Services: Software Tools

Development of the software plattform for MassBank, a database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da).

Parallel and scalable workflow for the analysis of Oxford Nanopore direct RNA sequencing datasets. Nextflow pipeline for analysis of Nanopore reads (from RNA/cDNA/DNA).

MatrixDB is a database focused on molecular interactions of extracellular matrix proteins and glycosaminoglycans. The advanced query interface allows users to browse MatrixDB data, to build and to visualize specific interaction networks based on transcriptomic or quantitative proteomic data, diseases, biological processes or molecular functions. MatrixDB hosts the GAG builder tool to build on line 3D models of GAG sequences binding to proteins. 

Efficient graph clustering tool with a collection of use cases for protein family detection, orthology assignment and protein interaction module discovery (Emerging Service) 

Mechismo is a tool that allows rapid predictions of how genetic variants impact on biomolecular function. This is done by a pre-computed collection of protein-protein, protein-DNA/RNA, protein-chemical interactions of known three-dimensional structure mapped to proteomes from major model organisms. Users can input any number of variants to get a ranked list of genes and specific positions that have a functional impact on biomolecular interactions.

MeDeCom is an R package for reference-free decomposition of heterogeneous DNA methylation profiles. 

A tool for genome scaffolding that exploits information obtained from a set of (draft or closed) genomes to determine the correct order and orientation of the contigs.

Analysis of raw GC- and LC-MS metabolome data against the either the GMD database or user defined libraries in NIST.

MEM is a web-based multi experiment gene expression query and visualization tool. It gathers thousands of publicly available gene expression data sets from ArrayExpress database.

A method for estimating disordered stretches in transmembrane proteins

Mercator is a web server that is able to assign functional terms to protein or nucleotide sequences.

An online platform for pooling the results of research with the same objectives

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.

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.

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

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.