Projects

Latest Project: Dedicated Protein and RNA Structure Prediction Capabilities for the Wagner Lab

  • Project Information
  • Principal Investigator: Samuel Wagner
  • Research Topics: Small molecules Microbiology Pathogens Transmembrane protein prediction

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. You can find all published projects below.

SSAM-lite-server
  • Project Information
  • Research Topics: Imaging High-throughput sequencing Transcriptomics
Metagenomics Summerschool 2021
  • Project Information
  • Research Topics: Sequence analysis Metagenomics
FlowSoFine
  • Project Information
  • Principal Investigator: Stefan Janssen
  • Workgroup: Algorithmic Bioinformatics
  • Affiliations:
  • Research Topics: Microbial ecology
SILVA release
  • Project Information
  • Research Topics: Biological databases rRNA
Analysis of flavonoid biosynthesis pathway across plant species
  • Project Information
  • Principal Investigator: Boas Pucker
  • Workgroup: Plant Biotechnology and Bioinformatics
  • Project Type: Simple Vm
  • Project Lifetime: 6
  • Affiliations:
  • Research Topics: Phylogeny Genomics Splice sites
  • Resources
  • Available virtual machines: 1
  • Total RAM: 32 GB
  • Total VCPU Cores: 14 GB
  • Number of Volumes: 1
  • Amount of volume storage: 100 GB
Generative models to disentangle spatial components of cellular variation
  • Project Information
  • Research Topics: Computational biology Machine learning
Genetic analysis of Cercospora leaf spot resistance in wild and cultivated beets
  • Project Information
  • Research Topics: Agricultural science
LIFS Portal
  • Project Information
  • Research Topics: Lipids Bioinformatics Mass spectrometry
GPU_BASE
  • Project Information
  • Research Topics: Genomics Plant biology
BaktaWeb
  • Project Information
  • Research Topics: Sequence annotation Genome annotation
4D Controls-based denoising
  • Project Information
  • Research Topics: Medical imaging MRI Applied mathematics
Computational Psychiatry
  • Project Information
  • Principal Investigator: Tobias Kaufmann
  • Research Topics: Computational biology Medical imaging Genetics Neurobiology Psychiatry
Extending cross-linking mass spectrometry with cleavable cross-linkers
  • Project Information
  • Research Topics: Protein interactions Proteomics Protein structure analysis
HTS of Xcc mutant strains using CellProfiler
  • Project Information
  • Research Topics: Imaging Microbiology
Machine Learning for Protein Identification
  • Project Information
  • Research Topics: Proteomics Machine learning
Bioimage.io Model Zoo
  • Project Information
  • Principal Investigator: Florian Jug
  • Workgroup: Jug Lab
  • Project Type: Openstack
  • Project Lifetime: 12
  • Affiliations: BMBF
  • Research Topics: Cell biology Bioinformatics Bioimaging Machine learning
  • Resources
  • Available virtual machines: 7
  • Total RAM: 800 GB
  • Total VCPU Cores: 172 GB
  • Number of Volumes: 20
  • Amount of volume storage: 1024 GB
  • Amount of Object Storage: 100
Determination of the conformational loop flexibility of strongly neutralizing COV-2 antibody fragments.
