Service list

Server that performs functional enrichment analysis of a list of chemical compounds derived from a metabolomics experiment, which allows this list to be interpreted in biological terms.

Interactive viewer of metadynamics results.

METAGEN performs meta-analysis using fixed- and random-effects logistic regression models, treating the multiple genotypes as independent variables

METALizer predicts the coordination geometry of metals in metalloproteins.

MetaNetX is a repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from a number of major resources imported into a common namespace of chemical compounds, reactions, cellular compartments - namely MNXref - and proteins. The MetaNetX.org website (http://www.metanetx.org/) provides access to these integrated data as well as a variety of tools that allow users to import their own GSMNs, map them to the MNXref reconciliation, and manipulate, compare, analyze, simulate (using flux balance analysis) and export the resulting GSMNs. MNXref and MetaNetX are regularly updated and freely available.

A public repository of phylogeny-based orthologs and paralogs that were computed using phylogenetic trees available in twelve public repositories. 

Automated inference of elemental fluxes in microbial communities, now integrated as TOPP into OpenMS

MetaProteomeAnalyzer is an intuitive open-source tool for metaproteomics data analysis and interpretation, which includes multiple search engines and the ability to decrease data redundancy by grouping protein hits into so-called metaproteins. 

Analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms with optimized tradeoff between true and false hits.

MetExplore is a free and open webserver for the analysis of omics data in the context of genome scale metabolic networks. MetExplore allows the collaborative curation of metabolic networks. In the specific case of metabolomics, it provides mining algorithms such as MetaboRank, a recommendation system for enhanced metabolic fingerprinting. Overall, Metexplore orginality relies in its ability to allow taylor made metabolic network visualisation using an open source javascript library: MetExploreViz.

MetFrag is a system for the annotation of tandem mass spectra of metabolites, performing in silico fragmentation and scoring.

methview.qc allows you to generate quality control plots from your methylation array dataset.

Formerly called EBI Metagenomics, MGnify is an automated pipeline for the analysis and archiving of metagenomic data.

Providing a large infrastructure for the analysis and interpretation of metagenomics data

The MHC Motif Atlas helps visualize, analyse, and compare the different binding specificities of thousands of class I and class II MHC molecules, and includes binding motifs, peptide length distributions, motifs of phosphorylated ligands, multiple specificities, or links to X-ray crystallography structures.

OpenMS workflow for identification and quantification of HLA ligands.

A software pipeline for the processing of amplicon sequencing data, from raw sequences to OTU tables, taxonomy classification and phylogenetic tree inference

Micro-tomography (micro-computed tomography or microCT) is a method of non-destructive 3D x-ray microscopy, which allows the users to create 3D models of objects from a series of x-ray projection images, similar to the conventional clinical computer tomography. The MicroCT Service offers a collection of virtual galleries of taxa which will be displayed and disseminated through a web-based framework, and allows the user to manipulate the 3D models through a series of online tools or to download the datasets for local manipulations.

A compilation of tools offering identification and quantification of microorganisms, working with cellular pathways, phylogenetic trees and microbial communities, including: 

• MOCAT - a modular and scalable software pipeline for analyzing shotgun metagenomics datasets generated with Illumina technology. 
• mOTUs - Metagenomic operational taxonomic units (mOTUs) allow for the quantification of known (sequenced) and unknown microorganisms at species-level resolution from shotgun sequencing data. 
• SIAMCAT -  a modular framework for the statistical inference of associations between microbial communities and host phenotypes, such as disease states in clinical case-control studies. 
• eggNOG - a database of nested orthologous gene groups (NOGs) infered using unsupervised clustering applied to >2,000 complete genomes followed by comprehensive characterization and analysis of the resulting gene families. 
• Enterotyping - uses computational methods to detect and characterise densely populated regions in a high-dimensional space of microbiome community composition, by which human individuals can be stratified. 
• iPATH - a web-based tool for the visualization and analysis of cellular pathways. Based on current annotations (such as KEGG), it provides pathway maps for primary cellular metabolism as well as for some additional secondary metabolite synthesis and regulatory pathways. 
• iTOL - Interactive Tree Of Life (iTOL) is an online tool for the display and manipulation of phylogenetic trees. 

MicroMiner searches mutations in protein structure databases like the PDB. Retrieved mutant structures can be easily analysed and compared. 

MicroScope is an integrated Web platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. It supports submissions of newly assembled genomes and metagenomes, and also provides analysis services for RNA-seq data. The user interface of MicroScope enables collaborative work in a rich comparative context to improve community-based curation efforts.

microTSS is a machine-learning algorithm that provides highly accurate, single-nucleotide resolution predictions for intergenic miRNA transcription start sites (TSSs)

The Molecular INTeraction Database of protein-protein interactions curated from peer-reviewed papers. An ELIXIR Core Data Resources and founder member of the IMEx Consortium.

A manually curated database of animal small non-coding RNAs

The Missense3D portal hosts resources developed to characterise and prioritise missense variants (amino acid substitutions) using protein three-dimensional structural information from models or experimental coordinates. Missense3D predicts the structural changes introduced by an amino acid substitution.

MITOchondrial genome database of metaZOAns, a resource for comparative analyses of metazoan mitochondrial genomes at the sequence and genomic levels.

A database of protein disorder and mobility annotations, designed centralize resources for annotations of intrinsic protein disorder and its function. Part of the InterPro consortium, an ELIXIR Core Data Resource.

MobiDB-lite is an optimized method for highly specific predictions of long intrinsically disordered regions.

The archive for structural models which are not based on experimental data and complements the PDB archive for experimental structures and PDB- Dev for integrative structures. Any type of macromolecular structure which would otherwise be suitable for the PDB but whose coordinates are not based on experimental data can be deposited in ModelArchive. This includes single chains or complexes consisting of proteins, RNA, DNA, or carbohydrates including small molecules bound to them.

Intuitively, MOFA can be viewed as a versatile and statistically rigorous generalization of principal component analysis (PCA) to multi-omics data. Given several data matrices with measurements of multiple ‘omics data types on the same or on overlapping sets of samples, MOFA infers an interpretable low-dimensional data representation in terms of (hidden) factors. These learnt factors represent the driving sources of variation across data modalities, thus facilitating the identification of cellular states or disease subgroups.