==Annotated Bibliography==
+
==Week 10 Assignment==
 
===Used Resources===
 
===Used Resources===
 
*[http://www.ncbi.nlm.nih.gov/pubmed Pubmed]
 
*[http://www.ncbi.nlm.nih.gov/pubmed Pubmed]
 
*[https://apps.webofknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch&SID=4EqdZnb3BBocMP6y1Te&preferencesSaved= Web of Science]
 
*[https://apps.webofknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch&SID=4EqdZnb3BBocMP6y1Te&preferencesSaved= Web of Science]
 
===Keyword Searches===
 
===Keyword Searches===
*'''Pubmed''' was entered, on 11/5, and the keywords <code>Burkholderia cenocepacia genome</code> were utilized and a search was conducted; '''150 records''' were found with these keywords and most of the results were related to ''Burkholderia cenocepacia'' genes and their characterization. The results seemed very broad and covered a wide variety of topics (the observed papers covered the purpose of certain genetic regions, the virulence of the bacteria, and protein characterization, among many other topics). A paper related to the sequencing of the entire genome of a ''Burkholderia cenocepacia'' strain was found on the second page of the search results (was result #21).  
+
*'''Pubmed''' was entered, on 11/5, and the keywords <code>Burkholderia cenocepacia genome</code> were utilized and a search was conducted; '''150 records''' were found with these keywords and most of the results were related to ''Burkholderia cenocepacia'' genes and their characterization. The results seemed very broad and covered a wide variety of topics (the observed papers covered the purpose of certain genetic regions, the virulence of the bacteria, and protein characterization, among many other topics). A paper related to the sequencing of the entire genome of a ''Burkholderia cenocepacia'' strain was found on the second page of the search results (was result #21). The keyword <code>sequence</code> was added to the search, which now yielded '''106 results'''. The results appeared to be very similar to the previous search (lots of topics were still covered, which appear to be related to the use of genome data). The same paper that was previously found, which announced the complete genome sequencing of a ''B. cenocepacia'' strain (H111), was found earlier. Reading through the genome sequence paper (titled "Genome Sequence of ''Burkholderia cenocepacia'' H111, a Cystic Fibrosis Airway Isolate"), the term ''Burkholderia cepacia complex'' was noticed (abbreviated BCC), which is a name of a group of bacteria (composed of at least 18 species) to which ''Burkholderia cenocepacia'' belongs. Using the search terms <code>burkholderia cenocepacia genome sequence BCC</code> led to '''25 results''' (genome paper appeared as the second result); BCC was effective in filtering the results.
**The keyword <code>sequence</code> was added to the search, which now yielded '''106 results'''. The results appeared to be very similar to the previous search (lots of topics were still covered, which appear to be related to the use of genome data). The same paper that was previously found, which announced the complete genome sequencing of a ''B. cenocepacia'' strain (H111), was found earlier. Reading through the genome sequence paper (titled "Genome Sequence of ''Burkholderia cenocepacia'' H111, a Cystic Fibrosis Airway Isolate"), the term ''Burkholderia cepacia complex'' was noticed (abbreviated BCC), which is a name of a group of bacteria (composed of at least 18 species) to which ''Burkholderia cenocepacia'' belongs. Using the search terms <code>burkholderia cenocepacia genome sequence BCC</code> led to '''25 results''' (genome paper appeared as the second result); BCC was effective in filtering the results.
+
 
*'''Google Scholar''' was entered, on 11/5, and the search query <code>burkholderia cenocepacia sequenced genome</code> was used, this search led to '''16,400 results''' which were fairly similar to what was previously found using Pubmed; the vast majority of results, on the first couple of pages, appear to be papers related to ''B. cenocepacia'' genes (which used data from a genome paper). The second result was a paper detailing the full genome of the J2315 strain of ''B. cenocepacia'' (which is possibly the "model" strain for work related to the bacteria). Using the keywords <code>burkholderia cenocepacia genome bcc cystic fibrosis</code> led to '''1,070 results''', with the paper regarding the J2315 strain being the first result.
 
*'''Google Scholar''' was entered, on 11/5, and the search query <code>burkholderia cenocepacia sequenced genome</code> was used, this search led to '''16,400 results''' which were fairly similar to what was previously found using Pubmed; the vast majority of results, on the first couple of pages, appear to be papers related to ''B. cenocepacia'' genes (which used data from a genome paper). The second result was a paper detailing the full genome of the J2315 strain of ''B. cenocepacia'' (which is possibly the "model" strain for work related to the bacteria). Using the keywords <code>burkholderia cenocepacia genome bcc cystic fibrosis</code> led to '''1,070 results''', with the paper regarding the J2315 strain being the first result.
Exception encountered, of type "Error"
[8d8d1ee4] /biodb/fall2015/index.php?diff=5931&oldid=5767&title=Blitvak_Week_10 Error from line 434 of /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php: Call to undefined function each()
Backtrace:
#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(111): 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/diff/DifferenceEngine.php(632): DifferenceEngine->getDiff()
#14 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(453): DifferenceEngine->showDiff()
#15 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(795): DifferenceEngine->showDiffPage()
#16 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(506): Article->showDiffPage()
#17 /apps/xmlpipedb/biodb/fall2015/includes/actions/ViewAction.php(44): Article->view()
#18 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(395): ViewAction->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}