  • Project Information
  • Research Topics: Protein interactions Protein structure analysis Structure prediction Molecular dynamics
Machine Learning for Antibiiotic Resistance 2
  • Project Information
  • Research Topics: Bioinformatics Machine learning
RNA-RNA interaction prediction evaluation
  • Project Information
  • Research Topics: Nucleic acid structure analysis
Identification of causative variants in patients with genetically unclassified severe congenital neutropenia
  • Project Information
  • Principal Investigator: Maksim Klimiankou
  • Workgroup: Internal Medicine II, Division of Translational Oncology
  • Project Type: Openstack
  • Project Lifetime: 12
  • Research Topics: Sequencing Molecular genetics
  • Resources
  • Available virtual machines: 1
  • Total RAM: 256 GB
  • Total VCPU Cores: 32 GB
  • Number of Volumes: 1
  • Amount of volume storage: 4000 GB
WebDECIMER
  • Project Information
  • Principal Investigator: Christoph Steinbeck
  • Workgroup: Steinbeck group
  • Project Type: Openstack
  • Project Lifetime: 12
  • Affiliations:
  • Research Topics: Small molecules Literature analysis Literature data resources
  • Resources
  • Available virtual machines: 1
  • Total RAM: 64 GB
  • Total VCPU Cores: 16 GB
  • Number of Volumes: 1
  • Amount of volume storage: 80 GB
  • Amount of Object Storage: 10
Automated Analysis of Microscopy Images Using Deep Learning
  • Project Information
  • Principal Investigator: Rohr Karl
  • Workgroup: Biomedical Computer Vision Group
  • Affiliations: BMBF Elixir Project
  • Research Topics: Cell biology Biomedical science Bioimaging Light microscopy Machine learning
de.NBI Training Event: "The Linux Command Line: From Basic Commands to Shell Scripting"
  • Project Information
  • Workgroup: Bioinformatics Core
  • Research Topics: Computational biology Bioinformatics Computer science
Diatom Virtual Slide Storage
  • Project Information
  • Research Topics: Ecology Taxonomy Bioimaging Light microscopy Machine learning Freshwater biology
Bellman's GAP for deep learning
  • Project Information
  • Principal Investigator: Stefan Janssen
  • Workgroup: Algorithmic Bioinformatics
  • Project Type: Simple Vm
  • Project Lifetime: 12
  • Affiliations:
  • Research Topics: Computer science
  • Resources
  • Available virtual machines: 2
  • Total RAM: 80 GB
  • Total VCPU Cores: 24 GB
  • Number of Volumes: 3
  • Amount of volume storage: 50 GB
RNAProNet - Infer regulatory behavior from RNA protein binding events
  • Project Information
  • Principal Investigator: Rolf Backofen
  • Workgroup: Chair for Bioinformatics
  • Project Type: Simple Vm
  • Project Lifetime: 12
  • Affiliations: BMBF
  • Research Topics: Protein interactions High-throughput sequencing Machine learning
  • Resources
  • Available virtual machines: 1
  • Total RAM: 64 GB
  • Total VCPU Cores: 16 GB
  • Number of Volumes: 3
  • Amount of volume storage: 1000 GB
ECF Hub - An interactive database for ECF sigma factors
  • Project Information
  • Principal Investigator: Alexander Goesmann
  • Workgroup: Professur für Systembiologie
  • Project Type: Openstack
  • Project Lifetime: 12
  • Affiliations: BMBF
  • Research Topics: Biological databases Protein databases Synthetic biology
  • Resources
  • Available virtual machines: 3
  • Total RAM: 48 GB
  • Total VCPU Cores: 24 GB
  • Number of Volumes: 20
  • Amount of volume storage: 750 GB
  • Amount of Object Storage: 750
EMIC sequencing pipeline
  • Project Information
  • Research Topics: Sequence analysis Microbial ecology Environmental science
Evaluation of genome assembly tools for Triticeae
  • Project Information
  • Principal Investigator: HARMEET SINGH CHAWLA
  • Workgroup: Plant Genome and System Biology
  • Project Type: Openstack
  • Project Lifetime: 6
  • Affiliations:
  • Research Topics: Plant biology Whole genome sequencing
  • Resources
  • Available virtual machines: 1
