* [[User:Mpetredi|Mitchell Petredis]]: [[Sinorhizobium_meliloti|''Sinorhizobium meliloti'']]
 
* [[User:Mpetredi|Mitchell Petredis]]: [[Sinorhizobium_meliloti|''Sinorhizobium meliloti'']]
 
* [[User:Ksherbina|Katrina Sherbina]]: [[Chlamydia_trachomatis|Team H(oo)KD, ''Chlamydia trachomatis'']]
 
* [[User:Ksherbina|Katrina Sherbina]]: [[Chlamydia_trachomatis|Team H(oo)KD, ''Chlamydia trachomatis'']]
* [[User:Taur.vil|Tauras Vilgalys]]: [[Streptococcus_pneumoniae|''Streptococcus pneumoniae'']]
+
* [[User:Taur.vil|Tauras Vilgalys]]: [[Streptococcus_pneumoniae|Team ATK ''Streptococcus pneumoniae'']]
    
== Milestones ==
 
== Milestones ==
 
#*** Note that you need to use 32-bit Java
 
#*** Note that you need to use 32-bit Java
 
#* GenMAPP (http://genmapp.org)
 
#* GenMAPP (http://genmapp.org)
 +
#** We will be using GenMAPP and MAPPFinder version 2.1.  This software is already installed on the Windows machines in the Keck lab annex and in the Seaver 120 computer lab.
 +
#*** This version is now called "GenMAPP Classic" and can be downloaded [http://www.genmapp.org/download_v2.1.php from this page].
 +
#*** Follow the instructions in the installer.
 +
#*** During installation, the installer will open a window called the GenMAPP Data Acquisition Tool.  It will not function because it cannot connect to the server.  This is OK.
 
#* XMLPipeDB ''match'' utility for counting IDs in XML files
 
#* XMLPipeDB ''match'' utility for counting IDs in XML files
 
#* Microsoft Access or any other tool that can read .mdb files
 
#* Microsoft Access or any other tool that can read .mdb files
 
# Go to Eclipse’s menu bar’s ''Window'' > ''Open Perspective'' and choose ''SVN Repository Exploring'' either from the ''Open Perspective'' submenu if it is there, or from ''Other...''.  If you don't see this, double-check your installation of Subclipse.
 
# Go to Eclipse’s menu bar’s ''Window'' > ''Open Perspective'' and choose ''SVN Repository Exploring'' either from the ''Open Perspective'' submenu if it is there, or from ''Other...''.  If you don't see this, double-check your installation of Subclipse.
 
# Define a new Subversion repository by clicking on the ''Add Repository'' button (this is the icon with the little yellow canister with small ''SVN'' and ''+'' badges to its right).
 
# Define a new Subversion repository by clicking on the ''Add Repository'' button (this is the icon with the little yellow canister with small ''SVN'' and ''+'' badges to its right).
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(895): 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/diff/DifferenceEngine.php(566): DifferenceEngine->getDiff()
#13 /apps/xmlpipedb/biodb/fall2013/includes/diff/DifferenceEngine.php(409): DifferenceEngine->showDiff()
#14 /apps/xmlpipedb/biodb/fall2013/includes/Article.php(725): DifferenceEngine->showDiffPage()
#15 /apps/xmlpipedb/biodb/fall2013/includes/Article.php(478): Article->showDiffPage()
#16 /apps/xmlpipedb/biodb/fall2013/includes/actions/ViewAction.php(37): Article->view()
#17 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(427): ViewAction->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}