https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?action=history&feed=atom&title=Ksherbina_Project_Notebook Ksherbina Project Notebook - Revision history 2026-04-15T10:22:37Z Revision history for this page on the wiki MediaWiki 1.20.3 https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Ksherbina_Project_Notebook&diff=7047&oldid=prev Ksherbina: /* Week 15 */ Finalized the testing report 2013-12-13T07:42:03Z <p>‎<span dir="auto"><span class="autocomment">Week 15: </span> Finalized the testing report</span></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;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 07:42, 13 December 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 455:</td> <td colspan="2" class="diff-lineno">Line 455:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Synchronized again.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Synchronized again.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Committed the changes I made to the gmbuilder.properties code.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Committed the changes I made to the gmbuilder.properties code.</div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">==Week 16==</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">===December 12, 2013===</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">The gene database&#160; Ct-Std_v2_KS_20131121.gdb was renamed to Ct-Std_External_20131121.gdb in preparing the final delivarables for the project. The testing report was accordingly modified:</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">====Testing Report====</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">Version of GenMAPP Builder: 2.0b71</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">Computer on which export was run: Personal computer</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">Postgres Database name: CT_KS_20131119_32bit_gmb2b71</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">UniProt XML filename: Uniprot_XML_C.trachomatis_serovar_A_KS_20131114.xml</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_11</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">::*Original file name from [http://www.uniprot.org/uniprot/?query=organism:315277+keyword:181 UniProt site]: uniprot-organism%3A315277+keyword%3A181.xml</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">* Time taken to import: 1.20 min</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">GO OBO-XML filename: Go_daily-termdb_v2_HD_20131107.obo-xml</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped): 11/06/2013</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">::*Original file name as listed in beta.geneontology.org: go_daily-termdb.obo-xml.gz</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">* Time taken to import: 13.05 min</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">* Time taken to process: 10.80 min</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">GOA filename: 22183.C_trachomatis_A_KS_20131114.goa</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): 11/12/13</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">::*Original file name as listed in the FTP site: 22183.C_trachomatis_A.goa</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">* Time taken to import: 0.04 min</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">*Name of .gdb file: Ct-Std_v2_KS_20131121.gdb</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">*Time taken to export .gdb:</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">:*Start Time: 10:56 AM (approximately)</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">:*End Time: 11:14:26 AM</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">*Upload your file and link to it here: [[Media:Ct-Std External 20131121.gdb|Ct-Std_External_20131121.gdb]]</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">Note: There is one ID &quot;CTA_0406/CTA_0407/CTA_0408&quot; that is a combination of three predicted genes that are actually one gene. The Tally Engine and PostgreSQL count this as one gene resulting in a total gene count of 917. However, through Access and xmlpipedb &#039;&#039;match&#039;&#039;, the ID is separated into three separate genes bringing the total count to 919.</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Journal Entry]] &#160;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Journal Entry]] &#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Individual Homework]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Individual Homework]]</div></td></tr> </table> Ksherbina https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Ksherbina_Project_Notebook&diff=6799&oldid=prev Ksherbina: /* Customize Tally Engine for C. trachomatis */ Finished recording steps. 2013-12-06T06:35:02Z <p>‎<span dir="auto"><span class="autocomment">Customize Tally Engine for C. trachomatis: </span> Finished recording steps.</span></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;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 06:35, 6 December 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 440:</td> <td colspan="2" class="diff-lineno">Line 440:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Opened gmbuilder and set the database to CT_KS_20131119_32bit_gmb2b71.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Opened gmbuilder and set the database to CT_KS_20131119_32bit_gmb2b71.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Ran TallyEngine.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Ran TallyEngine.</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*Got the same <del class="diffchange diffchange-inline">results </del>as those from November 21, 2013 despite the fact that I received an error that the species specified in the added code could not be found. However, the error also specified that the correct species ID is chlamydiatrachomatisservoara.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*Got the same <ins class="diffchange diffchange-inline">counts </ins>as those from November 21, 2013 despite the fact that I received an error that the species specified in the added code could not be found. However, the error also specified that the correct species ID is chlamydiatrachomatisservoara.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Accordingly, I went back to Eclipse and modified the code added to gmbuilder.properties:</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Accordingly, I went back to Eclipse and modified the code added to gmbuilder.properties:</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; # Chlamydia trachomatis</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; # Chlamydia trachomatis</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 450:</td> <td colspan="2" class="diff-lineno">Line 450:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; chlamydiatrachomatisserovara_table_name_level0=Ordered Locus</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>&#160; chlamydiatrachomatisserovara_table_name_level0=Ordered Locus</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*Built a distribution version of gmbuilder and then ran Tally Engine again. I got the same counts but no error message about the species ID as before.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*Went back to Eclipse. Synchronized the code on my computer with the code on SourceForge.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*Built a new distribution of gmbuilder.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*Synchronized again.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*Committed the changes I made to the gmbuilder.properties code.</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Journal Entry]] &#160;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Journal Entry]] &#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Individual Homework]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Individual Homework]]</div></td></tr> </table> Ksherbina https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Ksherbina_Project_Notebook&diff=6798&oldid=prev Ksherbina: /* December 5, 2013 */ Recorded some of the steps taken to customize the Tally Engine 2013-12-06T06:29:48Z <p>‎<span dir="auto"><span class="autocomment">December 5, 2013: </span> Recorded some of the steps taken to customize the Tally Engine</span></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;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 06:29, 6 December 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 419:</td> <td colspan="2" class="diff-lineno">Line 419:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>===December 5, 2013===</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>===December 5, 2013===</div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">====Customize Tally Engine for &#039;&#039;C. trachomatis&#039;&#039;====</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">*Opened Eclipse.