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<p class=MsoNormal>PostgreSQL is default for Chado<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>http://gmod.org/wiki/Databases_and_GMOD<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal> and MySQL is recommended for GBrowse<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>http://gmod.org/wiki/GBrowse_Install_HOWTO<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>That seems a bit complicated to me. Does this mean
that we should populate and maintain our genome DB with PostgreSQL and use
MySQL for the browsing?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>On the other hand, the Pg adaptor was supposed to be part of
BioPerl 1.3.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/docs/pod/ORACLE_AND_POSTGRESQL.pod<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Does BioPerl now have a Pg adaptor?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Can we use Gbrowse with PostgreSQL without too much
difficulty? Has it or is it being tested? Is there any support if
we want to use and/or test it?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>More basically, I see a list of adaptors<o:p></o:p></p>
<p class=MsoNormal>http://gmod.org/wiki/GBrowse#About_Databases<o:p></o:p></p>
<p class=MsoNormal>But at this point, I haven't seen a set of supported schema
for GBrowse. Has anybody compiled a list of supported schema? Do I
just need to get them from the adaptor links above?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>What about Jbrowse? Does that do all of its queries
with perl modules, ie BioSQL or BioPerl? Does it require or support any
DBMS?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Additionally, what about Apollo? Does it need a DBMS
or does it rely only on JAVA classes?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Finally, since I mentioned JAVA, do any of the tools have
HQL functionality. Is there any HQL development in gmod? Is there
any interest in HQL?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks for the range of tools and any help you can provide
with my questions.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Tom Walk<o:p></o:p></p>
<p class=MsoNormal>tom.walk@ars.usda.gov<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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