ELIXIR-UK Node Services

The UK Node represents UK strengths in bioinformatics within ELIXIR and provides a route for UK bioinformatics resources to participate in ELIXIR. The Node’s activities and services span the ELIXIR Platforms for training, interoperability and standards, tools and data.

ELIXIR-UK offers services to the rest of ELIXIR members, which come from two streams:

  • an annual, open and transparent process to conform to a set of criteria designed to ensure high service quality and match UK priorities as identified by its funders
  • project commitments made to ELIXIR, notably ELIXIR-EXCELERATE

ELIXIR-UK contributes to four of the five ELIXIR platforms: Training, Interoperability and Standards, Data and Tools. The UK services also reflect and link to the strategic themes of ELIXIR, its Technical Platforms and its Scientific Communities, as well as engaging with a number of key international initiatives and national and international organisations.

If you have a service that could help the life sciences community deal with current data challenges it faces and would like to submit an Expression of Interest please click here.

ELIXIR-UK Node Services:

Cambridge Bioinformatics Training Programme The Cambridge Bioinformatics Training Facility provides a broad range of postgraduate, hands-on, training courses focused on data science, bioinformatics and computational biology. Machine Learning, Metagenomics, Molecular Phylogenetics, Proteomics, Services, training, Transcriptomics
Birmingham Metabolomics Training Centre The Birmingham Metabolomics Training Centre provides training to the metabolomics community in both analytical and computational methods, via face-to-face and online workshops, and at introductory to advanced levels Biochemistry, Data and tools, Human health, Metabolomics, Training
CATH Gene 3D CATH is a classification of protein structures downloaded from the Protein Data Bank. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. Data and tools, Interoperability and standards, Structural Bioinformatics
COPO COPO is a portal for scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results.
DRASP: Dundee Resource for Sequence Analysis and Structure Prediction DRSASP’s flagship services are the JPred4 webserver for protein secondary structure and solvent accessibility prediction and the JABAWS 2.2 webserver for multiple sequence alignment, disorder prediction, amino acid conservation calculations, and specificity‐determining site prediction. DRSASP resources are available through conventional web interfaces and APIs but are also integrated into the Jalview sequence analysis workbench, which enables the composition of multitool interactive workflows. Biochemistry, Data and tools, Machine Learning, Structural Bioinformatics
Edinburgh Genomics Training To enable researchers to analyse their next generation sequencing data themselves, Edinburgh Genomics offers a range of hands-on bioinformatics workshops Training
ENSEMBL Farmed and Domestic Animals Emsembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation Data and tools
FAIRDOM: SEEK The SEEK platform is a web-based resource for sharing heterogeneous scientific research datasets, models or simulations, processes and research outcomes. It preserves associations between them, along with information about the people and organisations involved. Interoperability and standards
FAIRsharing A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resource more discoverable, more widely adopted and cited. Interoperability and standards
FAIR Cookbook Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable and Reusable (FAIR).
FlyBase FlyBase is a model organism database for the fruit fly, Drosophila melanogaster. It provides comprehensive genetic, genomic and functional information through manual curation of the literature and integration of selected datasets.
GWAS Central The GWAS Central resource provides a toolkit for integrative access and visualisation of summary-level genome-wide association study data gathered from various public sources and submitted by GWAS authors, while ensuring safe open access to prevent research participant identification. Data and tools, Human Genomics, Human Health
HGNC The HUGO Gene Nomenclature Committee is the only worldwide authority that assigns standardised nomenclature to human genes. Data and tools, Gene Nomenclature, Human Genomics, Human Health, Interoperability and standards
Intermine InterMine is a software system that you can install on your own servers to make data available on the web. It integrates biological data sources, making it easy to query and analyse data. Data and tools, Gene Ontology, Human Genomics, Human Health, Interoperability and standards, Machine Learning, Model Organism Biology, Plant Biology, Transcriptomics
