Bioinformatics and computation
Protein structure and function
Systems approaches to biology
Data sharing and data resources
We have funded and invested in a number of resources that are available for the bioscience community to use. Some of them are listed below. The operators of these resources should be contacted directly regarding their use.
European Bioinformatics Institute (EBI)
An academic organisation, based in Hinxton, Cambridgeshire that forms part of the European Molecular Biology Laboratory.
EBI is a centre for research and services in bioinformatics, and manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.
EBI undertakes a series of training activities throughout the year. Details of these can be found on the EBI website.
Collaborative Computational Projects (CCP)
CCP intends to bring together leading UK expertise in key fields of computational research to tackle large-scale scientific software development, maintenance and distribution projects. BBSRC currently supports 3 CCPs:
- CCP4 Software for Macromolecular X-Ray Crystallography (currently funded 2008-2013)
CCP4 was initially set up in 1979 to support collaboration between computational and macromolecular crystallography researchers. It has a large number of software resources for people to access. Further details can be found on the CCP4 website
- CCPN Collaborative Computational Project for NMR (currently funded 2009-2012)
CCPN was set up in 1999 to establish a CCP for the NMR community. It aims to promote interchange of data between different users and software, as well as to develop and maintain a suite of software for processing, analysing and interpreting macromolecular NMR date. Further details can be found on the CCPN website
- CCPB Collaborative Computational Project for Biomolecular Simulation (currently funded 2005-2009)
CCPB’s aim is to build and strengthen the UK capacity in biomolecular simulations.
Nottingham Arabidopsis Stock Centre (NASC)
BBSRC supports the NASC, which provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. NASC provides free access to GARNet, a UK Arabidopsis functional genomics network, and UK CropNet, a crop bioinformatics network.
A small charge is made for seeds to cover the cost of production, storage and postage.
The Roslin Institute Transmissible Spongiform Encephalopathy (TSE) Resource Centre
The Roslin TSE Resource Centre collects, stores, characterises, produces and distributes a range of reagents needed for TSE research. These reagents range from monoclonal antibodies to infective materials.
Functional genomics for farm and domestic animals
BBSRC supports ARK-Genomics Centre for Comparative and Functional Genomics, a not-for-profit organisation based at Roslin in Scotland. Projects will be carried out as collaborative ventures with ARK-Genomics. The resources are available for use at Roslin or in your own laboratory. In line with BBSRC policy, all biological resources submitted to ARK-Genomics will be made freely available to all users.
Resources for the investigating gene function initiative
- Arabidopsis: GARNET: co-ordinator Ruth Bastow, PI Professor Jim Beynon, The University of Warwick
- Drosophila: Flychip: Professor M Ashburner, Cambridge University
- Brassica: Dr Graham King, Rothamsted Research
- COGEME: Yeast and plant fungal pathogens – Professor S Oliver, The University of Manchester
- Streptomyces: Professor K Chater, John Innes Centre
- Cereals: Dr Graham Moore, John Innes Centre, joint programme with the Scottish Executive Rural Affairs Department (Scottish Crop Research Institute)
Online atlas of gene expression in Drosophila – www.flyatlas.org
Functional genetics research and reverse genetics – http://revgenuk.jic.ac.uk
Web-based application for QTL mapping on a variety of population types – www.gridqtl.org.uk
Annotated database of published miRNA sequences – www.mirbase.org
UEA small RNA Workbench
Resource for analysing small RNA data – http://rna-workbench.cmp.uea.ac.uk
Online resource for protein circular dichroism deconvolution software – http://dichroweb.cryst.bbk.ac.uk
Protein structure classification database – www.cathdb.info
Database of structural and functional annotation for proteins and genomes – http://supfam.cs.bris.ac.uk/SUPERFAMILY
A protein modelling resource for the prediction of protein structure – www.sbg.bio.ic.ac.uk/~phyre
Web-based workbench for predicting protein structure and function – http://bioinf.cs.ucl.ac.uk/psipred
A Java multiple amino-acid sequence alignment editor – www.jalview.org
Data resource that allows biologists to store, search and retrieve published mathematical models of biological interest – www.ebi.ac.uk/biomodels-main.
A modelling portal for the UK Plant Systems Biology community
The PlaSMo Plant Systems Biology Modelling Portal provides access to crop mathematical models in a standardised format. The portal aims to ensure that mathematical models found in legacy formats do not become lost.
BioLayout Express 3D
BioLayout Express 3D is a tool for the visualisation and analysis of biological data networks.
The Open Microscopy Environment (OME)
OME Remote Objects (OMERO) is a client-server software platform for the visualisation, management and analysis of biological microscope images.
The Electron Microscopy Data Bank (EMDB)
The EMDB is a data bank for electron microscopy data produced by a variety of techniques including single-particle analysis, electron tomography and electron (2D) crystallography.
A curated catalogue of life science services – www.biocatalogue.org
MIBBI: Minimum Information for Biological and Biomedical Investigations
A website collecting together Mimimal Information resources from across a number of biological disciplines – http://biosharing.org/standards/mibbi
The European Molecular Biology Open Software Suite (EMBOSS)
EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
Chemical Entities of Biological Interest (ChEBI)
ChEBI is a dictionary of molecular entities focused on small chemical compounds.
The following resources may be of use when planning your data sharing strategy:
- EMBL-Bank – also known as the EMBL Nucleotide Sequence Database constitutes Europe's primary nucleotide sequence resource
- EMBL-Align – multiple sequence alignment database
- FlyBase – database of the Drosophila Genome
- Biosharing – Repository and community, linked to journals, of data sharing statements and standards in genomics and post-genomics
- UniProt knowledgebase – complete annotated protein sequence database
- IntAct – protein interaction database and analysis system
- Expert Protein Analysis System (ExPASy) – a proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE
- Protein Circular Dichroism Data Bank – open access archiving facility for circular dichroism spectra
- Protein Data Bank (PDB) – provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function and disease
- ArrayExpress – for gene expression data
- NCBI Geo – curated online database for gene expression data
- NASC Affymetrix service – the European Arabidopsis Stock Centre provides an international Affymetrix service
- PRoteomics IDEntifications database (PRIDE) – allows you to submit proteomic data in PRIDE XML format or retrieve data using the search page
- NASC proteomic database – the European Arabidopsis Stock center
- Model repositories – contains links to resources where biological models generated using systems approaches can be deposited
Organism specific databases
- FlyBase – see the genome databases section above
- WormBase – the central data repository for information about Caenorhabditis elegans and related nematodes
- ComBase – database for the growth kinetics of food borne pathogens
- Monogram – provides links to a number of wheat tools and resources
- BioGrid – database and repository for biological interactions
- ISAinfrastructure – A general-purpose format and freely available desktop software suite that allows users to manage experimental metadata and uptake minimal information checklists and ontologies
BBSRC funds a number of community resources through responsive mode. These are not listed. If grant holders of currently funded facilities/resources wish to be listed, please provide the following details to the contact below:
- Name of the resource
- Access provision
- BBSRC grant reference number (if possible)