  • Total RAM: 3000 GB
  • Total VCPU Cores: 64 GB
  • Number of Volumes: 3
  • Amount of volume storage: 50000 GB
Cis-regulatory atlas of Brassica napus
  • Project Information
  • Research Topics: Gene expression Genetic variation Genomics Bioinformatics Gene regulation Plant biology DNA structural variation
SIMBA Metagenome Training Course
  • Project Information
  • Principal Investigator: Alexander Sczyrba
  • Workgroup: Computational Metagenomics
  • Project Type: Simple Vm
  • Project Lifetime: 3
  • Affiliations: Horizon 2020
  • Research Topics: Sequence analysis Metagenomics
  • Resources
  • Available virtual machines: 2
  • Total RAM: 96 GB
  • Total VCPU Cores: 42 GB
  • Number of Volumes: 2
  • Amount of volume storage: 500 GB
SFB1324 - Data Exchange and Collaborative Analysis
  • Project Information
  • Research Topics: Sequence analysis Protein structure analysis Cell biology Imaging Functional genomics Signaling pathways
VascuShare: a vascular imaging data repository
  • Project Information
  • Principal Investigator: Kyle Harrington
  • Research Topics: Imaging Bioinformatics Bioimaging
Applying - Helixer, Gene Structural Prediction with Deep Learning
  • Project Information
  • Principal Investigator: Andreas Weber
  • Workgroup: Institute of Plant Biochemistry
  • Project Type: Openstack
  • Project Lifetime: 10
  • Affiliations:
  • Research Topics: Sequence analysis Gene structure Machine learning
  • Resources
  • Available virtual machines: 3
  • Total RAM: 384 GB
  • Total VCPU Cores: 60 GB
  • Number of Volumes: 6
  • Amount of volume storage: 3000 GB
  • Amount of Object Storage: 1000
Covalent and kinetic trapping repair machinery for structural and functional studies
  • Project Information
  • Research Topics: Protein interactions Protein structure analysis Enzymes Nucleic acids
ChIP-seq / ATAC-seq workshop
  • Project Information
  • Principal Investigator: Herrmann Carl
  • Workgroup: HDSU
  • Project Type: Simple Vm
  • Project Lifetime: 15
  • Affiliations:
  • Research Topics: Computational biology
  • Resources
  • Available virtual machines: 2
  • Total RAM: 512 GB
  • Total VCPU Cores: 64 GB
  • Number of Volumes: 2
  • Amount of volume storage: 500 GB
Decoding Context-Dependent Genetic Networks in vivo
  • Project Information
  • Principal Investigator: Stegle Oliver
  • Workgroup: ERC Decode Project
  • Project Type: Openstack
  • Affiliations: Horizon 2020
  • Research Topics: Computational biology
de.NBI - CeBiTec Nanopore Workshop - Best Practice and SARS-CoV-2 applications
  • Project Information
  • Principal Investigator: Alexander Sczyrba
  • Workgroup: BiGi
  • Project Type: Simple Vm
  • Project Lifetime: 3
  • Affiliations: BMBF
  • Research Topics: Sequence analysis Sequencing Sequence assembly Virology
  • Resources
  • Available virtual machines: 22
  • Total RAM: 704 GB
  • Total VCPU Cores: 352 GB
  • Number of Volumes: 30
  • Amount of volume storage: 1500 GB
Using machine learning approaches to predict antimicrobial resistance from bacterial genome sequences
  • Project Information
  • Principal Investigator: Oliver Kohlbacher
  • Project Type: Simple Vm
  • Project Lifetime: 9
  • Research Topics: Pathogens Machine learning
Alignment- and reference-free Phylogenomics
  • Project Information
  • Principal Investigator: Jens Stoye
  • Workgroup: Genome Informatics
  • Project Type: Simple Vm
  • Project Lifetime: 24
  • Affiliations:
  • Research Topics: Sequence analysis Phylogeny
  • Resources
  • Available virtual machines: 1
  • Total RAM: 1024 GB
  • Total VCPU Cores: 32 GB
  • Number of Volumes: 1
  • Amount of volume storage: 1000 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 Information
  • Principal Investigator: Ulisses Nunes da Rocha
  • Workgroup: Microbia Data Science
  • Project Type: Openstack
  • Project Lifetime: 22
  • Affiliations:
