Service list

MolArt (MOLeculAR structure annoTator) - molecular structure annotation and visualization tool.

Toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in (bio)macromolecular structures, e.g., proteins, RNA, DNA and biomacromolecular assemblies. 

Web interface providing a direct access to MOLE 2.0 functionality and enabling on-line and easy-to-use interactive channel analysis. 

A software package to help researchers set up an online database application that supports data queries and allows data sharing.

MolMeDB is an open chemistry database about interactions of molecules with membranes.

Mol* is a web application for visualization of biomacromolecular structures including experimental data (for example electron densities) and annotations. Can visualize also molecular dynamics.

A web application for validation of annotation of ligands and
residues.

The mOTUs tool uses phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) to profile microorganisms at species-level resolution when using metagenomic data as input. Since the MGs represent housekeeping genes, mOTUs can also be used to profile transcriptionally active community members when using metatranscriptomic data as input. Furthermore, MG-based SNV profiling provides an efficient alternative to using whole genome sequences to compare microbial strain populations.

Tool to predict peptide fragment ion intensities for mass spectrometry-based proteomics data.

A highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from NGS data. Predicts mitochondrial haplogroups.

A tool for life science researchers to correct multiple hypothesis testing

A tool for analyzing PCR primer compatibility and automatically finding optimal multiplexing (grouping) solution.  It uses nearest neighbour DNA binding thermodynamics to estimate unwanted pairings between PCR samples.

A platform linking gene expression changes and mutational status in solid tumours  

Nucleic acid search engine to reliably identify a wide range of modified RNA sequences.

The NERC Environmental Omics Facility (NEOF) will enable environmental researchers in the UK to access the full range of omics supporting technology.

A tool to visualize the output from the database for annotation, visualization and integrated discovery DAVID in order to reveal overlapping biological connections for a list of relevant genes.

Enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.

An innovative knowledge platform dedicated to human proteins. It contains a wealth of data on all the human proteins that are produced by the 20'000 protein- coding genes found in the human genome. 

Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Our goal is to aid epidemiological understanding and improve outbreak response. This resource supports COVID-19 / SARS-CoV-2 research.

Textmining tools

The NNCR (National Network of Computing Resources) is a distributed infrastructure providing computing and storage services to french and international users and consisting of the IFB-core resources (cloud and cluster) and nine high-performance computing platforms located in different regions.

Norine has been and remains the unique resource dedicated to nonribosomal peptides (NRPs). It contains a database complemented with analysis tools (structure comparison, inference of monomer structure from chemical structure, mass spectrum analysis, NRP annotation for submission to the database). NRPs are secondary metabolites produced by bacteria and fungi and display a diverse spectrum of biological activity.

The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping raw sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive world maps and ecological plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.

Curated database of oligogenic diseases and genetic variants causing these diseases. The successor of DIDA, a similar database for digenic diseases

OMA identifies orthologs among 2000 genomes from all domains of life. Other distinctive characteristics are the high quality of its inferences, the feature-rich web interface, and frequent update schedule of two releases per year. 

The Omics Discovery Index provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics). It indexes metadata from more than 20 omics resources across four continents.

A database of causal protein-protein interactions, transcriptional and post-transcriptional regulation, enzyme-PTM interactions, protein complexes, annotations (function, disease roles, expression, localization, structure) and intercellular communication. Integrates data from more than 100 resources.

OMPdb is a database of beta-barrel outer membrane proteins from Gram-negative bacteria.

Terms that are commonly encountered while conducting, reporting, storing, harmonizing, integrating, and describing nutritional studies. ONS builds upon a subset of the Ontology for Biomedical Investigations (OBI), reuses already formalized information by importing terms already defined in other ontologies, and defines de novo key classes/terms to tailor concept to the nutritional field

Open source software underlying the technology for SURF's single sign-on and facilitating national and international online collaboration in education and research.