Latest project: Metagenomics Summerschool 2021

Project: Research Topics: Sequence analysis, Metagenomics


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

FlowSoFine

Project: Principal Investigator: Stefan Janssen, Workgroup: Algorithmic Bioinformatics, Research Topics: Microbial ecology


SILVA release

Project: Research Topics: Biological databases, rRNA


Analysis of flavonoid biosynthesis pathway across plant species

Project: Principal Investigator: Boas Pucker, Institution: Institute of Plant Biology, TU Braunschweig, Workgroup: Plant Biotechnology and Bioinformatics, Lifetime: 6 months, Research Topics: Phylogeny, Genomics, Splice sites

Resources: Project type: Simple Vm, Number of possible VMs: 1, Total number of cores: 14, Total amount of RAM: 32 GB, Amount of Object Storage: 0 GB


Generative models to disentangle spatial components of cellular variation

Project: Research Topics: Computational biology, Machine learning


Genetic analysis of Cercospora leaf spot resistance in wild and cultivated beets

Project: Research Topics: Agricultural science


LIFS Portal

Project: Research Topics: Lipids, Bioinformatics, Mass spectrometry


GPU_BASE

Project: Research Topics: Genomics, Plant biology


BaktaWeb

Project: Research Topics: Sequence annotation, Genome annotation


4D Controls-based denoising

Project: Institution: Nuclear Medicine and Molecular Imaging, Tuebingen, Research Topics: Medical imaging, MRI, Applied mathematics


Computational Psychiatry

Project: Principal Investigator: Tobias Kaufmann, Institution: Department of Psychiatry and Psychotherapy, University of Tübingen, Research Topics: Computational biology, Medical imaging, Genetics, Neurobiology, Psychiatry


Bioimage.io Model Zoo

Project: Principal Investigator: Florian Jug, Institution: CSBD/MPI-CBG Dresden, Workgroup: Jug Lab, Lifetime: 12 months, Research Topics: Cell biology, Bioinformatics, Bioimaging, Machine learning

Resources: Project type: Openstack, Number of possible VMs: 2, Total number of cores: 64, Total amount of RAM: 256 GB, Amount of Object Storage: 50 GB


HTS of Xcc mutant strains using CellProfiler

Project: Research Topics: Imaging, Microbiology


Extending cross-linking mass spectrometry with cleavable cross-linkers

Project: Research Topics: Protein interactions, Proteomics, Protein structure analysis


Machine Learning for Protein Identification

Project: Research Topics: Proteomics, Machine learning


Determination of the conformational loop flexibility of strongly neutralizing COV-2 antibody fragments.

Project: Research Topics: Protein interactions, Protein structure analysis, Structure prediction, Molecular dynamics


Machine Learning for Antibiiotic Resistance 2

Project: Research Topics: Bioinformatics, Machine learning


RNA-RNA interaction prediction evaluation

Project: Research Topics: Nucleic acid structure analysis


Identification of causative variants in patients with genetically unclassified severe congenital neutropenia

Project: Principal Investigator: Maksim Klimiankou, Institution: University Hospital Tuebingen, Workgroup: Internal Medicine II, Division of Translational Oncology, Lifetime: 12 months, Research Topics: Sequencing, Molecular genetics

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


WebDECIMER

Project: Principal Investigator: Christoph Steinbeck, Institution: Friedrich-Schiller University Jena, Workgroup: Steinbeck group, Lifetime: 12 months, Research Topics: Small molecules, Literature analysis, Literature data resources

Resources: Project type: Openstack, Number of possible VMs: 1, Total number of cores: 16, Total amount of RAM: 64 GB, Amount of Object Storage: 10 GB


Automated Analysis of Microscopy Images Using Deep Learning

Project: Principal Investigator: Rohr Karl, Institution: BioQuant Center and IPMB, Heidelberg University, Workgroup: Biomedical Computer Vision Group, 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: Institution: University Medical Center Hamburg-Eppendorf, Workgroup: Bioinformatics Core, Research Topics: Computational biology, Bioinformatics, Computer science


Diatom Virtual Slide Storage

Project: Research Topics: Ecology, Taxonomy, Bioimaging, Light microscopy, Machine learning, Freshwater biology


