Service list

A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form. 

SymCurv is a computational ab initio method for nucleosome positioning prediction. It is based on the structural property of natural nucleosome forming sequences, to be symmetrically curved around a local minimum of curvature.

Database of protein association networks representing a broad scala of biological associations between pairs of proteins that go beyond  direct protein interactions

TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.

Web tool for the prediction of T-cell receptor epitope recognition.

A training materials portal that helps you to discover, package and disseminate training resources. It aggregates training information from the ELIXIR nodes, and also from third-party content providers.

Transcription factor - target gene interaction and binding site database for multiple species

Contains tools for the functional classification of PLP-dependent enzymes in predicted protein sequences.

The European Nucleotide Archive (ENA) contains all the nucleotide sequences in the public domain and consolidates data from EMBL-Bank, the European Trace Archive and the Sequence Read Archive.

A web-based system for finding and testing relations between high-throughput sequencing and/or other genomic datasets (tracks), making use of statistical hypothesis testing and other advanced methodology.

The Ontology Lookup Service (OLS) provides a web service interface to query multiple ontologies from a single location with a unified output format.

Database of membrane localization of transmembrane protein structures estimated by AlphaFold2

A method for estimating the crystallizability of transmembrane proteins

Detection of transmembrane regions using 3D protein structure

Differential gene expression analysis in tumour, normal and metastatic tissues

Based on ICGC PanCancer infrastructure for organising and processing NGS data using workflow plugins including:  

• Workflow Plug-Ins - provide pipelines for the most common NGS processing tasks, including alignment (WES, WGS, WGBS, RNA-seq), quality control and variant calling (SNV, indel, CNV, SV).
• Cloud/HPC - IT Infrastructure for de.NBI users based on ICGC and TCGA PanCancer technology
• OTP - "One Touch Pipeline" is a comprehensive framework for NGS project organization and processing.
• Roddy - a framework for large scale NGS processing pipelines on Petabyte scale for the management of workflows in the Pan-Cancer Analysis of Whole Genomes (PCAWG) project.

Diverse tools under development, in use in BYOD events to facilitate making data FAIR using linked data technology.

Database of experimentally determined topological data of transmembrane proteins

The OpenMS Proteomics Pipeline making a range of tools available, including MetaProSIP and TOPPview. 

Visualising own data through OpenMS tools, including spectra, chromatograms, 2D LC-MS data and annotations. 

Training events about tools developed in ELIXIR-EE (usually g:Profiler, MEM, ClustVis are taught).

Courses in bioinformatics and HPC at CSC are open for academics, government and industry participants.

• Bioinformatics tools and resources
• Computational skills
• (bio)data science
• Data management, annotation and analysis
• Data interoperability and FAIRification
• bio.tools and Bioschemas

Training provided by ELIXIR-LU focuses on the usage of the Node services, data management, efficient use of high-performance computing to analyse complex biomedical data, and reproducibility in research.

Most of the training organised in DTL/ELIXIR-NL and the associated Dutch research school on bioinformatics and systems biology (BioSB) are open to participants from any ELIXIR country. Training and training materials available are listed on dtls.nl and TeSS. Training and materials are developed on a diverse range of topics, including specific bioinformatics skills and workflows, as well as generic FAIR data knowledge and data stewardship.

Interdisciplinary trainings in post‐genome technologies and computation

SIB Training offers courses and workshops on various bioinformatics and data science-related fields to life scientists, clinicians and bioinformaticians. 

Courses providing fundamental data skills for research, basic skills for research computing, and knowledge for research data management and ELIXIR Belgium’s Node Services.

Either as a cooperation or consultancy service.

Either as a cooperation or consultancy service.

contact [at] denbi.de