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<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3><STRONG>Ensembl Usage Survey</STRONG></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><?xml:namespace prefix = o ns =
"urn:schemas-microsoft-com:office:office" /><o:p><FONT face="Times New Roman"
size=3> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>We are currently developing a Java API to Ensembl as an alternative
</FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>to Ensembl’s Perl API for data access (<A
href="http://jensembl.sourceforge.net/">http://jensembl.sourceforge.net/</A>).</FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman"
size=3> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>Our prototype code architecture accesses various demonstration data types
</FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>from the Core and Compara schema, and we would like to prioritize future
</FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>functionality.</FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman"
size=3> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>To help us do this we are keen to discover how bioinformaticians
currently </FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>use </FONT><FONT face="Times New Roman" size=3>the Ensembl datasources
and Perl API in particular, and which features </FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT
face="Times New Roman"><FONT size=3><FONT>of<SPAN class=966405508-05072011>
</SPAN></FONT><FONT>a Java API might be of most use to future application
developers. </FONT></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman"
size=3> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>Please take a few minutes to complete our online survey at<SPAN
class=966405508-05072011>:</SPAN> </FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><A
href="http://www.surveymonkey.com/s/MFD9G36"><FONT face="Times New Roman"
size=3>http://www.surveymonkey.com/s/MFD9G36</FONT></A><FONT
face="Times New Roman" size=3> </FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>and help us to prioritize future development of our JEnsembl
API.</FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman"
size=3> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>Please forward this email to colleagues that might be interested,
</FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>or let us know of any mail lists that might be relevant.</FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3></FONT> </P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>If you are interested in seeing how the JEnsembl API might be used in
</FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>graphical applications to provide access to Ensembl datasources,
</FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>we have made use of JEnsembl in two demonstration
applications:</FONT></P>
<OL style="MARGIN-TOP: 0cm" type=1>
<LI class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; mso-list: l0 level1 lfo1; tab-stops: list 36.0pt"><FONT
face="Times New Roman" size=3>ArkMAP, a map drawing tool that can download,
draw and align <BR></FONT><FONT face="Times New Roman" size=3>homologies
between chromosome maps from any Ensembl Datasource <BR>and from
ArkDB<BR></FONT><A href="http://jensembl.sourceforge.net/arkmap.html"><FONT
face="Times New Roman" color=#800080
size=3>http://jensembl.sourceforge.net/arkmap.html</FONT></A></LI>
<LI class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; mso-list: l0 level1 lfo1; tab-stops: list 36.0pt"><FONT
face="Times New Roman" size=3>A plug-in for the Savant Genome Browser that
allows gene maps <BR>and sequences to be downloaded from Ensembl<BR></FONT><A
href="http://jensembl.sourceforge.net/savant.html"><FONT
face="Times New Roman"
size=3>http://jensembl.sourceforge.net/savant.html</FONT></A></LI></OL>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman"
size=3> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>Thanks you for help.</FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman"
size=3> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>Trevor Paterson and Andy Law</FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3><SPAN style="COLOR: navy"><o:p><SPAN class=966405508-05072011><A
href="mailto:roslin.bioinformatics@roslin.ed.ac.uk">roslin.bioinformatics@roslin.ed.ac.uk</A></SPAN></o:p></SPAN></FONT></P>
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size=3><SPAN style="COLOR: navy"><o:p><SPAN
class=966405508-05072011></SPAN></o:p></SPAN></FONT> </P></FONT>
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