Home Project Objectives Project Development Source Code Design Architecture Downloads Code Examples Current JavaDocs Change Log Example Usage I: Savant Browser Plugin Example Usage II: ArkMAP Application Contact Roslin Bioinformatics
Get JEnsembl: a Java API for Ensembl at SourceForge.net. Fast, secure and Free Open Source software downloads
2015-01-13 Release version 1.78. Updated to handle up to Ensembl Schema 78 (Ensembl Genomes 25). Introduced searching for partial matches on species aliases/names. (Download)
JEnsembl API is published: JEnsembl: a version-aware Java API to Ensembl data systems. Paterson T, Law A. (2012) Bioinformatics 38(21):2724-2731. [PDF]
To help drive our development of the API we are running a poll to try and determine how potential users might use JEnsembl. Please add your opinion at Survey Monkey.

JEnsembl: Plug-In for Savant Genome Browser

In order to demonstrate how the JEnsembl API might be used by developers to embed access to Ensembl data sources into third party bioinformatics applications we have implemented a simple plug-in for the Savant Genome Browser that embeds JEnsembl functionality in a genome visualisation application. The plug-in allows the user to import any available chromosome, its sequence and gene annotations into the browser, from both the Ensembl and EnsemblGenomes data sources, from any available species and release version of the assembly annotation.

The source code for this plug-in is available form the JEnsembl project Subversion repository, and relies upon the JEnsembl API Jar library artifacts. The plug-in itself, bundled together with all dependencies into a single Jar library is available from the File Download Page. The plug-in Jar is simply added to the plug-ins directory of the Savant application.

SavantEnsembl Plug-In

Screenshots of the JEnsembl plug-in for Savant Genome Browser.  (A) The user chooses to connect to Ensembl, EnsemblGenomes or EnsemblGenomes-Bacterial data sources. (B) The desired species and release version are selected from those available for the current JEnsembl configuration. (C) A single chromosome/assembly is selected from those available for the chosen species/release. The chromosome is imported either as a simple coordinate skeleton, or with the associated genomic sequence. Currently the only feature annotation that can be imported from the data source is the gene track, which Savant shows aligned with the DNA Sequence.

Note that the requirements of the Savant Browser restricts the ability of JEnsembl to lazy load DNA sequences, consequently loading the genome sequence should be be avoided for large chromosomes.