• https://doi.org/10.7490/f1000research.1120270.1Copy DOI Icon

The de.NBI cloud federation in 2025

Show More
  • Abstract
  • Literature Map
  • Similar Papers
Abstract

To meet the rising demand for comprehensive bioinformatics tools in the life sciences, the German Network for Bioinformatics Infrastructure (de.NBI) was established in 2015 as a national bioinformatics consortium offering high quality bioinformatics services, comprehensive training and powerful computing capacities. The de.NBI Cloud is one of the flagship services for the de.NBI & ELIXIR Germany network with more than 4000 registered users, over 1350 projects, of which more than 620 are currently active, and over 1380 publications citing its use. Eight federated cloud centers adhere to a unified governance structure and utilize the centralized project application and management workflow available through the de.NBI Cloud Portal. Single sign-on and user management are provided via LifeScience Login and eduGAIN. PIs from German universities or research institutes may submit project applications, which are reviewed by the Cloud Access Committee and, upon approval, resources are allocated to one of the cloud centers. Regular staff training, mutual internal audits and external ISMS certification (ISO27001 or BSI C5) ensure secure operations of the data centers. The de.NBI Cloud offers various project types for your computing needs, covering different levels of expertise and experience in cloud computing: From the simple and fast start of pre-configured VMs with easy access (SimpleVM), to the use of bioinformatics tools and workflows (Galaxy), to the possibility of running your own infrastructures and services (OpenStack & Kubernetes). We offer pre-configured virtual research environments (VRE), which can be accessed easily when using our SimpleVM platform. They include integrated development environments, data science notebooks and virtual desktop environments. The VREs can be accessed in the web browser or by secure shell (ssh). VREs and images tailored for specific needs can also be used to provide uniform VMs for trainings and workshops. The cluster module makes it easy to set up a SLURM-based grid cluster for resource-intensive computations. Users can also provide recipes for custom VREs. The de.NBI Cloud provides computational resources for a diverse portfolio of projects within Europe (ELIXIR, EOSC, Horizon Europe) and Germany (NFDI projects), ranging from (web)service development and hosting, to execution of memory and CPU-intensive bioinformatics workflows, GPU resources for machine learning, resources for hackathons, workshops and trainings, as well as resources for proof-of-concept development, and secure environments for sensitive data processing. Regular trainings and workshops teach you how to use the cloud infrastructure effectively for your research. The annual Cloud User Meeting offers users the opportunity for networking and to get in touch with the administrators of the cloud locations and the cloud governance. Researchers present their work in the cloud and training courses expand the range of expertise for experienced cloud users, while also providing a comprehensive introduction for beginners. The de.NBI Cloud offers various project types for your computing needs, covering different levels of expertise and experience in cloud computing: From the simple and fast start of pre-configured VMs with easy access (SimpleVM), to the use of bioinformatics tools and workflows (Galaxy), to the possibility of running your own infrastructures and services (OpenStack & Kubernetes). Selection of training course topics: • VM basics: Linux & command line • SimpleVM & Research Environments • BioConda & BioContainers • CWL, Nextflow, Snakemake • Infrastructure as Code: Ansible, Terraform • Grid computing: BiBiGrid / SLURM

Similar Papers
  • Research Article
  • Citations8

Clinical validation of explainable AI for fetal growth scans through multi-level, cross-institutional prospective end-user evaluation

  • Jan 15, 2025
  • Scientific Reports
  • Zahra Bashir +10
  • Book Chapter
  • Citations1

Categorization of Emergent Processes by Students at Different Levels of Expertise

  • Apr 24, 2019
  • Randi A Engle +1
  • Journal Issue

ISSUES OF INTEGRATION OF SKILLS FAVOURABLE TO HEALTH IN PERSONS WITH DIABETES MELLITUS

  • Jan 01, 2018
  • Social Work
  • Vida Gudžinskienė +1
  • Research Article
  • Citations19

Assessing the reliability, validity and acceptance of a classification scheme of usability problems (CUP)

  • Sep 01, 2013
  • The Journal of Systems & Software
  • Sigurbjorg Groa Vilbergsdottir +2
  • Book Chapter
  • Citations6

A Conceptualisation of an Agent-Oriented Triage Decision Support System

  • Jan 01, 2012
  • Shamimi Halim +3
  • Research Article
  • Citations7

Who gains more: Experts or novices? The benefits of interaction under numerical uncertainty.

  • Aug 01, 2018
  • Journal of Experimental Psychology: Human Perception and Performance
  • Francesco Sella +4
  • Research Article
  • Citations14

Laparoscopic Common Bile Duct Exploration Four-Task Training Model: Construct Validity

  • Jan 01, 2012
  • JSLS : Journal of the Society of Laparoendoscopic Surgeons
  • Alexis Sánchez +5
  • Research Article
  • Citations48

Acquisition of flexible cystoscopy skills on a virtual reality simulator by experts and novices

  • Jan 01, 2010
  • BJU International
  • Barbara M.A Schout +6
  • Abstract

Kiosk 8R-FB-07 - Quantitative Segmentation Analysis in CMR Across Different Levels of Expertise – FBom Beginners to Experts

  • Jan 01, 2024
  • Journal of Cardiovascular Magnetic Resonance
  • Jan Gröschel +7
  • Research Article
  • Citations3

Reliability of Bigliani's Classification using Magnetic Resonance Imaging for Determination of Acromial Morphology.

  • Nov 01, 2022
  • Malaysian orthopaedic journal
  • Sahin K +5
  • Research Article
  • Citations24

Icon-function relationship in toolbar icons

  • Jul 24, 2008
  • Displays
  • Stefano Passini +2
  • Preprint Article

OpenEBench. TCGA: A community-led benchmarking use case.

  • Jan 16, 2020
  • F1000Research
  • Javier Garrayo Ventas +7
  • Dissertation
  • Citations3

Instructional computer use by COE faculty in Turkey: application of diffusion of innovations theory

  • Sep 09, 2014
  • Ismail Sahin
  • PDF
  • Research Article
  • Citations96

Video game telemetry as a critical tool in the study of complex skill learning.

  • Sep 18, 2013
  • PLoS ONE
  • Joseph J Thompson +3
  • Book Chapter
  • Citations8

Did You Forget Your Password?

  • Jan 01, 2011
  • Abbas Moallem
Cactus Communications logo

Copyright 2026 Cactus Communications. All rights reserved.