<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Victor,<div><br class="webkit-block-placeholder"></div><div>We're just starting to work on getting E. coli information into Chado. It may be good to share our experiences as we go along. I believe that TIGR has done a bit with Chado and bacteria as well. </div><div><br class="webkit-block-placeholder"></div><div>Jim</div><div><br><div><div>On Jan 23, 2008, at 5:59 AM, Victor de Jager wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Scott and Dave,<br><br>thanks for your replies. I will contact Jim Hu and the genedb people<br>as these projects seem to resemble what we want to achieve in time. In<br>between I have been successful to get the schema into Postgresql. I<br>haven't looked at all the tools yet, but hope to do so next week (i'm<br>working only a few hours a week on this project)<br><br>Victor<br><br><br><br>On Jan 17, 2008 1:08 AM, Scott Cain <<a href="mailto:cain.cshl@gmail.com">cain.cshl@gmail.com</a>> wrote:<br><blockquote type="cite">Hi Victor,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Just to follow on a little bit: the web front end that we use in GMOD is<br></blockquote><blockquote type="cite">a tool based on Turnkey, a perl/Class::DBI tool. However, it is still<br></blockquote><blockquote type="cite">somewhat immature and a little difficult to install. It is currently in<br></blockquote><blockquote type="cite">use by ParameciumDB though (<a href="http://paramecium.cgm.cnrs-gif.fr/">http://paramecium.cgm.cnrs-gif.fr/</a> ).<br></blockquote><blockquote type="cite">Another option being worked on by someone in our group is a Drupal-based<br></blockquote><blockquote type="cite">front end which has the potential of doing as much as Django. Drupal is<br></blockquote><blockquote type="cite">php based and has a fairly large community of users and developers.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Scott<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Wed, 2008-01-16 at 15:56 -0800, Dave Clements, GMOD Help Desk wrote:<br></blockquote><blockquote type="cite"><blockquote type="cite">Hi Victor,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I've cross-posted my response to the GMOD Schema list, which is about<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Chado. People may have some additional comments.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">There are a number of bacterial projects using GMOD. Here are some:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">EcoliWiki: <a href="http://ecoliwiki.net/">http://ecoliwiki.net/</a> EcoliWiki uses GMOD components<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">including GBrowse and TableEdit. Jim Hu <<a href="mailto:jimhu@tamu.edu">jimhu@tamu.edu</a>>.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Pathema: <a href="http://pathema.tigr.org/Burkholderia/beta/">http://pathema.tigr.org/Burkholderia/beta/</a> Pathema uses<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Chado.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">GeneDB: <a href="http://www.genedb.org/">http://www.genedb.org/</a> GeneDB also uses Chado.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Take a look at <a href="http://gmod.org/GMOD_Users">http://gmod.org/GMOD_Users</a> for more. There may be<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">others on the mailing list who may also respond to your question.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">To answer your second question, as far as I know, there are no Python<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">based software tools in GMOD. We are mainly a Perl organization with<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">some prominent Java components. However, to use GMOD you shouldn't<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">have to do much if any Perl programming. You will, however, have to<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">understand how to do Perl installs.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Please let me know if you have any questions,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Dave C<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">GMOD Help Desk<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">On Jan 16, 2008 8:08 AM, Victor de Jager <<a href="mailto:victor.dejager@gmail.com">victor.dejager@gmail.com</a>><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi there,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I'm looking into options for using the chado scheme to build a<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">bacterial genome annotation database with experimental evidence<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">based<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">annotations.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I would like to know if there are groups who use the chado scheme<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">and<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">gmod tools for bacterial genomics. If so, who might I contact?<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">As a second question, are you aware of any python based software<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">tools<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">for the chado database (Using Django models maybe?). I am basically<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">a<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">python programmer so perl would mean an extra effort in learning.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">best regards<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Vic de Jager<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">------------------------------------------------------------------------<br></blockquote><blockquote type="cite">Scott Cain, Ph. D. <a href="mailto:cain@cshl.edu">cain@cshl.edu</a><br></blockquote><blockquote type="cite">GMOD Coordinator (<a href="http://www.gmod.org/">http://www.gmod.org/</a>) 216-392-3087<br></blockquote><blockquote type="cite">Cold Spring Harbor Laboratory<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><br>-------------------------------------------------------------------------<br>This SF.net email is sponsored by: Microsoft<br>Defy all challenges. Microsoft(R) Visual Studio 2008.<br><a href="http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/">http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/</a><br>_______________________________________________<br>Gmod-schema mailing list<br>Gmod-schema@lists.sourceforge.net<br>https://lists.sourceforge.net/lists/listinfo/gmod-schema<br></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">=====================================</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Jim Hu</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Associate Professor</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Dept. of Biochemistry and Biophysics</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">2128 TAMU</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Texas A&M Univ.</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">College Station, TX 77843-2128</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">979-862-4054</font></p></div><br class="Apple-interchange-newline"></span> </div><br></div></body></html>