[BioMart Users] Ensembl Usage Survey for JEnsembl

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[BioMart Users] Ensembl Usage Survey for JEnsembl

Ensembl Usage Survey


We are currently developing a Java API to Ensembl as an alternative

to Ensembl’s Perl API for data access (http://jensembl.sourceforge.net/).


Our prototype code architecture accesses various demonstration data types

from the Core and Compara schema, and we would like to prioritize future



To help us do this we are keen to discover how bioinformaticians currently

use the Ensembl datasources and Perl API in particular, and which features

of a Java API might be of most use to future application developers.


Please take a few minutes to complete our online survey at:


and help us to prioritize future development of our JEnsembl API.


Please forward this email to colleagues that might be interested,

or let us know of any mail lists that might be relevant.


If you are interested in seeing how the JEnsembl API might be used in

graphical applications to provide access to Ensembl datasources,

we have made use of JEnsembl in two demonstration applications:

  1. ArkMAP, a map drawing tool that can download, draw and align
    homologies between chromosome maps from any Ensembl Datasource
    and from ArkDB
  2. A plug-in for the Savant Genome Browser that allows gene maps
    and sequences to be downloaded from Ensembl


Thanks you for help.


Trevor Paterson and Andy Law

[hidden email]


The Roslin Institute
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Easter Bush
EH25 9RG

Scotland UK

phone +44 (0)131 651 9157


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