Service list

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.

The glycomic MS database and repository.

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

VarAFT is a software designed to annotate and filter Human NGS data. This system was developed within the RD-Connect project and was instrumental for the creation of the RD-Connect Genome-Phenome platform. As a stand-alone java system, it ensures full data protection, critical for clinical use. VarAFT provides experiments’ quality, annotates, and allows the filtration of VCF files. Data from multiple samples can be combined to address different Mendelian Inherited Disorders, Population Genetics or Cancers. It contains unique variant priorization features including OMIM, HPO, Gene Ontology, pathways and predictions from UMD-Predictor and Human Splicing Finder in addition to classical annotations from dbNSFP . It is used by many research and clinical laboratories worldwide.

Performs ranking of variants in genomic datasets, integrating information from multiple sources to prioritize each variant by its deleteriousness, novelty and existing information.

Accurate validation, mapping and formatting of sequence variant descriptions

A high recall search engine to support the curation of genomic variants.

https://academic.oup.com/bioinformatics/article/38/9/2595/6547047

VEuPathDB provides access to diverse genomic and other large scale datasets related to eukaryotic pathogens and invertebrate disease vectors.

Galaxy server for the functional annotation and prioritization of genetic variants.

A resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries. 

WarPP is a fully automated procedure to place water molecules in the active site of a protein structure.