  • Research Topics: Sequence analysis Computational biology Function analysis Biological databases Phylogenomics Metagenomics Microbiology Human disease Microbial ecology
  • Resources
  • Available virtual machines: 29
  • Total RAM: 4352 GB
  • Total VCPU Cores: 768 GB
  • Number of Volumes: 3
  • Amount of volume storage: 100000 GB
Cloud User Meeting 2020
  • Project Information
  • Principal Investigator: Alexander Sczyrba
  • Project Type: Openstack
  • Research Topics: Bioinformatics
  • Resources
  • Available virtual machines: 100
  • Total RAM: 1300 GB
  • Total VCPU Cores: 650 GB
  • Number of Volumes: 50
  • Amount of volume storage: 275 GB
  • Amount of Object Storage: 100
Meet-U 4EU+ Teaching project
  • Project Information
  • Principal Investigator: Herrmann Carl
  • Research Topics: Computational biology
Using NLP-Networks (Transformers) for human genome data
  • Project Information
  • Research Topics: Computational biology Bioinformatics Biomedical science Sequence classification
SIRIUS back end
  • Project Information
  • Workgroup: Chair of Bioinformatics
  • Project Type: Openstack
  • Affiliations:
  • Research Topics: Metabolites Computer science Mass spectrometry Metabolomics Computational chemistry
Sequence-based prediction of Translational Efficiency
  • Project Information
  • Principal Investigator: Pascal Falter-Braun
  • Workgroup: Network Biology
  • Research Topics: Sequence analysis Protein interactions Computational biology
SDC BioDATEN
  • Project Information
  • Research Topics: Ontology and terminology Computational biology Database management
Generation of Mass Spectrometry Decoy Spectra with Adversarial Autoencoders
  • Project Information
  • Research Topics: Proteomics Mass spectrometry
CovRadar: a web application for SARS-CoV-2 molecular surveillance
  • Project Information
  • Principal Investigator: Stephan Fuchs
  • Workgroup: Methodology and Research Infrastructure - MF1: Bioinformatics
  • Project Type: Openstack
  • Project Lifetime: 24
  • Affiliations:
  • Research Topics: Sequence analysis Data visualisation Bioinformatics Virology Protein variants Public health and epidemiology
  • Resources
  • Available virtual machines: 7
  • Total RAM: 360 GB
  • Total VCPU Cores: 180 GB
  • Number of Volumes: 3
  • Amount of volume storage: 1550 GB
Innovative benchmarking approaches to improve Computational Methods for big data analysis in Health.
  • Project Information
  • Principal Investigator: Herrmann Carl
  • Workgroup: Health Data Science Unit, Medical Faculty
  • Affiliations:
  • Research Topics: Computational biology Genomics Gene regulation Oncology
Proteomics of the Springtail Folsomia Candida
  • Project Information
  • Principal Investigator: Oliver Kohlbacher
  • Workgroup: Applied Bioinformatics
  • Research Topics: Proteomics Protein expression
Modeling and simulation of multicellular processes during tissue morphogenesis
  • Project Information
  • Principal Investigator: Lutz Brusch
  • Workgroup: Center for Information Services and High Performance Computing
  • Research Topics: Computational biology Personalised medicine
Myzel - Medical Cloud Platform
  • Project Information
  • Principal Investigator: Maier-Hein Klaus
  • Workgroup: Medical Image Computing
  • Project Type: Openstack
  • Project Lifetime: 12
  • Affiliations:
  • Research Topics: Medical imaging Natural language processing
  • Resources
  • Available virtual machines: 2
  • Total RAM: 384 GB
  • Total VCPU Cores: 60 GB
  • Number of Volumes: 2
  • Amount of volume storage: 2000 GB
Ganon in the 2 nd round of the CAMI II challenge
  • Project Information
  • Research Topics: Sequence analysis Metagenomics
Wheat Structural Variant Calling
  • Project Information
  • Research Topics: Structure analysis Genetic variation
A R Shiny based web server for performing BLAST queries on novel SARS-CoV2 sequences
  • Project Information
  • Principal Investigator: Herrmann Carl
