The participation of the German Network for Bioinformatics Infrastructure (de.NBI) in research projects to fight the pandemic triggered by SARS-CoV-2

The current corona pandemic is a major challenge for our society and therefore requires special attention from the established scientific structures. It is important to advance molecular biological research of corona viruses, especially of SARS-CoV-2, and to investigate both medical and epidemiological aspects of the infection process in COVID-19 disease. These research areas generate large amounts of data requiring intensive informatics analysis. Here, the German Network for Bioinformatics Infrastructure (de.NBI), which is funded by the BMBF, is obliged to provide both the wide collection of analysis programs and the compute capacities of the network's own de.NBI cloud. Both, analysis programs and compute capacities can be used free of charge by all researchers in the life sciences. In addition, working groups within the de.NBI network are directly involved in corona research projects. A survey among the PIs of the de.NBI network resulted in a list of a total of 29 projects that are presented on the de.NBI website. The projects show the important role the de.NBI network for the current corona research.

512px SARS CoV 2 without background

Source: CDC/ Alissa Eckert, MS; Dan Higgins, MAM

 

The recent establishment of the European Virus Bioinformatics Center - EVBC in Jena also helps to advance research on coronaviruses and curates a list of bioinformatics tools designed explicitly for SARS-CoV-2 and coronaviruses. Members of the de.NBI network are also part of EVBC, which pursues issues related to find the best strategies to control and treat viral diseases but also to understand the role of viruses in different ecosystems.

For further information, visit http://evbc.uni-jena.de/

 

Sequence variants and geographical distribution of the SARS-CoV-2 virus

Analyzing SARS-CoV-2 chromatograms and mutations using the genome analysis server GEAR

J. Korbel, EMBL Heidelberg

HD-HuB 

MapMyCorona

R. Eils, HiDiH Berlin  

 HD-HuB

Characterizing CoV-2 coronavirus substrains by nanopore sequencing for a spacio-temporal epidemiology

J. Kalinowski, A. Sczyrba, Bielefeld University

BiGi

Interactions of the SARS-CoV-2 virus with human cells

(Gen)omics of SARS-CoV-2 infection: joint forces of GHGA/DeCOI and the de.NBI Cloud

Joint initiative of de.NBI/GHGA in Heidelberg and Tübingen: O. Kohlbacher, J. Korbel, O. Stegle, I. Buchhalter 

 HD-HuB / CIBI
Virus-induced lung injury: Pathobiology and novel therapeutic strategies A. Goesmann, Gießen University BiGi
RNA viruses: RNA metabolism, host response and pathogenesis A. Goesmann, Gießen University BiGi 
Excellence Cluster “Cardio Pulmonary Institute” (2019 – 2026) A. Goesmann, Gießen University BiGi 
Magellan: COVID-19 Omics Explorer R. Eils, HiDiH Berlin HD-HuB
The relevance of de.NBI tools in COVID-19 research of HiDiH  R. Eils, HiDiH Berlin  HD-HuB
Single-cell transcriptome dynamics of SARS-CoV-2 infection A. Akalin and N. Rajewsky, Max Delbruck Center For Molecular Medicine, Berlin RBC

Analysis of the COVID-19 disease

Artificial Intelligence for advancing precision medicine in severe cases of COVID-19 (CovidDataNet.NRW) M. Eisenacher, Ruhr University Bochum BioInfra.Prot
Provision of data and expertise to the Research Network of German University Hospitals on COVID-19  M. Eisenacher, Ruhr University Bochum BioInfra.Prot
Local initiative against COVID-19 at the Ruhr-University Bochum  M. Eisenacher, Ruhr University Bochum BioInfra.Prot
Covid-19 disease map construction and text mining for drug prediction  M. Hoch, S. Gupta, J. Scheel, University of Rostock RBC
Genome-wide Association Study of Severe Covid-19 with Respiratory Failure D. Ellinghaus, A. Franke, and The Severe Covid-19 GWAS Group, Kiel University RBC

Development of drugs for SARS-CoV-2 infections

Cloud-based analysis of high-throughput image-based SARS-CoV-2 screens M. Boutros, DKFZ Heidelberg  HD-HuB
Identify potential drugs and drug targets against SARS-CoV-2 by host factor siRNA screening H. Erfle, Ruprecht Karl University of Heidelberg  HD-HuB
COVID-19 Drug Design and Target Screening S. Bray, Albert Ludwigs University Freiburg   RBC
COVID-19 Drug Repurposing and Inhibitor Design Utilizing the ProteinsPlus Toolbox M. Rarey, Hamburg University BioData

Support for classical epidemiological studies

Online monitor for parameterized modeling of the SARS-CoV2 pandemic S. Hoffmann, Fritz Lipmann Institute, Jena   RBC
The role of aggressive testing and strict quarantining to avoid a total lockdown  O. Wolkenhauer, S. Bej, University of Rostock RBC
Modelling of epidemiological developments of COVID-19 U. Kummer, Heidelberg University de.NBI-SysBio

Tool development to analyze COVID-19 related data

Publication of SARS-CoV-2 Proteomics Datasets: Cooperation in the context of a de.NBI-service and ELIXIR collaboration M. Eisenacher, Ruhr University Bochum BioInfra.Prot
Convenient Access to Data, Tools and Compute resources R. Backofen,  Albert Ludwigs University Freiburg RBC
Transparent and reproducible Analysis of biomedical Data Using Galaxy, BioConda and Public Research Infrastructure  B. Grüning, Albert Ludwigs University Freiburg RBC
Galaxy Training Material, workshops, webinars, and hackathons W. Maier, B. Batut, R. Backofen, Albert Ludwigs University of Freiburg RBC
Data management for COVID-19 initiatives: NFDI4Health study hub, COVID-19 disease maps and Research Data Alliance recommendations W. Müller, M. Golebiewski, M. Rey, A. Weidemann, U. Wittig, Heidelberg Institute for Theoretical Studies, Heidelberg de.NBI-SysBio
de.NBI cloud compute and storage resources predominantly reserved to fight COVID-19 A. Sczyrba, P. Belmann, Bielefeld University BiGi
Automated quality control of COVID-19 proteomics data on the PRIDE archive O. Kohlbacher, Eberhard Karls Universität Tübingen CIBI