Services by Associated Partners

IKMB Kiel University

Animal genome assembly and annotation

Genomic data has become a corner stone in modern biological research. However, while sequencing is becoming increasingly affordable, the technical details in generating a draft assembly and its subsequent annotation require a wide range of bioinformatics tools – including assembly validation, transcriptome assembly, repeat analysis, gene structure prediction and functional annotation. Within de.NBI, this service project provides guidance and hands-on support for groups interested in conducting a de novo genome project, with a particular focus on metazoan species and farm animals.

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Large-scale genome-wide association studies

Over the past decade, genetic epidemiology studies of complex polygenic traits and diseases have progressed from studying single genetic variants in candidate genes to investigating millions of genetic variants in genome-wide association studies (GWAS). Within de.NBI, this service project provides guidance for planning (and execution) of SNP array genotyping and hands-on support for large-scale quality control, variant annotation, imputation and association analysis of GWAS data. Our expertise builds on more than 90 completed GWA studies in the past 10 years. Besides providing specific GWAS services our service project may also help the users to obtain access to various large control data sets.

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Friedrich Schiller University Jena

Cloud-based data analysis in metabolomics

Metabolomics, like almost any omics area, is characterised by the need to analyse increasingly large datasets. Workflows for such analyses are often composed of a plethora of different tools of varying provenance, which a bioinformatician needs to install, maintain, resolve dependencies and ultimately wire together and use. In the PhenoMeNal infrastructure, we are providing a cloud-based workflow system which can be deployed on public and private cloud and releaves the user from most the above mentioned steps. Within de.NBI, we are providing advice and assistance to use and adapt PhenoMeNal to your needs.

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Metabolomics data management and deposition

Deposition of research data has become a mandatory step in publicly funded scientific projects. The hurdle to learn about the tools and requirements for data deposition, however, can be daunting. As a service within de.NBI we are offering advice on the use of the ISA tools suite to create well-annotated datasets that can be uploaded into the MetaboLights database at the European Bioinformatics Institute (EMBL-EBI).

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A main goal of de.NBI is to provide excellent bioinformatics services and resources for life sciences research in academia and industry. de.NBI maintains and develops almost 100 software tools and four internationally recognized databases. In this section, the eight de.NBI units provide brief overviews of their de.NBI services including links to webpages and contact details. The de.NBI services include among others the analysis of high-throughput data in genomics, transcriptomics and proteomics, bioinformatics and statistical support of research projects, the development of algorithms and access to computational space. The Service Table provides information at a glance.

de.NBI services are also registered and searchable in the ELIXIR Tools and Data Services Registry that provides more detailed information in standardized format.

Table of Services within de.NBI

Area of activityHD-HuBBiGiBioinfra.ProtCIBIRBCGCBNDatabase NodeNBI-SysBio
Microorganisms
 
Plants  
 
Human
 
 
Agriculture  
 
 
Biotechnology  
Environment
 
Medicine
 
Genomics
 
Metagenomics
   
Transcriptomics
   
Proteomics
 
 
Metabolomics  
 
Modeling
         
Systematic phenotyping
             
Programs and workflows
Software libraries
   
 
Standards
 
Consulting
Databases
 
 
Project data management
     
Compute resources
 
   
Training