Bellman's GAP for deep learning

Project: Principal Investigator: Stefan Janssen, Institution: Justus-Liebig-University Gießen, Germany, Workgroup: Algorithmic Bioinformatics, Lifetime: 12 months, Research Topics: Computer science

Resources: Project type: Simple Vm, Number of possible VMs: 2, Total number of cores: 24, Total amount of RAM: 80 GB, Amount of Object Storage: 0 GB


RNAProNet - Infer regulatory behavior from RNA protein binding events

Project: Principal Investigator: Rolf Backofen, Institution: Freiburg University, Workgroup: Chair for Bioinformatics, Lifetime: 12 months, Research Topics: Protein interactions, High-throughput sequencing, Machine learning

Resources: Project type: Simple Vm, Number of possible VMs: 1, Total number of cores: 16, Total amount of RAM: 64 GB, Amount of Object Storage: 0 GB


ECF Hub - An interactive database for ECF sigma factors

Project: Principal Investigator: Alexander Goesmann, Institution: Professur für Systembiologie, Workgroup: Professur für Systembiologie, Lifetime: 12 months, Research Topics: Biological databases, Protein databases, Synthetic biology

Resources: Project type: Openstack, Number of possible VMs: 3, Total number of cores: 24, Total amount of RAM: 48 GB, Amount of Object Storage: 750 GB


EMIC sequencing pipeline

Project: Research Topics: Sequence analysis, Microbial ecology, Environmental science


Evaluation of genome assembly tools for Triticeae

Project: Principal Investigator: HARMEET SINGH CHAWLA, Institution: Helmholtz Centre Munich, Workgroup: Plant Genome and System Biology, Lifetime: 6 months, Research Topics: Plant biology, Whole genome sequencing

Resources: Project type: Openstack, Number of possible VMs: 1, Total number of cores: 64, Total amount of RAM: 3000 GB, Amount of Object Storage: 0 GB


Cis-regulatory atlas of Brassica napus

Project: Research Topics: Gene expression, Genetic variation, Genomics, Bioinformatics, Gene regulation, Plant biology, DNA structural variation


SIMBA Metagenome Training Course

Project: Principal Investigator: Alexander Sczyrba, Institution: Center for Biotechnology, Bielefeld University, Workgroup: Computational Metagenomics, Lifetime: 3 months, Research Topics: Sequence analysis, Metagenomics

Resources: Project type: Simple Vm, Number of possible VMs: 2, Total number of cores: 42, Total amount of RAM: 96 GB, Amount of Object Storage: 0 GB


SFB1324 - Data Exchange and Collaborative Analysis

Project: Research Topics: Sequence analysis, Protein structure analysis, Cell biology, Imaging, Functional genomics, Signaling pathways


VascuShare: a vascular imaging data repository

Project: Principal Investigator: Kyle Harrington, Institution: Max Delbrueck Center for Molecular Medicine, Berlin, Research Topics: Imaging, Bioinformatics, Bioimaging


Applying - Helixer, Gene Structural Prediction with Deep Learning

Project: Principal Investigator: Andreas Weber, Institution: Heinrich Heine University, Workgroup: Institute of Plant Biochemistry, Lifetime: 10 months, Research Topics: Sequence analysis, Gene structure, Machine learning

Resources: Project type: Openstack, Number of possible VMs: 3, Total number of cores: 60, Total amount of RAM: 384 GB, Amount of Object Storage: 1000 GB


Covalent and kinetic trapping repair machinery for structural and functional studies

Project: Research Topics: Protein interactions, Protein structure analysis, Enzymes, Nucleic acids


ChIP-seq / ATAC-seq workshop

Project: Principal Investigator: Herrmann Carl, Institution: Medical Faculty Heidelberg, Workgroup: HDSU, Lifetime: 15 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


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


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: 22, Total number of cores: 352, Total amount of RAM: 704 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, Machine learning

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 Nunes da Rocha, Institution: Helmholtz Centre for Environmental Research, Workgroup: Microbia Data Science, Lifetime: 22 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: 29, Total number of cores: 768, Total amount of RAM: 4352 GB, Amount of Object Storage: 0 GB


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


Using NLP-Networks (Transformers) for human genome data

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


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: 24 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


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


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


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


Ganon in the 2 nd round of the CAMI II challenge

Project: Research Topics: Sequence analysis, Metagenomics


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: 21 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: 24 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