[Biojava-dev] Ensembl Usage Survey for JEnsembl

Hello, Jalviewers.

I just saw an interesting post on the biojava lists about JEnsembl (see below).
Would anyone be interested in exploring whether they can integrate it into Jalview ? My plate is full at the moment, but I am happy to point people in the right direction.


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-------- Original Message --------
Subject: [Biojava-dev] Ensembl Usage Survey for JEnsembl
Date: Tue, 5 Jul 2011 10:28:19 +0100
From: PATERSON Trevor <trevor.paterson@roslin.ed.ac.uk>
To: biojava-dev <biojava-dev@lists.open-bio.org>, "'biojava-l@lists.open-bio.org'" <biojava-l@lists.open-bio.org>

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

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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