The number of SARS-CoV-2 infections increases dramatically in Germany and worldwide from day to day. This poses immense challenges for society and for each of us.
Scientists involved in projects to curb the corona pandemic, prevent and treat COVID-19, or other corona virus related work will be given priority access to de.NBI cloud resources. de.NBI encourages scientists who need compute resources for their work to contact us at email@example.com.
Project applications can be submitted via the de.NBI Cloud Portal (https://cloud.denbi.de/get-started/). Applications include a short description (less than one page) of the proposed project and a list of required resources. The research proposals will then be checked for compliance with the resources at the respective de.NBI Cloud sites. Access to resources will be provided ASAP. Teams who get access to de.NBI Cloud resources are expected to publish their results in the open scientific literature.
The de.NBI Cloud Federation provides computing resources for the life sciences. This includes more than 20,000 CPUs and 30 PB storage. We want to give researchers from Germany and across Europe the opportunity to improve our understanding of the SARS-CoV-2 virus and to accelerate the development of treatments and vaccines to combat COVID-19.
COVID-19 related research requires extensive involvement from areas such as epidemiology, bioinformatics, molecular modeling, etc. In this context, enormous computing capacities are necessary. The de.NBI Cloud supports these research activities with one of the most powerful academic clouds in Europe by providing compute resources to combat the virus.
Types of de.NBI Cloud services
The de.NBI Cloud provides different types of projects, starting from pre-configured VMs (de.NBI Cloud SimpleVMs), where software packages for certain use cases are pre-installed and accessible through a remote desktop. Larger projects can utilize Openstack projects (Infrastructure as a Service) or Kubernetes or SLURM clusters (Platform as a Service). If you are unsure which project type would fit your needs, contact us at firstname.lastname@example.org.
COVID-related projects supported by the de.NBI Cloud
CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance
CovRadar is a tool for molecular surveillance of the Corona spike protein. The spike protein contains the receptor binding domain (RBD) that is used as a target for most vaccine candidates. CovRadar consists of a workflow pipeline and a web application that enable the analysis and visualization of over 250,000 sequences.
ELIXIR’s services to support COVID-19 research
de.NBI Cloud resources are offered to ELIXIR services to support COVID-19 research, including deposition of databases, data analysis and provisioning of compute resources.
Magellan: COVID-19 Omics Explorer
Magellan is a web application developed by the Hub for Innovations in Digital Health (HiDiH) for the display and analysis of next-generation sequencing data with a focus on COVID-19 diseases. The application runs on the de.NBI Cloud infrastructure.The focus of the omics data is on single-cell sequencing data, but other omics data, such as epigenetic data, will also be integrated in the long term. The visualization of bulk Whole Genome Bisulfite Sequencing (WGBS) Data will allow an analysis of condition dependent methylation patterns in promotor regions of coding genes and certain enhancer regions. The average CpG methylation of a genetic region is used as a marker for the specific region.
The goal is to provide free access to the highly relevant data of COVID-19 patients for the community. The data can be freely accessed via customizable plots. This enables scientists and medical professionals to test their own hypotheses or generate new ones. If required, extended direct access to the data can be requested and checked. Magellan currently provides access to previously published data on gene expression in various lung tissue samples (https://www.biorxiv.org/content/10.1101/2020.03.13.991455v1). Magellan will soon provide access to data on the temporal gene expression of COVID-19 patients.
German Human Genome Phenome Archive GHGA
The DFG funded NGS competence centers Kiel, Dresden, Tübingen, and the West German Genome Center recently decided to sequence more than 1000 host human genomes to tackle questions regarding host genomics and the influence on the course of the COVID-19 disease and possible treatments. The resulting data will be stored in the infrastructure of the German Human Genome Phenome Archive GHGA at the de.NBI Cloud sites in Heidelberg and Tübingen. Scientists from different German Universities and research centers will get controlled access to these data. This project is part of the broader association of the German NGS Centers and partners of the NFDI GHGA to fight the Covid 19 pandemia.
Also developed by HiDiH, the MapMyCorona website provides the possibility to compute similarities of any sequence (protein or nucleotide) to already available viral SARS-CoV-2 sequences. The website displays the matching hits on a world map, together with temporal information and offers various display options. Hence, using this website, one can follow the geographical and temporal distribution of SARS-CoV-2 sequences and track the spread of viral strains.
The COV2Imaging project aids the computational analysis of image-based drug screens against SARS-COV2. In the project, high-throughput cell-based assays are performed that result in large numbers of fluorescence imagery. These will be analysed in a distributed computing infrastructure and shared between groups at the German Cancer Research Center (DKFZ) and Heidelberg University. Experiments should eventually result in novel compound/drug candidates for treatment of COVID-19.
Best practices for the analysis of SARS-CoV-2 data: Genomics and Cheminformatics
The de.NBI Cloud site Freiburg is part of the global Galaxy project providing publicly accessible infrastructure and workflows for SARS-CoV-2 data analyses, using open source tools and public cyberinfrastructure for transparent, reproducible analyses of viral datasets.
COVID19 Pangenome Visualization
The aim of the project is to build an interactive pangenome visualization tool for COVID-19 data that includes annotation and metadata. The VirtualBiohackathon COVID19 2020, taking place from 5th-11th April 2020 presents a cohesive effort to create tools for COVID-19 analysis. The major deliverable of the hackathon is a public sequence resource for COVID-19 following the FAIR guidelines. See the landing page for potential project participants.
Folding@home supporting COVID-19 research
The de.NBI Cloud sites Bielefeld and Heidelberg are providing free compute resources to the Folding@home COVID-19 initiative, a world-wide endeavour to solve protein structures and simulate protein structure dynamics. New insights from these simulations can reveal new therapeutic opportunities. Contributions by de.NBI Cloud are monitored here.
The #WirVsVirus Hackathon
Supported by the federal government, the digital #wirvsvirus hackathon has been organized March 20-22, 2020. All across Germany, individuals have been working on solutions for the corona crisis. The #WirVsVirus Online Hackathon is a digital space where we can all develop, test and improve solutions for emerging challenges.
Citizens as well as the ministries had the opportunity to submit their challenges until the Thursday before the hackathon. They asked themselves: What are the most pressing challenges we’re currently facing? What are the problems you would like to see solved? The challenges represent the ideas of individuals from all walks of life in Germany.
The de.NBI Cloud offers “company support” during the hackathon and afterwards.