ELIXIR-UK

ELIXIR-UK Node Services

The UK Node supports the bioinformatics and broader biological research community by providing training and resources that help researchers to find and share data, exchange expertise, and agree on best practices at national, European and International level.

If you have a service that could help the life sciences community deal with current data challenges it faces please get in contact.

Following a call for services in 2016 the ELIXIR-UK currently has services in 6 strategic areas

Through these prioritised themes ELIXIR-UK contributes to four of the ELIXIR’s 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 Use Cases/Communities, as well as engaging with a number of key international initiatives and national and international organisations.

ELIXIR-UK Node Services:

Biomedical Atlas Centre

Expression Atlases for mouse embryo (emouseatlas.org), human embryo (hudsen.org), chick (echickatlas.org), pig (www.macrophages.com/pig-atlas) and sheep

Strategic area:
Training
Expression Atlases
Organisations:
Heriot-Watt University
Newcastle University
University of Edinburgh

Bioinformatics Training Program

The Bioinformatics Training Program of the University of Cambridge offers a broad range of undergraduate and postgraduate hands-on training courses focused on bioinformatics and computational biology. These training activities aim at enabling life scientists to effectively handle and interpret biological data.

Strategic area:
Training
Organisations:
University of Cambridge

Birmingham Metabolomics Training Centre

The Birmingham Metabolomics Training Centre offers a wide range of introductory to advanced training courses in metabolomics, including in analytical and computational methods and their application to medicine, microbiology and the environmental sciences. Courses are relevant to academia, industry and government scientists and include face-to-face, hands-on and online training.

Strategic area:
Training
Organisations:
The University of Birmingham

CATH-Gene3D

CATH is a classification of protein structures downloaded from the Protein Data Bank.

Strategic area:
Protein Structure & Function
Organisations:
University College London

Dundee Resource for Sequence Analysis and Structure Prediction

The Dundee Resource for Sequence Analysis and Structure Prediction is a collection of services provided by the Barton Group. The Dundee Resource includes services such as Jpred, JABAWS, AACon, and others currently under development.

Strategic area:
Protein Structure & Function
Organisations:
University of Dundee

Edinburgh Genomics Advanced Training in Bioinformatics

Edinburgh Genomics Advanced Training in Bioinformatics offers a range of hands-on workshops, focusing on core bioinformatics skills and the analysis of second- and third-generation sequencing data. Workshops are aimed at scientists from academia as well as industry.

Strategic area:
Training
Organisations:
Edinburgh Genomics
The Roslin Institute

ELIXIR 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. For ELIXIR Nodes, TeSS provides opportunities to promote training events and news, and to contribute to a growing catalogue of materials.

Strategic area:
Training
Organisations:
The University of Manchester
The University of Oxford - Oxford e-Research Centre
Formal links with external initiatives:
GOBLET

ENSEMBL Farmed and Domesticated Animals

Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

Strategic area:
Agri-data
Organisations:
The Roslin Institute

FAIRsharing

A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies.

Strategic area:
Interoperability & Standards
Organisations:
The University of Oxford - Oxford e-Research Centre

Intermine

InterMine is an open source data warehouse system that enables the integration and analysis of complex biological data through sophisticated web interfaces and web services.

Strategic area:
Interoperability & Standards
Organisations:
University of Cambridge

ISA Tools& Commons

The open source ISA framework and tools help to manage an increasingly diverse set of life science, environmental and biomedical experiments that employing one or a combination of technologies.

Strategic area:
Agri-data
Organisations:
The University of Oxford

IUPHAR/BPS guide to Pharmacology

An expert-driven guide to pharmacological targets and the substances that act on them.

Strategic area:
Human Health & Disease
Organisations:
University of Edinburgh

Jalview

Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.

Strategic area:
Protein Structure & Function
Organisations:
University of Dundee

Pathogen Host Interactions Database

A web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts.

Strategic area:
Agri-data
Organisations:
Rothamsted Research

Phyre2

A web server for the prediction of protein 3D structure from sequence incorporating analyses of ligand binding and the effects of missense mutations.

Strategic area: Protein Structure & Function
Organisations:
Imperial College London

Road Mapped Services

EuPathDB

The EuPathDB Bioinformatics Resource Center provides a portal for accessing genomic-scale datasets associated with the diverse eukaryotic microbes

Strategic area:
Human Health & Disease Agri-data
Organisations:
The University of Liverpool

COPO

COPO is a brokering portal for plant scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results.

Strategic area:
Agri-data
Organisations:
Earlham Institute
The University of Oxford - Oxford e-Research Centre

Ionomics Hub

Improving our understanding of how plants take up, transport and store their nutrient and toxic elements, collectively known as the ionome, will benefit human health and the natural environment. Here you will find curated ionomic data on many thousands of plant samples freely available to the public.

Strategic area:
Agri-data
Organisations:
The University of Nottingham

SignaLink

An integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes

Strategic area:
Human Health & Disease
Organisations:
Earlham Institute

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