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.
| Project | Description | Code used |
|---|---|---|
| Vega | Website to present curated vertebrate annotation | Web front-end derived from Ensembl webcode; Ensembl database and Perl API |
| VectorBase | Bioinformatic Resource Centre for Invertebrate Vectors of Human Pathogens | Customised Ensembl webcode, Ensembl Compara pipeline, Ensembl annotation pipeline |
| DeCIFR legume project | Automated annotation and display of legume genomes | Customised Ensembl pipeline, API, and webcode |
| AtEnsembl | Arabidopsis thaliana genome browser | Customised Ensembl pipeline, API, and webcode |
| Otter | Database backend for interactive curation of annotation | Otter is an extension of the Ensembl database schema |
| 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. |
| 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 |
| S. pombe Gene Expression Viewer | Web display of S. pombe gene expression under various environmental conditions. | 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. |
| ISACGH | Web tool to detect chromosomal copy number alterations and relate them to gene expression and gene function. | Web front end to a CGI that uses APIs. DAS server. |
| 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. |
| 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).
