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.
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.
Note that we do not support these user-contributed packages - please contact the original developer if you have any questions or comments.
Ensembl-powered Websites
Some projects make use of the Ensembl software system, or are derived from it.
Projects based at WTSI or EBI
| Project | Description | Code used |
|---|---|---|
| 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 |
| Vega | Website to present curated vertebrate annotation | Web front-end derived from Ensembl webcode, Ensembl schema databases, Ensembl Compara pipeline and Perl API |
| 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 |
| Genome Reference Consortium PGPviewer | The GRC is creating reference assemblies of human, mouse and zebrafish that are accessible in the PGP viewer | Customised webcode, pipelines (not genebuild) and compara |
External projects
| Project | Description | Code used |
|---|---|---|
| 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 |
| Neanderthal Genome Browser | Preliminary assembly of Homo sapiens neanderthalensis. | Web front-end derived from Ensembl webcode, Ensembl schema databases. |
| 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 |
| HEROIC | Functional genomics data for Mouse (Mus musculus) | Data viewable on Ensembl via DAS. |
| 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. |
| 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. |
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).
