https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?action=history&feed=atom&title=Chlamydia_trachomatisChlamydia trachomatis - Revision history2026-06-02T15:13:31ZRevision history for this page on the wikiMediaWiki 1.20.3https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Chlamydia_trachomatis&diff=7156&oldid=prevDwilliams: /* Important Files */ Formatting2013-12-13T23:36:47Z<p><span dir="auto"><span class="autocomment">Important Files: </span> Formatting</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Final Excel Spreadsheet Containing Everything from GenMAPP and MAPPFinder'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Final Excel Spreadsheet Containing Everything from GenMAPP and MAPPFinder'''</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*Final Excel Sheet Used for Project.xls</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*<ins class="diffchange diffchange-inline">[[Media: </ins>Final Excel Sheet Used for Project.xls<ins class="diffchange diffchange-inline">]]</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">:Final excel sheet used for project. Includes all raw data, all EB to RB ratios in the presence and absence of rifampicin, statistical analysis of that data, for GenMAPP data, and all charts and tables used for GO terms and summaries of data</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Wiki Formatting==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Wiki Formatting==</div></td></tr>
</table>Dwilliamshttps://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Chlamydia_trachomatis&diff=7155&oldid=prevDwilliams: /* Important Files */ Added file2013-12-13T23:36:03Z<p><span dir="auto"><span class="autocomment">Important Files: </span> Added file</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Media: For GenMAPP Chlamydia V4 20131205 KS.gmf]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Media: For GenMAPP Chlamydia V4 20131205 KS.gmf]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: File created by MAPPFinder after creating the latest color set.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: File created by MAPPFinder after creating the latest color set.</div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">'''Final Excel Spreadsheet Containing Everything from GenMAPP and MAPPFinder'''</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">*Final Excel Sheet Used for Project.xls</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Wiki Formatting==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Wiki Formatting==</div></td></tr>
</table>Dwilliamshttps://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Chlamydia_trachomatis&diff=6868&oldid=prevKsherbina: /* Deliverable and Final Paper Assignments */ Removed a section2013-12-10T04:09:34Z<p><span dir="auto"><span class="autocomment">Deliverable and Final Paper Assignments: </span> Removed a section</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*How well did the GenMAPP Builder process work for your species? '''Katrina'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*How well did the GenMAPP Builder process work for your species? '''Katrina'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Discuss the statistical analysis and MAPPFinder results for your microarray dataset. '''Dillon'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Discuss the statistical analysis and MAPPFinder results for your microarray dataset. '''Dillon'''</div></td></tr>
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<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">=== References ===</del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">* Please use the [[Guidelines for Literature Citations in a Scientific Paper]].  The [http://en.wikipedia.org/wiki/APA_style#Citation APA format] is also very similar to these guidelines and will be acceptable.  Be consistent with your format for the in text citations and for your references list at the end.</del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Annotated Bibliography of Genomics Papers for ''C. trachomatis''==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Annotated Bibliography of Genomics Papers for ''C. trachomatis''==</div></td></tr>
</table>Ksherbinahttps://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Chlamydia_trachomatis&diff=6863&oldid=prevKsherbina: /* Final Paper */ Added some more assignments2013-12-08T06:43:26Z<p><span dir="auto"><span class="autocomment">Final Paper: </span> Added some more assignments</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Results</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Results</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Gene Database Schema '''Hilda'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Gene Database Schema '''Hilda'''</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Gene Database Testing Report on final version of Gene Database '''<del class="diffchange diffchange-inline">Dillon</del>'''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Gene Database Testing Report on final version of Gene Database '''<ins class="diffchange diffchange-inline">Katrina</ins>'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Report on quantity and identity of gene IDs that did not make it into the database '''Hilda'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Report on quantity and identity of gene IDs that did not make it into the database '''Hilda'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Report on what changes need to be made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs '''Katrina'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Report on what changes need to be made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs '''Katrina'''</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Report results of the DNA microarray statistical analysis</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Report results of the DNA microarray statistical analysis <ins class="diffchange diffchange-inline">'''Dillon'''</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Table of MAPPFinder results (from .xls) and MAPP of a pathway</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Table of MAPPFinder results (from .xls) and MAPP of a pathway <ins class="diffchange diffchange-inline">'''Dillon'''</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Discussion</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Discussion</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*How well did the GenMAPP Builder process work for your species? '''Katrina'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*How well did the GenMAPP Builder process work for your species? '''Katrina'''</div></td></tr>
</table>Ksherbinahttps://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Chlamydia_trachomatis&diff=6862&oldid=prevKsherbina: /* Final Paper */ Added assignments2013-12-08T06:42:55Z<p><span dir="auto"><span class="autocomment">Final Paper: </span> Added assignments</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Final Paper===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Final Paper===</div></td></tr>
