Service list

OpenEBench (https://openebench.bsc.es) is the ELIXIR benchmarking and technical monitoring platform for bioinformatics tools, web servers and workflows. 

OpenMS is an open-source C++ library (+ Python bindings) for LC/MS data management, analysis and visualization. 

OpenMS tool for the study of Protein-Protein interactions.

Open source software environment for development of biomedical data mining applications and data analysis workflows.

A service‐oriented environment for data mining, integrating web services as workflow components

A Galaxy instance customized for data-intensive computational analyses in microbiology and metagenomics.

Orphadata provides the scientific community with comprehensive, quality data sets related to rare diseases and orphan drugs from the Orphanet knowledge base, in reusable formats.

Orphanet is the reference resource for information and data on rare diseases and orphan drugs. Orphanet derives from its knowledge base an ontology of rare diseases, information on rare diseases and data on rare diseases.

OrthoDB is a comprehensive catalog of evolutionary and functional annotations of orthologs, covering over 22 million genes from over 5000 species of animals, fungi, plants, archaea, bacteria, and viruses. 

(Oligogenic Resource for Variant Analysis) is the first web bioinformatics platform for the exploration of predicted candidate disease-causing variant combinations, aiming to aid in uncovering the causes of oligogenic diseases (i.e. diseases caused by variants in a small number of genes).

OTP = "One Touch Pipeline" is a comprehensive framework for NGS project organization and processing. The application provides support in all steps of this process, including data transfer from temporary to final storage, execution of data quality monitoring programs, alignment of reads to the reference genome and variant calling. It allows full automatization, extended project administration, and full processing control for operators.

PanDrugs is a method to prioritize anticancer drug treatments according to individual genomic data. PanDrugs current version integrates data from 24 primary sources and supports 56297 drug-target associations obtained from 4804 genes and 9092 unique compounds

A service for the publishing, archiving and re-using data.

ParameciumDB is a community model organism database for the ciliate Paramecium. The web site gives access to genomes of many Paramecium species and their annotations. ParameciumDB also  integrates  genome-wide datasets (DNA-seq, RNA-seq, ChIP-seq) provided by the community. This portal is used to query, retrieve, visualize and compare the most up-to-date public data.

Prediction of Amyloid STructure Aggregation is a web server predictor for amyloid aggregation propensity from protein sequences;

A collection of software solutions for pangenome analyses.

To searches user submitted sequences for any combination of Position Weight Matrices (PWMs), primary sequence patterns and structural motifs.

Software to identify defined fragments in biomacromolecules.

Our algorithm for identifying PCA-correlated SNPs takes as input a properly encoded SNP data matrix and outputs a score for each SNP. SNPs corresponding to the highest scores are typically the most informative in reproducing the structure of the population.

Database of membrane localization of transmembrane proteins with defined spatial structure

The Protein Ensemble Database (PED) is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins (IDPs). Manually curated data of structural ensembles measured with nuclear magnetic resonance spectroscopy, small-angle X-ray scattering, fluorescence resonance energy transfer are annotated in PED.

Bioinformatics Docker Images Project, a library of over 50 Docker images. 

A platform for interpretation of proteomics identification results from multiple search engines.

Predictor of human deleterious Single Nucleotide Polymorphisms.

A binary classifier for predicting pathogenic variants in coding and non-coding regions.

A catalogue of experimentally-verified pathogenicity, virulence and effector genes involved in the infection of animal, plant, fungal and/or insect hosts.

phylogeny.fr is a web server intended to phylogenetic analyses.It has been designed to let non-specialist as well as expert users execute phylogenetic workflows. These workflows automatically chain programs to  perform different tasks: the identification of homologous sequences, their multiple alignment, the alignment curation, the phylogenetic reconstruction and the graphical representation of the inferred tree.

PhylomeDB is a public database for complete catalogs of gene phylogenie. It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments.

A phylogenetic inference platform for epidemiological investigations and population studies of bacterial pathogens.

PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. The main strength of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be processed. PhyML can process data sets made of multiple genes and fit sophisticated substitution models with heterogeneous components across partition elements.