Service list

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

The Training Metrics Database  aims to describe the audience demographic being reached by ELIXIR training events, assess the quality of the training events  after they have taken place, and evaluate the long-term impact that the training events have had on the work of training participants.

This catalogue lists available Translational Medicine datasets, coming from academic and industry research projects as well as from clinical cohorts and genome consortia. 

Template-based RNA secondary structure visualization.

A multiple sequence alignment package that can be used for DNA, RNA and protein sequences. It can be used to align sequences or to combine the output of other alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment.

Trimmomatic is a flexible read trimming tool for NGS data.

The Norwegian services for sensitive data, is a platform enabling collection, storage and analysis of sensitive research data in a secure environment.

Database of key transmembrane target proteins

Type (Strain) Genome Server allows you to identify or classify prokaryotic strains and provides genome-based phylogenies with branch support, (sub-)species delineation via digital DDH, differences in genomic G+C content and much more.

Universal Catalog Database for biological findings

UniLectin is a platform integrating information regarding non-enzymatic carbohydrate-binding proteins usually referred to as lectins with the prospect of building and refining a structural and functional classification of these proteins. It includes the reference Lectin3D a database of 3D structures curated from the PDB. Interactive resource for the exploration of lectins

Platform for metaproteomics data analysis with a focus on interactive data visualizations

UniProt produces and maintains automatic and manually curated annotation of all publicly available protein sequences and serves these to users through various interfaces. 

UniProt Related Documents (UniReD): assisting wet lab biologists
in their quest on finding novel counterparts in a protein network

Tools for processing the topology and structure of transmembrane proteins

• A. Constrained Consensus TOPology prediction server (CCTOP) 
• B. Transmembrane helices and protein topology prediction (HMMTOP),
• C. Detection of transmembrane regions (TMDET)
• D. Transmembrane proteins’ membrane segments folding recognizing (TmFoldWeb)

UseGalaxy.fr is the national Galaxy instance for ELIXIR-FR and deployed on the IFB Core Cluster and enabling reproducible analysis for french and international researchers in different domains: genomics, metagenomics, metabolomics, proteomics, ecology.

Public Galaxy instance enabling reproducible data analysis through workflows

CSC offers versatile and high-quality training in scientific computing, data management, and information networks - from cutting-edge technologies to widely used methods and practical IT skills.

Curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, with experimentally validated functional motifs and cross-links to interacting regulatory proteins.

V-pipe is the bioinformatics pipeline that integrates various open-source software packages for assessing viral genetic diversity from next-generation sequencing (NGS) data derived from intra-host virus populations. V-pipe enables reliable and comparable viral pathogen genomics and epidemiological studies and facilitates clinical diagnostics of viruses.

Collection of validation results for the entire Protein Data Bank.

A web database of biomacromolecular structure validation trends