I would try to find the newly opened window, either through $mech->application->openTabs() or by finding the opened Window from within the opening window, depending on whether Javascript is used to open that window or not.

Then, closing that window is a simple matter of calling the ->close method on it:

$window->close(); # this is window.close() from Javascript
[download]

Thanks, Corion. Can I ask you another question? I can't figure out how to make a particular selection. I know JavaScript is involved on this page, but that's about all I know. I would love a quick answer, but I also would like to find resources to help me better understand the nuts and bolts. If you run this script (remember to have MozRepl 1.1 running), the selection I want is "Saccharomyces cerevisiae(25)", which is on the left side of the page in the scrollbar. It would work equally well for me to select this option by a name or label, or by its position, being the second selection in the list. In the page source, I can see the relevant section (involving a JS function "document.createElement"), but I don't know how to access these elements. I would greatly appreciate help with a solution, and/or simply some advice on resources to help me figure out a solution.

#!/usr/bin/perl 
use strict;
use warnings;
use WWW::Mechanize::Firefox;

my $mech = WWW::Mechanize::Firefox->new(autoclose => 0);
$mech->allow( javascript => 1 );
$mech->get("http://david.abcc.ncifcrf.gov/summary.jsp");
$mech->click({ xpath => ('//*[@href="Upload a Gene List or Population"
+]', single => 1), synchronize => 0 });
$mech->form_name('frmManager');
$mech->set_fields( 
    'pasteBox' =>     "RRI1, YLR149C, FUN19, YBR285W, ALD3, CUE5, RTC3
+, AIM3, YDL199C, FMP45, AST2, GIP2,
            YKL091C, YKL133C, GLG2, SYM1, VHS3, YJR124C, MCH1, MHO1, I
+KS1, RKM1, STF2, SAC1, ATG7, YAK1",    
    'Identifier' => "OFFICIAL_GENE_SYMBOL",
);
$mech->click ({ xpath => ('//input[@name="rbUploadType" and @value="li
+st"]', single => 1), synchronize => 0 }); 
$mech->click({xpath => ('//*[@value="Submit List"]', single => 1), syn
+chronize => 0});
$mech->back;
[download]

In such cases, it is most helpfull to use the Firefox Document Inspector, which is invoked using F12 or CTRL+SHIFT+I. With it, you can point the mouse to a document element and it shows you the (generated) HTML source code that corresponds to that element.

In the case of the sidebar, this would be the following HTML, which you can then manipulate using the usual WWW::Mechanize::Firefox methods:

<select class="lists" style="z-index: -1;" name="speciesList" multiple
+="" size="4"><option value="- Use All Species -"></option><option val
+ue="0"></option><option value="1"></option><option value="2"></option
+><option value="3"></option><option value="4"></option><option value=
+"5"></option><option value="6"></option><option value="7"></option><o
+ption value="8"></option><option value="9"></option><option value="10
+"></option><option value="11"></option><option value="12"></option><o
+ption value="13"></option><option value="14"></option><option value="
+15"></option><option value="16"></option><option value="17"></option>
+<option value="18"></option><option value="19"></option><option value
+="20"></option><option value="21"></option><option value="22"></optio
+n><option value="23"></option><option value="24"></option><option val
+ue="25"></option><option value="26"></option><option value="27"></opt
+ion><option value="28"></option><option value="-1"></option></select>
[download]

Here's a more robust solution. It's possible to have multiple web browser windows with the same title. In that case, I wouldn't want to close all windows with a given title, just the last window that opened. So, the last three lines in this script identify the numeric value associated with the last window that opened containing "DAVID" in the title, then uses the system command to close that window.

#!/usr/bin/perl 
use strict;
use warnings;
use WWW::Mechanize::Firefox;

my $mech = WWW::Mechanize::Firefox->new();
$mech->get("http://david.abcc.ncifcrf.gov/summary.jsp");
$mech->click({ xpath => ('//*[@href="Upload a Gene List or Population"
+]', single => 1), synchronize => 0 });
$mech->form_name('frmManager');
$mech->set_fields( 
    'pasteBox' =>     "RRI1, YLR149C, FUN19, YBR285W, ALD3, CUE5, RTC3
+, AIM3, YDL199C, FMP45, AST2, GIP2,
            YKL091C, YKL133C, GLG2, SYM1, VHS3, YJR124C, MCH1, MHO1, I
+KS1, RKM1, STF2, SAC1, ATG7, YAK1",    
    'Identifier' => "OFFICIAL_GENE_SYMBOL",
);
$mech->click ({ xpath => ('//input[@name="rbUploadType" and @value="li
+st"]', single => 1), synchronize => 0 }); 
$mech->click({xpath => ('//*[@value="Submit List"]', single => 1), syn
+chronize => 0});
$mech->back;
my $retries = 100;
while ($retries-- and ! $mech->is_visible( xpath => '//*[@value="Funct
+ional Annotation Clustering"]' )) {
    sleep 1;
};
die "Timeout" unless $retries;
$mech->click({xpath => ('//*[@value="Functional Annotation Clustering"
+]', single => 1), synchronize => 0});
$mech->get("http://david.abcc.ncifcrf.gov/term2term.jsp?annot=52,9,79,
+85,25,32,39,3,47,45,63,76&currentList=1");
my $var = `wmctrl -l | grep \"DAVID\" | tail -1 | cut -f1 -d\" \"`;
chomp $var;
system("wmctrl -i -c \"$var\"");
[download]

I figured out a solution. I installed the "WMCTRL" package, a linux windows manager, using "sudo apt-get install wmctrl". Now I use the "wmctrl -c "title of window"" system command in my perl script to close only the browser window with that title. See the 2 new lines of code below.

#!/usr/bin/perl 
use strict;
use warnings;
use WWW::Mechanize::Firefox;

my $mech = WWW::Mechanize::Firefox->new();
$mech->get("http://david.abcc.ncifcrf.gov/summary.jsp");
$mech->click({ xpath => ('//*[@href="Upload a Gene List or Population"
+]', single => 1), synchronize => 0 });
$mech->form_name('frmManager');
$mech->set_fields( 
    'pasteBox' =>     "RRI1, YLR149C, FUN19, YBR285W, ALD3, CUE5, RTC3
+, AIM3, YDL199C, FMP45, AST2, GIP2,
            YKL091C, YKL133C, GLG2, SYM1, VHS3, YJR124C, MCH1, MHO1, I
+KS1, RKM1, STF2, SAC1, ATG7, YAK1",    
    'Identifier' => "OFFICIAL_GENE_SYMBOL",
);
$mech->click ({ xpath => ('//input[@name="rbUploadType" and @value="li
+st"]', single => 1), synchronize => 0 }); 
$mech->click({xpath => ('//*[@value="Submit List"]', single => 1), syn
+chronize => 0});
$mech->back;
my $retries = 100;
while ($retries-- and ! $mech->is_visible( xpath => '//*[@value="Funct
+ional Annotation Clustering"]' )) {
    sleep 1;
};
die "Timeout" unless $retries;
$mech->click({xpath => ('//*[@value="Functional Annotation Clustering"
+]', single => 1), synchronize => 0});
$mech->get("http://david.abcc.ncifcrf.gov/term2term.jsp?annot=52,9,79,
+85,25,32,39,3,47,45,63,76&currentList=1");
my $title = 'DAVID: Database for Annotation, Visualization, and Integr
+ated Discovery (Laboratory of Immunopathogenesis and Bioinformatics (
+LIB); National Institute of Allergies and Infectious Diseases (NIAID)
+; Science Applications International Corporation (SAIC)';
system("wmctrl -c \"$title\"");
[download]