de.NBI Cloud federation through ELIXIR AAI

Belmann, Peter; Fischer, Björn; Kruger, Jan Walters; Procházka, Michal; Rasche, Helena; Prinz, Manuel; Hanussek, Maximilian; Lang, Martin; Bartusch, Felix; Gläßle, Benjamin; Krüger, Jens; Pühler, Alfred; Sczyrba, Alexander

doi:10.12688/f1000research.19013.1

Cited by 16 publications

(13 citation statements)

References 5 publications

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“…Since the establishment of the de.NBI Cloud 17 , 18 , all partners work on different cloud-based applications such as tailor-made images for specific bioinformatics analysis (Metagenomics, Nanopore sequencing, ASA 3 P 19 ) that also play a key role in many of the workshops provided.…”

Section: Bioinformatics Training In Germany By Denbimentioning

confidence: 99%

“…Training and outreach activities. Researchers, who are interested in the analysis of genomic, metagenomic or postgenomic data or who want to get familiar with the use of the de.NBI Cloud 17 , 18 are welcome to join one of the workshops offered by BiGi. Nanopore best practice workshop.…”

Section: Bioinformatics Training In Germany By Denbimentioning

confidence: 99%

“… Introduction to the de.NBI Cloud. There are basic courses on the use of the de.NBI Cloud 17 , 18 , which are offered in Bielefeld and Gießen or also as dedicated workshops on scientific conferences. In these courses, participants learn to setup a research project on the de.NBI Cloud, to work with virtual instances, to efficiently utilize cloud computing resources, about networking and security issues and means of deploying bioinformatics tools in the cloud.…”

Section: Bioinformatics Training In Germany By Denbimentioning

confidence: 99%

“…Through a cloud federation setup, the six cloud sites including Bielefeld, Gießen, Freiburg, Heidelberg, Berlin and Tübingen are integrated into a single cloud platform and offer more than 33000 cores and 38 PB of storage capacity in total. A single sign-on (SSO) mechanism enables the user to access any de.NBI Cloud service via their home institution account using the ELIXIR authentication and authorization infrastructure system (ELIXIR AAI) and in particular Perun, the identity and access management system of ELIXIR 17 .…”

Section: Denbi Cloud-based Trainingmentioning

confidence: 99%

“…Currently, the de.NBI Cloud offers the project types SimpleVM and OpenStack 17 . Both project types are using virtual machines (VM), where a VM is an emulation of an operating system and represents one of the main building blocks of the cloud.…”

Section: Denbi Cloud-based Trainingmentioning

confidence: 99%

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The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

et al. 2020

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The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF). The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics community with international network structures. The de.NBI members also run the German node (ELIXIR-DE) within the European ELIXIR infrastructure. The de.NBI / ELIXIR-DE training platform, also known as special interest group 3 (SIG 3) ‘Training & Education’, coordinates the bioinformatics training of de.NBI and the German ELIXIR node. The network provides a high-quality, coherent, timely, and impactful training program across its eight service centers. Life scientists learn how to handle and analyze biological big data more effectively by applying tools, standards and compute services provided by de.NBI. Since 2015, more than 300 training courses were carried out with about 6,000 participants and these courses received recommendation rates of almost 90% (status as of July 2020). In addition to face-to-face training courses, online training was introduced on the de.NBI website in 2016 and guidelines for the preparation of e-learning material were established in 2018. In 2016, ELIXIR-DE joined the ELIXIR training platform. Here, the de.NBI / ELIXIR-DE training platform collaborates with ELIXIR in training activities, advertising training courses via TeSS and discussions on the exchange of data for training events essential for quality assessment on both the technical and administrative levels. The de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.

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Section: Bioinformatics Training In Germany By Denbimentioning

confidence: 99%

Section: Bioinformatics Training In Germany By Denbimentioning

confidence: 99%

Section: Bioinformatics Training In Germany By Denbimentioning

confidence: 99%

Section: Denbi Cloud-based Trainingmentioning

confidence: 99%

Section: Denbi Cloud-based Trainingmentioning

confidence: 99%

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The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

et al. 2020

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Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions

et al. 2022

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Third-generation long-read sequencing is transforming plant genomics. Oxford Nanopore Technologies and Pacific Biosciences are offering competing long-read sequencing technologies and enable plant scientists to investigate even large and complex plant genomes. Sequencing projects can be conducted by single research groups and sequences of smaller plant genomes can be completed within days. This also resulted in an increased investigation of genomes from multiple species in large scale to address fundamental questions associated with the origin and evolution of land plants. Increased accessibility of sequencing devices and user-friendly software allows more researchers to get involved in genomics. Current challenges are accurately resolving diploid or polyploid genome sequences and better accounting for the intra-specific diversity by switching from the use of single reference genome sequences to a pangenome graph.

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ARTS-DB: a database for antibiotic resistant targets

Mungan

Blin

Ziemert

2021

Nucleic Acids Research

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As a result of the continuous evolution of drug resistant bacteria, new antibiotics are urgently needed. Encoded by biosynthetic gene clusters (BGCs), antibiotic compounds are mostly produced by bacteria. With the exponential increase in the number of publicly available, sequenced genomes and the advancements of BGC prediction tools, genome mining algorithms have uncovered millions of uncharacterized BGCs for further evaluation. Since compound identification and characterization remain bottlenecks, a major challenge is prioritizing promising BGCs. Recently, researchers adopted self-resistance based strategies allowing them to predict the biological activities of natural products encoded by uncharacterized BGCs. Since 2017, the Antibiotic Resistant Target Seeker (ARTS) facilitated this so-called target-directed genome mining (TDGM) approach for the prioritization of BGCs encoding potentially novel antibiotics. Here, we present the ARTS database, available at https://arts-db.ziemertlab.com/. The ARTS database provides pre-computed ARTS results for >70,000 genomes and metagenome assembled genomes in total. Advanced search queries allow users to rapidly explore the fundamental criteria of TDGM such as BGC proximity, duplication and horizontal gene transfers of essential housekeeping genes. Furthermore, the ARTS database provides results interconnected throughout the bacterial kingdom as well as links to known databases in natural product research.

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de.NBI Cloud federation through ELIXIR AAI

Cited by 16 publications

References 5 publications

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions

ARTS-DB: a database for antibiotic resistant targets

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