data analysis and collaboration . In: Nature Reviews Genetics . tape 19 , no. 4 , April 2018, ISSN  1471-0064 , p. 208–219 , doi : 10.1038 / nrg.2017.113 ( nature.com [accessed February 12, 2019]).
23. ↑ de.NBI summer school 2015. de.NBI, accessed on February 12, 2019 . 
24. ↑ de.NBI summer school 2016. Accessed on February 12, 2019 . 
25. ↑ de.NBI summer school 2017. Accessed on February 12, 2019 . 
26. ↑ de.NBI Summer School 2018. Accessed on February 12, 2019 . 
27. ↑ de.NBI Summer School 2019. Accessed on February 12, 2019 . 
28. ↑ de.NBI Summer School 2020 - Metagenomics. Retrieved March 3, 2020 . 
29. ↑ de.NBI Cloud Summer School 2017. Accessed on February 12, 2019 . 
30. ↑ de.NBI Winterschule 2018. Accessed on February 12, 2019 . 
31. ↑ Summer school for curious students who want to discover the natural sciences of the future. Martin Luther University Halle-Wittenberg, accessed on March 3, 2020 .