</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">*Double-clicked xmlpipedb-gmbuilder &gt; src &gt; edu.lmu.xmlpipedb.gmbuilder.resource.properties &gt; gmbuilder.properties.</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">*Found the following part of the code:</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"> #</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"> # wizard.properties</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"> #</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; 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color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;"> chlamydiatrachomatisserovara_table_name_level0=Ordered Locus</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Journal Entry]] &#160;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Journal Entry]] &#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Individual Homework]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Individual Homework]]</div></td></tr> </table> Ksherbina https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Ksherbina_Project_Notebook&diff=6797&oldid=prev Ksherbina: /* Week 15 */ Created another section 2013-12-06T05:58:20Z <p>‎<span dir="auto"><span class="autocomment">Week 15: </span> Created another section</span></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;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 05:58, 6 December 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 417:</td> <td colspan="2" class="diff-lineno">Line 417:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Worked with Hilda to separate the gene IDs from the Affymetrix IDs appended to them in the microarray data.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Worked with Hilda to separate the gene IDs from the Affymetrix IDs appended to them in the microarray data.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Worked with Dillon to run GenMAPP and MAPPFinder with the microarray data and the gene database created for &#039;&#039;C. trachomatis&#039;&#039;.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Worked with Dillon to run GenMAPP and MAPPFinder with the microarray data and the gene database created for &#039;&#039;C. trachomatis&#039;&#039;.</div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">===December 5, 2013===</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Journal Entry]] &#160;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Journal Entry]] &#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Individual Homework]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Individual Homework]]</div></td></tr> </table> Ksherbina https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Ksherbina_Project_Notebook&diff=6796&oldid=prev Ksherbina: /* Week 15 */ Recorded work done on December 3, 2013 2013-12-06T05:57:35Z <p>‎<span dir="auto"><span class="autocomment">Week 15: </span> Recorded work done on December 3, 2013</span></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;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 05:57, 6 December 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 412:</td> <td colspan="2" class="diff-lineno">Line 412:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==Week 15==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==Week 15==</div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">===December 3, 2013===</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">*Worked with Hilda to separate the gene IDs from the Affymetrix IDs appended to them in the microarray data.</ins></div></td></tr> <tr><td colspan="2">&#160;</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;">*Worked with Dillon to run GenMAPP and MAPPFinder with the microarray data and the gene database created for &#039;&#039;C. trachomatis&#039;&#039;.</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Journal Entry]] &#160;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Journal Entry]] &#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Individual Homework]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Individual Homework]]</div></td></tr> </table> Ksherbina https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Ksherbina_Project_Notebook&diff=6795&oldid=prev Ksherbina: Added section for Week 15 2013-12-06T05:55:39Z <p>Added section for Week 15</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;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 05:55, 6 December 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 410:</td> <td colspan="2" class="diff-lineno">Line 410:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Note: There is one ID &quot;CTA_0406/CTA_0407/CTA_0408&quot; that is a combination of three predicted genes that are actually one gene. The Tally Engine counts this as one gene that contributes to the total count of 917. However, through Access and xmlpipedb &#039;&#039;match&#039;&#039;, the ID is separated into three separate genes bringing the total count to 919.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Note: There is one ID &quot;CTA_0406/CTA_0407/CTA_0408&quot; that is a combination of three predicted genes that are actually one gene. The Tally Engine counts this as one gene that contributes to the total count of 917. However, through Access and xmlpipedb &#039;&#039;match&#039;&#039;, the ID is separated into three separate genes bringing the total count to 919.</div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;">==Week 15==</ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td colspan="2">&#160;</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;"></ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Journal Entry]] &#160;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Journal Entry]] &#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Individual Homework]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Individual Homework]]</div></td></tr> </table> Ksherbina  
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   Unexpected non-MediaWiki exception encountered, of type "Error"
Error: Call to undefined function each() in /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php:374
Stack trace:
#0 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(480): _DiffEngine->_diag()
#1 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(291): _DiffEngine->_compareseq()
#2 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(175): _DiffEngine->diff_local()
#3 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(653): _DiffEngine->diff()
#4 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(820): Diff->__construct()
#5 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(1240): MappedDiff->__construct()
#6 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(1458): WordLevelDiff->__construct()
#7 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(952): TableDiffFormatter->_changed()
#8 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(924): DiffFormatter->_block()
#9 /apps/xmlpipedb/biodb/fall2013/includes/diff/DifferenceEngine.php(765): DiffFormatter->format()
#10 /apps/xmlpipedb/biodb/fall2013/includes/diff/DifferenceEngine.php(655): DifferenceEngine->generateDiffBody()
#11 /apps/xmlpipedb/biodb/fall2013/includes/diff/DifferenceEngine.php(593): DifferenceEngine->getDiffBody()
#12 /apps/xmlpipedb/biodb/fall2013/includes/FeedUtils.php(147): DifferenceEngine->getDiff()
#13 /apps/xmlpipedb/biodb/fall2013/includes/actions/HistoryAction.php(303): FeedUtils::formatDiffRow()
#14 /apps/xmlpipedb/biodb/fall2013/includes/actions/HistoryAction.php(268): HistoryAction->feedItem()
#15 /apps/xmlpipedb/biodb/fall2013/includes/actions/HistoryAction.php(121): HistoryAction->feed()
#16 /apps/xmlpipedb/biodb/fall2013/includes/Action.php(541): HistoryAction->onView()
#17 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(427): FormlessAction->show()
#18 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(304): MediaWiki->performAction()
#19 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(536): MediaWiki->performRequest()
#20 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(446): MediaWiki->main()
#21 /apps/xmlpipedb/biodb/fall2013/index.php(59): MediaWiki->run()
#22 {main}