https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?action=history&feed=atom&title=Bklein7_Week_15 Bklein7 Week 15 - Revision history 2026-04-04T04:36:06Z Revision history for this page on the wiki MediaWiki 1.25.1 https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Bklein7_Week_15&diff=7820&oldid=prev Bklein7: added details regarding what I worked on in the database testing report 2015-12-14T09:00:22Z <p>added details regarding what I worked on in the database testing report</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td> <td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 09:00, 14 December 2015</td> </tr><tr><td colspan="2" class="diff-lineno" id="L145" >Line 145:</td> <td colspan="2" class="diff-lineno">Line 145:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Running and Testing a New Gene Database Export (cw20151210)==</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Running and Testing a New Gene Database Export (cw20151210)==</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Using version &quot;3.0.0-build-5-cw20151210&quot; of GenMAPP Builder ([[File:Dist cw20151210.zip]]), I conducted a new import-export cycle to create an updated gene database for &#039;&#039;Bordetella pertussis&#039;&#039;. The Gene Database Testing Report for this new gene database can be found here: [[Gene Database Testing Report- cw20151210]].</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Using version &quot;3.0.0-build-5-cw20151210&quot; of GenMAPP Builder ([[File:Dist cw20151210.zip]]), I conducted a new import-export cycle to create an updated gene database for &#039;&#039;Bordetella pertussis&#039;&#039;. The Gene Database Testing Report for this new gene database can be found here: [[Gene Database Testing Report- cw20151210]]<ins class="diffchange diffchange-inline">. I wrote sections 1-5.2 of the testing report</ins>.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Final Project Deliverables==</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Final Project Deliverables==</div></td></tr> </table> Bklein7 −
==To Do==
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*emails
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*deliverables!
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**ReadMe file (finish editing)
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*EC question
  −
   
==TallyEngine Customization (cw20151203)==
 
==TallyEngine Customization (cw20151203)==
 
In GenMAPP Builder version 3.0.0 Build 5 - cw20151203, the ''Bordetella pertussis'' species profile was customized to import 11 ORF gene IDs that were not exported in previous versions. To account for this change, the TallyEngine was customized for ''Bordetella pertussis'' to count "ORF" gene listings separately from "Ordered Locus Names". To do this, I followed the procedure documented below:
 
In GenMAPP Builder version 3.0.0 Build 5 - cw20151203, the ''Bordetella pertussis'' species profile was customized to import 11 ORF gene IDs that were not exported in previous versions. To account for this change, the TallyEngine was customized for ''Bordetella pertussis'' to count "ORF" gene listings separately from "Ordered Locus Names". To do this, I followed the procedure documented below:
 
Using version "3.0.0-build-5-cw20151210" of GenMAPP Builder ([[File:Dist cw20151210.zip]]), I conducted a new import-export cycle to create an updated gene database for ''Bordetella pertussis''. The Gene Database Testing Report for this new gene database can be found here: [[Gene Database Testing Report- cw20151210]].
 
Using version "3.0.0-build-5-cw20151210" of GenMAPP Builder ([[File:Dist cw20151210.zip]]), I conducted a new import-export cycle to create an updated gene database for ''Bordetella pertussis''. The Gene Database Testing Report for this new gene database can be found here: [[Gene Database Testing Report- cw20151210]].
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#0 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(544): DiffEngine->diag()
#1 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(344): DiffEngine->compareSeq()
#2 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(227): DiffEngine->diffLocal()
#3 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(721): DiffEngine->diff()
#4 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(859): Diff->__construct()
#5 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(980): MappedDiff->__construct()
#6 /apps/xmlpipedb/biodb/fall2015/includes/diff/TableDiffFormatter.php(194): WordLevelDiff->__construct()
#7 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(140): TableDiffFormatter->changed()
#8 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(82): DiffFormatter->block()
#9 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(888): DiffFormatter->format()
#10 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(802): DifferenceEngine->generateTextDiffBody()
#11 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(733): DifferenceEngine->generateContentDiffBody()
#12 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(662): DifferenceEngine->getDiffBody()
#13 /apps/xmlpipedb/biodb/fall2015/includes/FeedUtils.php(155): DifferenceEngine->getDiff()
#14 /apps/xmlpipedb/biodb/fall2015/includes/actions/HistoryAction.php(325): FeedUtils::formatDiffRow()
#15 /apps/xmlpipedb/biodb/fall2015/includes/actions/HistoryAction.php(290): HistoryAction->feedItem()
#16 /apps/xmlpipedb/biodb/fall2015/includes/actions/HistoryAction.php(130): HistoryAction->feed()
#17 /apps/xmlpipedb/biodb/fall2015/includes/actions/FormlessAction.php(43): HistoryAction->onView()
#18 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(395): FormlessAction->show()
#19 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(273): MediaWiki->performAction()
#20 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(566): MediaWiki->performRequest()
#21 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(414): MediaWiki->main()
#22 /apps/xmlpipedb/biodb/fall2015/index.php(44): MediaWiki->run()
#23 {main}