Latest project: Decoding Context-Dependent Genetic Networks in vivo

Project: Principal Investigator: Stegle Oliver, Institution: University of Heidelberg / EMBL / DKFZ, Workgroup: ERC Decode Project, Research Topics: Computational biology

Resources: Project type: Openstack

Description: The evolutionary success of multicellular organisms is based on the division of labor between cells. While some of the molecular determinants for cell fate specification have been identified, a fundamental understanding of which genetic activities are required in each cell of a developing tissue is still outstanding. The DECODE project will develop and apply leading-edge system genetics methods to Arabidopsis and Drosophila, two major model systems from the plant and animal kingdoms to decode context-dependent genetic networks in vivo. To achieve this, DECODE will bring together experimental and theoretical groups with complementary expertise in model organism genetics and cellular phenotyping, single-cell genomics, statistics and computational biology. Building on our combined expertise, we will create functional genetic maps using conditional CRISPR/Cas9-based single- and higher order knockout perturbations in vivo combined with single-cell expression profiling and imaging. Coupled with powerful computational analysis, this project will not only define, predict and rigorously test the unique genetic repertoire of each cell, but also unravel how genetic networks adapt their topology and function across cell types and external stimuli. With more than thousand conditional knockouts, characterized by several million single-cell transcriptome profiles and high-resolution imaging this project will create the largest single-cell perturbation map in any model organism and will provide fundamental insights into the genetic architecture of complex tissues. Analyzing two tissues with divergent organization and regulatory repertoire will enable us to uncover general principles in the genetic circuits controlling context dependent cell behavior. Consequently, we expect that the DECODE project in model organisms will lay the conceptual and methodological foundation for perturbation-based functional atlases in other tissues or species.


This is the latest project for which the PI has agreed to publish the data on this page. The project shown here is therefore not necessarily the most recent project for which the project application has been approved.


All projects

ChIP-seq / ATAC-seq workshop

Project: Principal Investigator: Herrmann Carl, Institution: Medical Faculty Heidelberg, Workgroup: HDSU, Lifetime: 3 months, Research Topics: Computational biology

Resources: Project type: Simple Vm, Number of possible VMs: 2, Total number of cores: 64, Total amount of RAM: 512 GB, Amount of Object Storage: 0 GB


de.NBI - CeBiTec Nanopore Workshop - Best Practice and SARS-CoV-2 applications

Project: Principal Investigator: Alexander Sczyrba, Institution: Center for Biotechnology - Bielefeld University, Workgroup: BiGi, Lifetime: 3 months, Research Topics: Sequence analysis, Sequencing, Sequence assembly, Virology

Resources: Project type: Simple Vm, Number of possible VMs: 17, Total number of cores: 272, Total amount of RAM: 544 GB, Amount of Object Storage: 0 GB


Using machine learning approaches to predict antimicrobial resistance from bacterial genome sequences

Project: Principal Investigator: Oliver Kohlbacher, Institution: Bioinformatics, Tubingen, Lifetime: 9 months, Research Topics: Pathogens

Resources: Project type: Simple Vm


Alignment- and reference-free Phylogenomics

Project: Principal Investigator: Jens Stoye, Institution: Center for Biotechnology / Faculty of Technology, Bielefeld University, Workgroup: Genome Informatics, Lifetime: 12 months, Research Topics: Sequence analysis, Phylogeny

Resources: Project type: Simple Vm, Number of possible VMs: 1, Total number of cores: 32, Total amount of RAM: 1024 GB, Amount of Object Storage: 0 GB


Integrative analysis of common and rare high-impact variants for a more comprehensive genetic risk assessment.

