[ensembl-dev] JEnsembl publication

[PATERSON Trevor]

We are pleased to announce (pre)publication of our paper describing our JEnsembl API

JEnsembl: a version-aware Java API to Ensembl data systems
Trevor Paterson; Andy Law
Bioinformatics 2012; doi: 10.1093/bioinformatics/bts525

Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts525
PDF: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts525

The current release of the JEnsembl API is version 1.13, and the most recent release of the EnsemblConfig module is 1.68, which configures the API to recognize releases up to Ensembl 68  / EnsemblGenomes 15 whilst retaining compatibility with  previous schema versions.  We aim to maintain configuration with successive releases of the Ensembl schema, by updating this EnsemblConfig module as the Ensembl schema evolves.

JEnsembl can be used to access data for all of the Species held in Ensembl and EnsemblGenomes: 'Core' functions are backward compatible to release50, 'Compara' back to release 57 and 'Variation'  back to release 62.

Currently implemented functionality includes: retrieval of chromosomes, sequences, genes, exon structure, transcripts, translated sequences, SNP variation data, gene homologies and chromosomal regions of conserved synteny.

Source and binary releases, and full documentation, including code examples, are available at our development site: http://jensembl.sourceforge.net/ where developers can get involved or join our distribution list. We are keen for (potential) users of the API to provide feedback about other features that should be implemented, and any improvements that could be made.

We now provide a Maven repository for downloading JEnsembl release artifacts (detailed on http://jensembl.sourceforge.net/download.html ).


Trevor Paterson PhD
trevor.paterson at roslin.ed.ac.uk<mailto:trevor.paterson at roslin.ed.ac.uk>
Bioinformatics
The Roslin Institute
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Easter Bush
Midlothian
EH25 9RG
Scotland UK

phone +44 (0)131 651 9157

http://bioinformatics.roslin.ed.ac.uk/

Please consider the environment before printing this e-mail
The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336
Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20121001/a2e3acba/attachment.html>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20121001/a2e3acba/attachment.ksh>