3D interacting domains

Collection of protein interactions for which high-resolution three-dimensional structures are known. The interface residues are presented for each interaction type individually, plus global domain interfaces at which one or more partners bind.

3DBIONOTES-WS and COVID19 Structural Hub

Web based application designed to integrate protein structure, protein sequence and protein annotations in a unique graphical environment. Moving towards integrating a quality-checking environment on experimental structures and relate them to predicted ones.

Agile Protein Interactomes DataServer Interactomes

Web-server that provides a comprehensive collection of protein interactomes based on the integration of known experimentally validated protein-protein physical interactions (PPIs).

Annotation of Pathological Mutations on Proteins

The PMut predictor is a web-based tool for the annotation of pathological variants on proteins. It allows the fast and accurate prediction of the pathological character of single point amino acid mutations based on the use of AI.

APPRIS (Annotating principal splice isoforms)

Annotates coding transcripts with protein structural information, functionally important residues, conservation of functional domains and evidence of cross-species conservation. Selects the most important coding transcript for each gene (principal) and generates scores for functional relevance of each coding transcript.

Beyondcell

Computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and spatial transcriptomics data and proposing cancer-specific treatments.

BioExcel Building Blocks

Python building blocks wrapping popular computational biomolecular tools. Includes workflow execution platform.

BSC Text Mining Unit tools

Collection of NLP and text mining componenst to process medical literature and clinical texts

CANcer TExt Mining SharedTask

Resource to evaluate and promote the development of resources for named entity recognition, concept normalization and clinical coding specifically focusing on cancer data in Spanish.

Collaborative Spanish Variant Server

Crowdsourcing initiative to provide information about the genomic variability of the Spanish population to the scientific/medical community.

Drug REpositioning for IMmune Transcriptome

Bioinformatics tool for hypothesis generation and prioritization of drugs capable of modulating immune cell activity from transcriptomics data.

EGA Beacon

Resource that will allow the discovery of datasets hosted at the European Genome-phenome Archive. It is based on Beacon v2, a specification that defines an open standard for federated discovery of genomic data in biomedical research and clinical applications.

Environment for Tree Exploration toolkit

Python package for the programmatic analysis and visualization of phylogenomic data

European Genome-phenome Archive

Service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.

Evolutionary genealogy of genes: Non-supervised Orthologous Groups

Public resource in which thousands of reference genomes are analyzed at once to establish orthology relationships between all their genes, providing also an easy-to-use interface for functional and evolutionary analysis by non-bioinformaticians.

FAIR Cookbook

Online resource for the Life Sciences that helps researchers make and keep data and services Findable, Accessible, Interoperable and Reusable (FAIR) through practical guides and recipes.

FAIRTracks Validation Service

Set of JSON Schemas developed through the ELIXIR implementation study "FAIRification of Genomic Tracks", as a minimal standard for genomic track metadata

footprintDB

Web server for assigning putative cis DNA motifs to input transcription factors (TFs) and conversely for predicting which TFs that might recognize input DNA motifs. Includes several collections of motifs which are also available from RSAT servers.

Genomes for Life. Cohort Study of the Genomes of Catalonia

Provides information from real-world- and research data from a population based cohort of 20K Spanish Resident Citizens (Catalonia region) to develop and support biomedical research focus on common disorders.

GET_HOMOLOGUES

Versatile software package for pan-genome analysis of microbes and plants, including GET_HOMOLOGUES and GET_HOMOLOGUES-EST

Hipathia suite

Web tool for the interpretation of the consequences of the combined changes of gene expression levels and/or genomic mutations in the context of signalling pathways.

INB Integrated platform for macromolecular flexibility

Web portal containing a series of tools and databases related to macromolecular structure flexibility, developed to offer an integrated approach to study flexibility.

Interactive Onco Genomics

Framework for automatic and comprehensive knowledge extraction based on mutational data from sequenced tumor samples from patients.

Interactome3D

Resource for the structural annotation and modeling of protein-protein interactions.

manta/mvgwas-nf

Pipeline for multi-trait genome-wide association studies (GWAS) using MANTA (Multivariate Asymptotic Non-parametric Test of Association)

Mapping human disease-mutations at systemic level

Resource that maps mutations related to human diseases on the structure of proteins and interactions in the human interactome

MasterOfPores

Nextflow pipeline for analysis of Nanopore data from direct RNA sequencing.

Metabolites Biological Role

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.

MetaPhOrs

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

Nextflow

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

OpenEBench

ELIXIR benchmarking and technical monitoring platform for bioinformatics tools, web servers and workflows.

PanDrugs

Method to prioritize anticancer drug treatments according to individual multiomics data.

PhylomeDB

Public database for complete catalogs of gene phylogenies. It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments.

Redundans

Pipeline that assists in the assembly of heterozygous genomes. It takes as input assembled contigs, sequencing libraries and/or a reference sequence and returns a scaffolded homozygous genome assembly.

Regulatory Sequence Analysis Tools Plants

Modular software which offers specialized options for researchers dealing with plant transcriptional regulation.

Ruby bioinformatics toolkit

Framework for software development in bioinformatics.

SQANTI

Tool for the analysis and quality control of long-read transcriptomic data (lrRNA-seq).

sqtlseeker2-nf

Nextflow pipeline for splicing quantitative trait loci (sQTL) mapping based on sQTLseekeR2.

Tree-based Consistency Objective Function for Alignment Evaluation

Multiple sequence alignment package that can be used for DNA, RNA, protein sequences and structures. The tool primary functionality it is to align sequences but it can also perform other operations such as combine the output of other alignment methods, data reformatting, results evaluation and methods benchmark.

Workflow Execution Service backend

High-level workflow execution command-line program which fetches and materializes all the elements needed to run workflows through permanent identifiers: workflow itself, engine, needed software containers and inputs.