  • Workgroup: Health Data Science Unit
  • Research Topics: Sequence analysis Infectious disease
kmer based spa typing
  • Project Information
  • Principal Investigator: Gunnar W. Klau
  • Workgroup: Algorithmische Bioinformatik
  • Project Type: Simple Vm
  • Project Lifetime: 3
  • Affiliations:
  • Resources
  • Available virtual machines: 1
  • Total RAM: 256 GB
  • Total VCPU Cores: 32 GB
  • Number of Volumes: 1
  • Amount of volume storage: 500 GB
Biohackathon Coivd19
  • Project Information
  • Principal Investigator: Alexander Sczyrba
  • Workgroup: Computational Metagenomics
  • Project Type: Openstack
  • Project Lifetime: 6
  • Affiliations:
  • Resources
  • Available virtual machines: 3
  • Total RAM: 192 GB
  • Total VCPU Cores: 96 GB
  • Number of Volumes: 3
  • Amount of volume storage: 20 GB
denbivsvirus Bielefeld
  • Project Information
  • Principal Investigator: Alexander Sczyrba
  • Workgroup: Computational Metagenomics
  • Project Type: Openstack
  • Project Lifetime: 21
  • Affiliations:
  • Resources
  • Available virtual machines: 15
  • Total RAM: 700 GB
  • Total VCPU Cores: 190 GB
  • Number of Volumes: 5
  • Amount of volume storage: 2000 GB
  • Amount of Object Storage: 500
WirVsVirus Hackathon der Bundesregierung
  • Project Information
  • Principal Investigator: Alexander Sczyrba
  • Workgroup: Computational Metagenomics
  • Project Type: Openstack
  • Affiliations:
Benchmarking proteomics nextflow workflows on PRIDE data
  • Project Information
  • Principal Investigator: Oliver Kohlbacher
  • Workgroup: Applied Bioinformatics
Performance improvements of DNA methylome deconvolution software MeDeCom
visualization webtool for deep learning features
de.NBI Training
  • Project Information
  • Principal Investigator: Malik Alawi
  • Workgroup: Bioinformatics Core
Petasearch Database Creation
Gene Structural Prediction with Deep Learning
  • Project Information
  • Principal Investigator: Andreas Weber
  • Workgroup: Plant Biochemistry
  • Project Type: Openstack
Understanding gluten related disorders at the molecular level
  • Project Information
  • Principal Investigator: Veronica Dodero
  • Affiliations:
Rheuma.Vor.Transcriptomics
  • Project Information
  • Principal Investigator: Schwarting Andreas
  • Workgroup: Ambulanz für Rheumatologie,
  • Project Type: Simple Vm
metagenomic analysis of human infant fecal sample
  • Project Information
  • Principal Investigator: Daniel Huson
  • Workgroup: algorithm in bioinformatics
  • Project Type: Openstack
  • Project Lifetime: 24
  • Affiliations:
  • Resources
  • Available virtual machines: 4
  • Total RAM: 1024 GB
  • Total VCPU Cores: 128 GB
  • Number of Volumes: 4
  • Amount of volume storage: 20000 GB
  • Amount of Object Storage: 150
Elucidating the origin of planktonic foraminifera
  • Project Information
  • Principal Investigator: Michal Kucera
  • Workgroup: Micropaleontology
  • Project Lifetime: 24
  • Resources
  • Available virtual machines: 10
  • Total RAM: 2560 GB
  • Total VCPU Cores: 320 GB
  • Number of Volumes: 10
  • Amount of volume storage: 10000 GB
Type Strain Genome Server (TYGS)
  • Project Information
  • Principal Investigator: Markus Göker
  • Workgroup: Phylogenomics (Department of Bioinformatics)
  • Project Type: Openstack
Bioschemas knowledge graph - BH2019Europe
GCB 2019 Cloud Tutorial
  • Project Information
  • Principal Investigator: Alexander Sczyrba
  • Workgroup: de.NBI Cloud Team
  • Project Type: Openstack
  • Project Lifetime: 1
  • Affiliations: BMBF
  • Resources
  • Available virtual machines: 60
  • Total RAM: 3840 GB
  • Total VCPU Cores: 1680 GB
  • Number of Volumes: 25
  • Amount of volume storage: 200 GB
  • Amount of Object Storage: 1000
Sustainable Innovation of Microbiome Applications in the Food System
  • Project Information
  • Principal Investigator: Alexander Sczyrba
  • Workgroup: Computational Metagenomics
  • Project Type: Openstack