HuMAGs - exploring how microbes co-exist in human microbiomes

Project: Principal Investigator: Ulisses Rocha, Institution: Helmholtz Centre for Environmental Research, Workgroup: Microbia Data Science, Lifetime: 10 months, Research Topics: Sequence analysis, Computational biology, Function analysis, Biological databases, Phylogenomics, Metagenomics, Microbiology, Human disease, Microbial ecology

Resources: Project type: Openstack, Number of possible VMs: 14, Total number of cores: 80, Total amount of RAM: 640 GB, Amount of Object Storage: 0 GB


Using NLP-Networks (Transformers) for human genome data

Project: Institution: University of Bielefeld, Research Topics: Computational biology, Bioinformatics, Biomedical science, Sequence classification


Cloud User Meeting 2020

Project: Principal Investigator: Alexander Sczyrba, Institution: Center for Biotechnology (CeBiTec), Bielefeld, Research Topics: Bioinformatics

Resources: Project type: Openstack, Number of possible VMs: 100, Total number of cores: 650, Total amount of RAM: 1300 GB, Amount of Object Storage: 100 GB


Meet-U 4EU+ Teaching project

Project: Principal Investigator: Herrmann Carl, Research Topics: Computational biology


SIRIUS back end

Project: Institution: Friedrich-Schiller-University Jena, Workgroup: Chair of Bioinformatics, Research Topics: Metabolites, Computer science, Mass spectrometry, Metabolomics, Computational chemistry

Resources: Project type: Openstack


Sequence-based prediction of Translational Efficiency

Project: Principal Investigator: Pascal Falter-Braun, Institution: Institute of Network Biology, Workgroup: Network Biology, Research Topics: Sequence analysis, Protein interactions, Computational biology


SDC BioDATEN

Project: Research Topics: Ontology and terminology, Computational biology, Database management


Generation of Mass Spectrometry Decoy Spectra with Adversarial Autoencoders

Project: Research Topics: Proteomics, Mass spectrometry


CovRadar: a web application for SARS-CoV-2 molecular surveillance

Project: Principal Investigator: Stephan Fuchs, Institution: Robert Koch Institut, Workgroup: Methodology and Research Infrastructure - MF1: Bioinformatics, Lifetime: 12 months, Research Topics: Sequence analysis, Data visualisation, Bioinformatics, Virology, Protein variants, Public health and epidemiology

Resources: Project type: Openstack, Number of possible VMs: 7, Total number of cores: 180, Total amount of RAM: 360 GB, Amount of Object Storage: 0 GB


Innovative benchmarking approaches to improve Computational Methods for big data analysis in Health.

Project: Principal Investigator: Herrmann Carl, Institution: Heidelberg University, Workgroup: Health Data Science Unit, Medical Faculty, Research Topics: Computational biology, Genomics, Gene regulation, Oncology


Proteomics of the Springtail Folsomia Candida

Project: Principal Investigator: Oliver Kohlbacher, Institution: Dept. of Computer Science, University of Tübingen, Workgroup: Applied Bioinformatics, Research Topics: Proteomics, Protein expression


Modeling and simulation of multicellular processes during tissue morphogenesis

Project: Principal Investigator: Lutz Brusch, Institution: Technische Universität Dresden, Workgroup: Center for Information Services and High Performance Computing, Research Topics: Computational biology, Personalised medicine


Ganon in the 2 nd round of the CAMI II challenge

Project: Research Topics: Sequence analysis, Metagenomics


Myzel - Medical Cloud Platform

Project: Principal Investigator: Maier-Hein Klaus, Institution: Deutsches Krebsforschungszentrum, Workgroup: Medical Image Computing, Lifetime: 12 months, Research Topics: Medical imaging, Natural language processing

Resources: Project type: Openstack, Number of possible VMs: 2, Total number of cores: 60, Total amount of RAM: 384 GB, Amount of Object Storage: 0 GB


Wheat Structural Variant Calling

Project: Research Topics: Structure analysis, Genetic variation


A R Shiny based web server for performing BLAST queries on novel SARS-CoV2 sequences

Project: Principal Investigator: Herrmann Carl, Institution: Heidelberg University, Workgroup: Health Data Science Unit, Research Topics: Sequence analysis, Infectious disease


kmer based spa typing

Project: Principal Investigator: Gunnar W. Klau, Institution: Heinrich-Heine-Universität Düsseldorf, Workgroup: Algorithmische Bioinformatik, Lifetime: 3 months

