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Projects using Ensembl

The Ensembl project is both a source of genome sequence related data (http://www.ensembl.org) and an open source software system that can be used to organise any such data.

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Collaborations

Ensembl are active collaborators in a number of projects, contributing code, know-how and a platform from which to distribute data.

Project Description Code used/data provided
1000 Genomes A web browser and ftp sites are provided to access human genetic variation catalogued by the project. Web front-end derived from Ensembl webcode
Blueprint Epigenomics project analysing samples from healthy and diseased individuals. Track Hub available on the Ensembl browser
Ensembl Genomes Websites presenting annotation for bacteria, protists, fungi, plants and invertebrate metazoa Web front-end derived from Ensembl webcode, Ensembl schema databases, Ensembl pipelines and Perl API
gEVAL This browser can be used to inspect the reference assemblies of human, mouse and zebrafish being created by the GRC Customised webcode, pipelines (not genebuild) and compara
HEROIC Functional genomics data for Mouse (Mus musculus) Data viewable on Ensembl via DAS.
Neanderthal Genome Browser Preliminary assembly of Homo sapiens neanderthalensis. Web front-end derived from Ensembl webcode, Ensembl schema databases.
NextGen A collaborative project investigating biodiversity of livestock species. Variant call sets produced using the Ensembl VEP, viewable in the Ensembl browser.
Quantomics Large-scale project to analyse sequence and variation in livestock genomes. Sequence alignments created using the Ensembl Compara pipelines.
Vega Website to present curated vertebrate annotation Web front-end derived from Ensembl webcode, Ensembl schema databases, Ensembl Compara pipeline and Perl API

External projects

Our open access data and open source code mean that many projects are able to make use of Ensembl data and software without our active involvement. We're happy to list those we know about here, but if your project is e!mpowered and you're not on this list, let us know.

Project Description Code used
SNPchiMp A multi-species database to disentangle the SNP chip jungle BioMart and VEP
mouse Genome Variation Identifier A simple web interface to the Ensembl VEP for mouse SNPs. Variant Effect Predictor script and mouse variation database
AutoPrime Automated design of RT primers Core API code and gene models
PomBase A resource for Schizosaccharomyces pombe that includes structural and functional annotation, literature curation and access to large-scale data sets. Customised webcode, pipeline, database schema and API
Ashyba Genome Database A genome/transcriptome database containing gene annotation and expression data for Ashbya gossypii and Saccharomyces cerevisiae Webcode
GermOnline Microarray expression database focused on germline development Webcode and underlying data
GRiD (Gene Regulators in Disease) Provides a web browser to investigate gene regulation and human disease. Webcode
Eagle Browser Provides installation of the Ensembl browser Webcode, API
Bgee Comparison of gene expression patterns between species Ensembl data and orthologues
InterologWalk Perl Modules Perl modules to determine protein-protein interactions from orthology and interaction data. API, compara
VectorBase Bioinformatic Resource Centre for Invertebrate Vectors of Human Pathogens Customised Ensembl webcode, Ensembl Compara pipeline, Ensembl annotation pipeline
Gramene A Comparative Mapping Resource for Grains Customised webcode, Ensembl Compara pipeline, Ensembl database used for annotation, import of the Arabidopsis Ensembl database from NASC.
AtEnsembl Arabidopsis thaliana genome browser Customised Ensembl pipeline, API, and webcode
CADRE Central Aspergillus Data REpository
Sigenae Sigenae EST ContigBrowser
COSMIC (Catalogue of Somatic Mutations in Cancer) Web display of somatic sequence variant/mutation data Customised Ensembl drawing code
MVP (Methylation Variable Positions) Web display of MVPs analysed in the Human Epigenome Project. Customised Ensembl drawing code
PupaSuite Interactive web tool for the selection of optimal sets of SNP for genotyping purposes, with prediction of functional effect and visualisation facilities. Web front end to a CGI that uses APIs.
OrthoMaM A database of alignments and trees based on orthologous exons and CDSs for mammalian species. 1-to-1 orthologues extracted from Ensembl.
Phylopat Web tool to show the presence or absence of certain genes or proteins in a set of eukaryote species. Uses orthologue data extracted from EnsMart.
DeCIFR legume project (retired) Automated annotation and display of legume genomes Customised Ensembl pipeline, API, and webcode
Otter Database backend for interactive curation of annotation Otter is an extension of the Ensembl database schema
Chromhome A database of chromosome map data, particularly chromosome painting data between species. Ensembl karyotype drawing code.
Selectome Database of positive selection. Uses Ensembl gene trees, gene data and xrefs extracted via the APIs.

'Powered by Ensembl' logo

If you are using Ensembl code in your project, you might like to download the 'empowered' logo (high-resolution PNG, suitable for use in print).

User-contributed code

Whilst we have developed a comprehensive Perl API in-house, we welcome contributions in other programming languages from the community.

Ruby

A Ruby API has been developed by Jan Aerts. A small example, showing what it can do (including coordinate transformation and reflecting on the types of associations for a given class) can be found on the wiki page.

Java

An open source Java API (JEnsembl) has been developed by the Bioinformatics Group at The Roslin Institute. The code has been designed to be version-aware (a single installation works against current and previous releases) and is hosted, together with documentation, examples and contact information for the Roslin group, at SourceForge.

Note that we do not support these user-contributed packages - please contact the original developer if you have any questions or comments.