ISA Tools and Commons Open source metadata model and authoring tools to describe, share, and publish life science, environmental and biomedical experiments using community-defined reporting standards. This FAIR-enabling framework is embedded in other data systems, such as institute-based (e.g. USA NASA GeneLab Data Repository), global repositories (e.g. EMBL-EBI MetaboLights), and other annotation software (e.g. InterMine and FAIRDOM). Data and tools, Interoperability and standards, Metagenomics, Proteomics, Transcriptomics
IUPHAR/BPS Guide to Pharmacology The IUPHAR/BPS Guide to PHARMACOLOGY is an expert-curated resource of ligand-activity-target relationships, the majority of which come from high-quality pharmacological and medicinal chemistry literature. It is a freely available, searchable database of pharmacological information that includes quantitative data on drug targets and the prescription medicines and experimental drugs that act on them. Biochemistry, Data and tools, Human Health
Jalview Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. It allows viewing and editing of sequence alignments, their analysis with phylogenetic trees and Principal Components Analysis (PCA) plots and exploration of molecular structures and annotation. Jalview also allows integration of variant data from genome sequencing together with interactive analysis of DNA, RNA and protein sequences, phylogenetics and three-dimensional structures of macromolecules. Biochemistry, Data and tools, Human Genomics, Microbial Genetics, Molecular Phylogenetics, Pathogen Biology, Plant Biology, Structural Bioinformatics
KnetMiner KnetMiner is a discovery platform that helps scientists search large volumes of scientific literature and Life Science data to unveil links between the genetic and biological properties of complex, polygenic traits and diseases. It allows users to effectively integrate, search, visualise and share biological knowledge in an accessible, transparent, yet concise format that can be easily interrogated to generate new insights.
LIPID MAPS LIPID MAPS® Lipidomics Gateway provide access to lipid nomenclature, databases, tools, protocols, standards, tutorials, meetings, publications, and other resources, serving the international lipid research community Biochemistry, Data and tools, Human Health, Interoperability and standards, Structural Bioinformatics
NEOF Training
Pathogen Host Interaction Database From mutant genes to phenotypes! The mission of PHI-base is to provide expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. Information is also given on the target sites of some anti-infective chemistries. Data and tools, Human Health, Pathogen Biology, Plant Biology
Phyre2 A server to predict protein structure from sequence with facilities for variant analysis and batch processing. Data and tools, Human Health, Structural Bioinformatics
PomBase PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation. Biochemistry, Data and tools, Gene Ontology, Microbial Genetics, Model Organism Biology
PSIPRED The PSIPRED Workbench is a Structural Bioinformatics service which offers a wide range of predictive methods to the bioscience community Data and tools, Machine Learning, Structural Bioinformatics
TeSS TeSS is ELIXIR’s training platform, providing a one-stop shop for trainers and trainees to discover online information and content, including training materials, events and interactive tutorials. Training
VEuPathDB VEuPathDB provides access to diverse genomic and other large scale datasets related to eukaryotic pathogens and invertebrate vectors of disease.
WorkflowHub WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows.

ELIXIR-UK Roadmapped Services:

Biomedical Atlas Centre Data and tools
Cafe Variome Cafe Variome is a flexible web-based, data discovery tool that can be quickly installed by any biomedical data owner to enable the “existence” rather than the “substance” of the data to be discovered.
Ionomics Hub Provide access to ionomics data on Arabidopsis thaliana leaf and seed from accessions, mapping populations, defined gene knockouts and various mutants. Along with ionomics data on the full genome-wide collection of Saccharomyces cerevisiae (yeast) gene knockouts and overexpressing strains. Data and tools, Plant Biology
Missense 3D Missense3D predicts the structural changes introduced by an amino acid substitution and is applicable to analyse both PDB coordinates and homology-predicted structures.
SignaLink SignaLink is a value-added knowledge-base providing both literature curated data on signaling pathways and integrated data from several different type of databases (interaction, regulation, localisation, diseases, etc.) for human and three major animal model organisms (C. elegans. D. melanogaster and D. rerio). Data and tools, Human health, Interoperability and Standards, Model Organism Biology