Resources: Project type: Simple Vm, Number of possible VMs: 1, Total number of cores: 32, Total amount of RAM: 256 GB, Amount of Object Storage: 0 GB


Biohackathon Coivd19

Project: Principal Investigator: Alexander Sczyrba, Institution: Center for Biotechnology, Bielefeld University, Germany, Workgroup: Computational Metagenomics, Lifetime: 6 months

Resources: Project type: Openstack, Number of possible VMs: 3, Total number of cores: 96, Total amount of RAM: 192 GB, Amount of Object Storage: 0 GB


denbivsvirus Bielefeld

Project: Principal Investigator: Alexander Sczyrba, Institution: Center for Biotechnology, Bielefeld University, Workgroup: Computational Metagenomics, Lifetime: 15 months

Resources: Project type: Openstack, Number of possible VMs: 15, Total number of cores: 190, Total amount of RAM: 700 GB, Amount of Object Storage: 500 GB


WirVsVirus Hackathon der Bundesregierung

Project: Principal Investigator: Alexander Sczyrba, Institution: Center for Biotechnology, Bielefeld University, Workgroup: Computational Metagenomics

Resources: Project type: Openstack


Benchmarking proteomics nextflow workflows on PRIDE data

Project: Principal Investigator: Oliver Kohlbacher, Institution: University of Tübingen, Workgroup: Applied Bioinformatics


Performance improvements of DNA methylome deconvolution software MeDeCom

visualization webtool for deep learning features

de.NBI Training

Project: Principal Investigator: Malik Alawi, Institution: University Medical Center Hamburg-Eppendorf, Workgroup: Bioinformatics Core


Petasearch Database Creation

Gene Structural Prediction with Deep Learning

Project: Principal Investigator: Andreas Weber, Institution: Heinrich Heine University, Workgroup: Plant Biochemistry

Resources: Project type: Openstack


Understanding gluten related disorders at the molecular level

Project: Principal Investigator: Veronica Dodero


Rheuma.Vor.Transcriptomics

Project: Principal Investigator: Schwarting Andreas, Institution: Universitätsmedizin der Johannes Gutenberg Universität Mainz, Workgroup: Ambulanz für Rheumatologie,

Resources: Project type: Simple Vm


metagenomic analysis of human infant fecal sample

Project: Principal Investigator: Daniel Huson, Institution: University of tuebingen, Workgroup: algorithm in bioinformatics, Lifetime: 24 months

Resources: Project type: Openstack, Number of possible VMs: 4, Total number of cores: 128, Total amount of RAM: 1024 GB, Amount of Object Storage: 150 GB


Elucidating the origin of planktonic foraminifera

Project: Principal Investigator: Michal Kucera, Institution: MARUM & Fachbereich Geowissenschaften, Workgroup: Micropaleontology, Lifetime: 18 months

Resources: Number of possible VMs: 10, Total number of cores: 320, Total amount of RAM: 2560 GB, Amount of Object Storage: 0 GB


Type Strain Genome Server (TYGS)

Project: Principal Investigator: Markus Göker, Institution: Leibniz Institute DSMZ, Braunschweig, Workgroup: Phylogenomics (Department of Bioinformatics)

Resources: Project type: Openstack


Bioschemas knowledge graph - BH2019Europe

GCB 2019 Cloud Tutorial

Project: Principal Investigator: Alexander Sczyrba, Institution: Center for Biotechnology, Bielefeld University, Workgroup: de.NBI Cloud Team, Lifetime: 1 months

Resources: Project type: Openstack, Number of possible VMs: 60, Total number of cores: 1680, Total amount of RAM: 3840 GB, Amount of Object Storage: 1000 GB


Sustainable Innovation of Microbiome Applications in the Food System

Project: Principal Investigator: Alexander Sczyrba, Institution: Bielefeld University, Center for Biotechnology, Workgroup: Computational Metagenomics

Resources: Project type: Openstack