<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>We are pleased to announce (pre)publication of our paper describing our JEnsembl API<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><b><u>JEnsembl: a version-aware Java API to Ensembl data systems <o:p></o:p></u></b></p><p class=MsoNormal>Trevor Paterson; Andy Law<o:p></o:p></p><p class=MsoNormal>Bioinformatics 2012; doi: 10.1093/bioinformatics/bts525<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Abstract: <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts525">http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts525</a><o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>PDF: <a href="http://bioinformatics.oxfordjournals.org/cgi/reprint/bts525">http://bioinformatics.oxfordjournals.org/cgi/reprint/bts525</a><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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. <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Source and binary releases, and full documentation, including code examples, are available at our development site<span style='color:#1F497D'>: </span><a href="http://jensembl.sourceforge.net/">http://jensembl.sourceforge.net/</a> 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.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>We now provide a Maven repository for downloading JEnsembl release artifacts (detailed on <a href="http://jensembl.sourceforge.net/download.html">http://jensembl.sourceforge.net/download.html</a> ).<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span style='font-size:12.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB'>Trevor Paterson PhD<br></span></b><span style='font-size:12.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB'><a href="mailto:trevor.paterson@roslin.ed.ac.uk"><span style='color:blue'>trevor.paterson@roslin.ed.ac.uk</span></a></span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:EN-GB'><o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:12.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB'>Bioinformatics <br>The Roslin Institute<br>Royal (Dick) School of Veterinary Studies<br>University of Edinburgh<br>Easter Bush<br>Midlothian<br>EH25 9RG<br>Scotland UK<br><br>phone +44 (0)131 651 9157<br><br><a href="http://bioinformatics.roslin.ed.ac.uk/"><span style='color:blue'>http://bioinformatics.roslin.ed.ac.uk/</span></a></span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";color:black;mso-fareast-language:EN-GB'><br></span><span style='font-size:10.0pt;font-family:"Times New Roman","serif";color:navy;mso-fareast-language:EN-GB'><br></span><span style='font-size:12.0pt;font-family:"Arial","sans-serif";color:green;mso-fareast-language:EN-GB'>Please consider the environment before printing this e-mail</span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:EN-GB'><o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><i><span style='font-size:10.0pt;font-family:"Times New Roman","serif";color:navy;mso-fareast-language:EN-GB'>The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336</span></i><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB'><br><b>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.</b></span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:EN-GB'> <o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>