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<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#Introduction</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#Introduction <ins class="diffchange diffchange-inline">'''Hilda'''</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Methods</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Methods</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Download the UniProt XML proteome set and GOA (GO association) files for your species.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Download the UniProt XML proteome set and GOA (GO association) files for your species. <ins class="diffchange diffchange-inline">'''Katrina'''</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Download GO terms from in the OBO-XML format.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Download GO terms from in the OBO-XML format. <ins class="diffchange diffchange-inline">'''Katrina'''</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Create the GenMAPP Builder tables in PostgreSQL.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Create the GenMAPP Builder tables in PostgreSQL. <ins class="diffchange diffchange-inline">'''Katrina'''</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Load files into PostgreSQL database via GenMAPP Builder.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Load files into PostgreSQL database via GenMAPP Builder. <ins class="diffchange diffchange-inline">'''Katrina'''</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Export into a GenMAPP Gene Database.  </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Export into a GenMAPP Gene Database. <ins class="diffchange diffchange-inline">'''Katrina'''</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Inspect/vet/validate Gene Database.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Inspect/vet/validate Gene Database. <ins class="diffchange diffchange-inline">'''Katrina'''</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Prepare microarray data (organize, normalize, perform statistical analysis) '''Dillon'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Prepare microarray data (organize, normalize, perform statistical analysis) '''Dillon'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Run GenMAPP and MAPPFinder using the Gene Database. '''Dillon'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Run GenMAPP and MAPPFinder using the Gene Database. '''Dillon'''</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Gene Database Schema '''Hilda'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Gene Database Schema '''Hilda'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Gene Database Testing Report on final version of Gene Database '''Dillon'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Gene Database Testing Report on final version of Gene Database '''Dillon'''</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Report on quantity and identity of gene IDs that did not make it into the database '''<del class="diffchange diffchange-inline">Katrina</del>'''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Report on quantity and identity of gene IDs that did not make it into the database '''<ins class="diffchange diffchange-inline">Hilda</ins>'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Report on what changes need to be made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs '''Katrina'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Report on what changes need to be made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs '''Katrina'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Report results of the DNA microarray statistical analysis</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Report results of the DNA microarray statistical analysis</div></td></tr>
</table>Ksherbinahttps://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Chlamydia_trachomatis&diff=6861&oldid=prevKsherbina: /* Final Paper */ Added more assignments2013-12-08T06:40:23Z<p><span dir="auto"><span class="autocomment">Final Paper: </span> Added more assignments</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Create the GenMAPP Builder tables in PostgreSQL.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Create the GenMAPP Builder tables in PostgreSQL.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Load files into PostgreSQL database via GenMAPP Builder.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Load files into PostgreSQL database via GenMAPP Builder.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Export into a GenMAPP Gene Database.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Export into a GenMAPP Gene Database.  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Inspect/vet/validate Gene Database.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Inspect/vet/validate Gene Database.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Prepare microarray data (organize, normalize, perform statistical analysis)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Prepare microarray data (organize, normalize, perform statistical analysis) <ins class="diffchange diffchange-inline">'''Dillon'''</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Run GenMAPP and MAPPFinder using the Gene Database.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Run GenMAPP and MAPPFinder using the Gene Database. <ins class="diffchange diffchange-inline">'''Dillon'''</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Results</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Results</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Gene Database Schema</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Gene Database Schema <ins class="diffchange diffchange-inline">'''Hilda'''</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Gene Database Testing Report on final version of Gene Database</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Gene Database Testing Report on final version of Gene Database <ins class="diffchange diffchange-inline">'''Dillon'''</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Report on quantity and identity of gene IDs that did not make it into the database</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Report on quantity and identity of gene IDs that did not make it into the database <ins class="diffchange diffchange-inline">'''Katrina'''</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#*Report on what changes need to be made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#*Report on what changes need to be made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs <ins class="diffchange diffchange-inline">'''Katrina'''</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Report results of the DNA microarray statistical analysis</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Report results of the DNA microarray statistical analysis</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Table of MAPPFinder results (from .xls) and MAPP of a pathway</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Table of MAPPFinder results (from .xls) and MAPP of a pathway</div></td></tr>
</table>Ksherbina
===Final Paper===
===Final Paper===
−
#Introductino
+
#Introduction
#Methods
#Methods
#*Download the UniProt XML proteome set and GOA (GO association) files for your species.
#*Download the UniProt XML proteome set and GOA (GO association) files for your species.
#*Table of MAPPFinder results (from .xls) and MAPP of a pathway
#*Table of MAPPFinder results (from .xls) and MAPP of a pathway